Starting phenix.real_space_refine on Sun Mar 10 15:15:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hds_34679/03_2024/8hds_34679.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hds_34679/03_2024/8hds_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_34679/03_2024/8hds_34679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hds_34679/03_2024/8hds_34679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hds_34679/03_2024/8hds_34679.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hds_34679/03_2024/8hds_34679.pdb" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 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. 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 19.77, per 1000 atoms: 0.37 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: 14.98 Conformation dependent library (CDL) restraints added in 7.0 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: 3.45 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: 13.05 Time building geometry restraints manager: 16.67 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 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: 1.000 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: 7.540 Check model and map are aligned: 0.570 Set scattering table: 0.360 Process input model: 96.170 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 % Allowed : 5.37 % Favored : 94.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP c 40 HIS 0.011 0.003 HIS J 383 PHE 0.021 0.003 PHE A 295 TYR 0.020 0.002 TYR b 113 ARG 0.008 0.001 ARG A 344 *********************** 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 : 4.356 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 REVERT: A 12 ARG cc_start: 0.7771 (ttm110) cc_final: 0.7223 (mtp180) REVERT: A 52 ARG cc_start: 0.7872 (ttt-90) cc_final: 0.7604 (ttt90) REVERT: A 60 LEU cc_start: 0.8852 (tt) cc_final: 0.8640 (tp) REVERT: A 84 LYS cc_start: 0.8407 (mttt) cc_final: 0.7992 (tttt) REVERT: A 94 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7793 (tm-30) REVERT: A 148 GLN cc_start: 0.7446 (pm20) cc_final: 0.7017 (mt0) REVERT: A 154 PHE cc_start: 0.8411 (p90) cc_final: 0.7929 (p90) REVERT: A 157 ARG cc_start: 0.6768 (mtp180) cc_final: 0.6383 (mtp180) REVERT: A 249 LYS cc_start: 0.8804 (tptt) cc_final: 0.8516 (ttmm) REVERT: A 293 ILE cc_start: 0.8572 (pp) cc_final: 0.8367 (tp) REVERT: A 315 MET cc_start: 0.1214 (ttp) cc_final: 0.0982 (ttm) REVERT: A 371 MET cc_start: 0.8220 (mmm) cc_final: 0.7502 (mmt) REVERT: A 375 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7057 (mt-10) REVERT: A 399 GLU cc_start: 0.6983 (tp30) cc_final: 0.6667 (tp30) REVERT: B 84 LYS cc_start: 0.8485 (mttt) cc_final: 0.8057 (tttt) REVERT: B 136 MET cc_start: 0.7602 (mtt) cc_final: 0.7013 (mtm) REVERT: B 148 GLN cc_start: 0.7574 (pm20) cc_final: 0.7101 (mt0) REVERT: B 154 PHE cc_start: 0.8485 (p90) cc_final: 0.8002 (p90) REVERT: B 157 ARG cc_start: 0.6683 (mtp180) cc_final: 0.6203 (mtp180) REVERT: B 189 MET cc_start: 0.8527 (mmm) cc_final: 0.8324 (mmm) REVERT: B 249 LYS cc_start: 0.8644 (tptt) cc_final: 0.8313 (ttmm) REVERT: B 294 LEU cc_start: 0.8669 (mm) cc_final: 0.8454 (mm) REVERT: B 371 MET cc_start: 0.8206 (mmm) cc_final: 0.7958 (mmt) REVERT: B 397 MET cc_start: 0.7577 (mmm) cc_final: 0.7374 (mmm) REVERT: C 47 ASN cc_start: 0.9026 (m-40) cc_final: 0.8807 (m110) REVERT: C 84 LYS cc_start: 0.8432 (mttt) cc_final: 0.8055 (tttt) REVERT: C 94 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7792 (tm-30) REVERT: C 249 LYS cc_start: 0.8707 (tptt) cc_final: 0.8421 (ttmm) REVERT: C 371 MET cc_start: 0.8008 (mmm) cc_final: 0.7075 (mmt) REVERT: C 399 GLU cc_start: 0.6742 (tp30) cc_final: 0.6256 (tp30) REVERT: D 12 ARG cc_start: 0.7797 (ttm110) cc_final: 0.7232 (mtp180) REVERT: D 52 ARG cc_start: 0.7856 (ttt-90) cc_final: 0.7563 (ttt90) REVERT: D 84 LYS cc_start: 0.8432 (mttt) cc_final: 0.7984 (tttt) REVERT: D 148 GLN cc_start: 0.7511 (pm20) cc_final: 0.7062 (mt0) REVERT: D 154 PHE cc_start: 0.8413 (p90) cc_final: 0.7895 (p90) REVERT: D 157 ARG cc_start: 0.6760 (mtp180) cc_final: 0.6392 (mtp180) REVERT: D 187 ASP cc_start: 0.6427 (t0) cc_final: 0.5826 (p0) REVERT: D 293 ILE cc_start: 0.8583 (pp) cc_final: 0.8357 (tp) REVERT: D 315 MET cc_start: 0.1146 (ttp) cc_final: 0.0922 (ttm) REVERT: D 371 MET cc_start: 0.8251 (mmm) cc_final: 0.7531 (mmt) REVERT: D 375 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6989 (mt-10) REVERT: D 379 ILE cc_start: 0.9168 (mt) cc_final: 0.8953 (mt) REVERT: D 399 GLU cc_start: 0.6880 (tp30) cc_final: 0.6509 (tp30) REVERT: E 84 LYS cc_start: 0.8494 (mttt) cc_final: 0.8062 (tttt) REVERT: E 148 GLN cc_start: 0.7579 (pm20) cc_final: 0.7085 (mt0) REVERT: E 154 PHE cc_start: 0.8414 (p90) cc_final: 0.7719 (p90) REVERT: E 157 ARG cc_start: 0.6777 (mtp180) cc_final: 0.6332 (mtp180) REVERT: E 189 MET cc_start: 0.8543 (mmm) cc_final: 0.8326 (mmm) REVERT: E 249 LYS cc_start: 0.8626 (tptt) cc_final: 0.8296 (ttmm) REVERT: E 273 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7386 (mt-10) REVERT: E 294 LEU cc_start: 0.8671 (mm) cc_final: 0.8430 (mm) REVERT: E 399 GLU cc_start: 0.6927 (tp30) cc_final: 0.6605 (tp30) REVERT: F 47 ASN cc_start: 0.9039 (m-40) cc_final: 0.8832 (m110) REVERT: F 84 LYS cc_start: 0.8469 (mttt) cc_final: 0.8093 (tttt) REVERT: F 249 LYS cc_start: 0.8731 (tptt) cc_final: 0.8319 (tttp) REVERT: F 324 LYS cc_start: 0.7920 (mtpt) cc_final: 0.6845 (mttm) REVERT: F 371 MET cc_start: 0.8036 (mmm) cc_final: 0.7572 (mmt) REVERT: F 399 GLU cc_start: 0.6756 (tp30) cc_final: 0.6224 (tp30) REVERT: G 12 ARG cc_start: 0.7810 (ttm110) cc_final: 0.7233 (mtp180) REVERT: G 52 ARG cc_start: 0.7854 (ttt-90) cc_final: 0.7563 (ttt90) REVERT: G 84 LYS cc_start: 0.8431 (mttt) cc_final: 0.7980 (tttt) REVERT: G 148 GLN cc_start: 0.7514 (pm20) cc_final: 0.7049 (mt0) REVERT: G 154 PHE cc_start: 0.8411 (p90) cc_final: 0.7902 (p90) REVERT: G 157 ARG cc_start: 0.6756 (mtp180) cc_final: 0.6407 (mtp180) REVERT: G 187 ASP cc_start: 0.6425 (t0) cc_final: 0.5808 (p0) REVERT: G 293 ILE cc_start: 0.8579 (pp) cc_final: 0.8354 (tp) REVERT: G 315 MET cc_start: 0.1142 (ttp) cc_final: 0.0916 (ttm) REVERT: G 371 MET cc_start: 0.8251 (mmm) cc_final: 0.7486 (mmt) REVERT: G 375 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7018 (mt-10) REVERT: G 399 GLU cc_start: 0.6882 (tp30) cc_final: 0.6503 (tp30) REVERT: H 84 LYS cc_start: 0.8496 (mttt) cc_final: 0.8084 (tttt) REVERT: H 148 GLN cc_start: 0.7575 (pm20) cc_final: 0.7068 (mt0) REVERT: H 154 PHE cc_start: 0.8411 (p90) cc_final: 0.7760 (p90) REVERT: H 157 ARG cc_start: 0.6781 (mtp180) cc_final: 0.6326 (mtp180) REVERT: H 189 MET cc_start: 0.8542 (mmm) cc_final: 0.8319 (mmm) REVERT: H 249 LYS cc_start: 0.8652 (tptt) cc_final: 0.8320 (ttmm) REVERT: H 294 LEU cc_start: 0.8670 (mm) cc_final: 0.8426 (mm) REVERT: H 397 MET cc_start: 0.7538 (mmm) cc_final: 0.7280 (mmm) REVERT: I 47 ASN cc_start: 0.9051 (m-40) cc_final: 0.8847 (m110) REVERT: I 84 LYS cc_start: 0.8469 (mttt) cc_final: 0.8100 (tttt) REVERT: I 94 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7729 (tm-30) REVERT: I 249 LYS cc_start: 0.8775 (tptt) cc_final: 0.8429 (ttmm) REVERT: I 324 LYS cc_start: 0.7920 (mtpt) cc_final: 0.6876 (mttm) REVERT: I 371 MET cc_start: 0.8044 (mmm) cc_final: 0.7572 (mmt) REVERT: I 399 GLU cc_start: 0.6712 (tp30) cc_final: 0.6224 (tp30) REVERT: J 12 ARG cc_start: 0.7778 (ttm110) cc_final: 0.7225 (mtp180) REVERT: J 52 ARG cc_start: 0.7892 (ttt-90) cc_final: 0.7611 (ttt90) REVERT: J 84 LYS cc_start: 0.8388 (mttt) cc_final: 0.7957 (tttt) REVERT: J 94 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7805 (tm-30) REVERT: J 148 GLN cc_start: 0.7449 (pm20) cc_final: 0.6978 (mt0) REVERT: J 154 PHE cc_start: 0.8402 (p90) cc_final: 0.7925 (p90) REVERT: J 157 ARG cc_start: 0.6736 (mtp180) cc_final: 0.6321 (mtp180) REVERT: J 249 LYS cc_start: 0.8803 (tptt) cc_final: 0.8511 (ttmm) REVERT: J 315 MET cc_start: 0.1280 (ttp) cc_final: 0.1014 (ttm) REVERT: J 371 MET cc_start: 0.8223 (mmm) cc_final: 0.7484 (mmt) REVERT: J 375 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7049 (mt-10) REVERT: J 399 GLU cc_start: 0.6890 (tp30) cc_final: 0.6641 (tp30) REVERT: K 84 LYS cc_start: 0.8481 (mttt) cc_final: 0.8053 (tttt) REVERT: K 136 MET cc_start: 0.7574 (mtt) cc_final: 0.6993 (mtm) REVERT: K 148 GLN cc_start: 0.7572 (pm20) cc_final: 0.7088 (mt0) REVERT: K 154 PHE cc_start: 0.8478 (p90) cc_final: 0.7722 (p90) REVERT: K 157 ARG cc_start: 0.6688 (mtp180) cc_final: 0.6260 (mtp180) REVERT: K 189 MET cc_start: 0.8530 (mmm) cc_final: 0.8324 (mmm) REVERT: K 249 LYS cc_start: 0.8657 (tptt) cc_final: 0.8314 (ttmm) REVERT: K 294 LEU cc_start: 0.8664 (mm) cc_final: 0.8415 (mm) REVERT: K 371 MET cc_start: 0.8131 (mmm) cc_final: 0.7922 (mmt) REVERT: K 397 MET cc_start: 0.7568 (mmm) cc_final: 0.7324 (mmm) REVERT: L 47 ASN cc_start: 0.9054 (m-40) cc_final: 0.8836 (m110) REVERT: L 84 LYS cc_start: 0.8443 (mttt) cc_final: 0.8051 (tttt) REVERT: L 94 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7729 (tm-30) REVERT: L 249 LYS cc_start: 0.8782 (tptt) cc_final: 0.8441 (ttmm) REVERT: L 324 LYS cc_start: 0.7921 (mtpt) cc_final: 0.6856 (mttm) REVERT: L 371 MET cc_start: 0.8046 (mmm) cc_final: 0.7503 (mmt) REVERT: L 399 GLU cc_start: 0.6707 (tp30) cc_final: 0.6216 (tp30) REVERT: a 9 ASP cc_start: 0.7657 (t0) cc_final: 0.7393 (t0) REVERT: a 35 MET cc_start: 0.8256 (mmm) cc_final: 0.8050 (mmt) REVERT: a 91 PHE cc_start: 0.8299 (m-10) cc_final: 0.8096 (m-10) REVERT: b 9 ASP cc_start: 0.7657 (t0) cc_final: 0.7405 (t0) REVERT: c 9 ASP cc_start: 0.7816 (t0) cc_final: 0.7554 (t0) REVERT: d 9 ASP cc_start: 0.7711 (t0) cc_final: 0.7351 (t0) REVERT: e 9 ASP cc_start: 0.7657 (t0) cc_final: 0.7395 (t0) REVERT: e 14 TYR cc_start: 0.8229 (m-10) cc_final: 0.8003 (m-10) REVERT: f 9 ASP cc_start: 0.7736 (t0) cc_final: 0.7483 (t0) REVERT: h 9 ASP cc_start: 0.7662 (t0) cc_final: 0.7412 (t0) REVERT: i 9 ASP cc_start: 0.7775 (t0) cc_final: 0.7496 (t0) REVERT: j 9 ASP cc_start: 0.7689 (t0) cc_final: 0.7434 (t0) REVERT: k 9 ASP cc_start: 0.7666 (t0) cc_final: 0.7420 (t0) REVERT: l 9 ASP cc_start: 0.7813 (t0) cc_final: 0.7541 (t0) outliers start: 36 outliers final: 1 residues processed: 2026 average time/residue: 0.5689 time to fit residues: 1832.9334 Evaluate side-chains 1314 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1313 time to evaluate : 4.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 135 VAL 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: 8.9990 chunk 207 optimal weight: 8.9990 chunk 325 optimal weight: 5.9990 chunk 399 optimal weight: 0.9990 chunk 621 optimal weight: 0.9980 overall best weight: 1.6742 ------------------------------------------------------------------------------- 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 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 B 325 ASN C 40 GLN C 70 GLN C 185 HIS C 325 ASN D 40 GLN D 47 ASN D 70 GLN ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN D 321 HIS D 325 ASN E 40 GLN E 70 GLN E 321 HIS E 325 ASN F 40 GLN F 70 GLN F 185 HIS F 321 HIS G 40 GLN G 47 ASN G 70 GLN ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN G 321 HIS H 40 GLN H 70 GLN H 321 HIS H 325 ASN I 40 GLN I 70 GLN I 185 HIS I 321 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 K 325 ASN L 40 GLN L 70 GLN L 185 HIS L 321 HIS L 325 ASN f 104 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 54576 Z= 0.193 Angle : 0.672 9.456 74028 Z= 0.346 Chirality : 0.043 0.151 8196 Planarity : 0.006 0.067 9804 Dihedral : 6.239 29.879 7465 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.64 % Allowed : 12.10 % Favored : 84.26 % 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: -4.76 (0.08), residues: 6816 helix: -3.34 (0.07), residues: 2436 sheet: -2.26 (0.22), residues: 420 loop : -3.26 (0.08), residues: 3960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP k 40 HIS 0.007 0.001 HIS F 185 PHE 0.025 0.002 PHE J 30 TYR 0.011 0.001 TYR h 113 ARG 0.006 0.001 ARG d 122 *********************** 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 1577 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1369 time to evaluate : 4.720 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: A 12 ARG cc_start: 0.7773 (ttm110) cc_final: 0.7390 (ttm110) REVERT: A 30 PHE cc_start: 0.7724 (m-80) cc_final: 0.7451 (m-10) REVERT: A 43 TYR cc_start: 0.8119 (m-10) cc_final: 0.7906 (m-10) REVERT: A 84 LYS cc_start: 0.8430 (mttt) cc_final: 0.7954 (tttt) REVERT: A 94 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7611 (tm-30) REVERT: A 157 ARG cc_start: 0.6804 (mtp180) cc_final: 0.6330 (mtp180) REVERT: A 160 ARG cc_start: 0.7783 (mmm-85) cc_final: 0.7576 (mmm-85) REVERT: A 189 MET cc_start: 0.8625 (mmm) cc_final: 0.8390 (mmm) REVERT: A 371 MET cc_start: 0.8171 (mmm) cc_final: 0.7431 (mmt) REVERT: A 375 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6878 (mt-10) REVERT: A 399 GLU cc_start: 0.6868 (tp30) cc_final: 0.6662 (tp30) REVERT: B 84 LYS cc_start: 0.8510 (mttt) cc_final: 0.8081 (tttt) REVERT: B 157 ARG cc_start: 0.7099 (mtp180) cc_final: 0.6702 (mtp180) REVERT: B 160 ARG cc_start: 0.7663 (mmm-85) cc_final: 0.7406 (mmm-85) REVERT: B 163 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.8171 (p) REVERT: B 378 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7591 (mt-10) REVERT: C 30 PHE cc_start: 0.7745 (m-80) cc_final: 0.7421 (m-10) REVERT: C 39 ARG cc_start: 0.7518 (ttm170) cc_final: 0.7307 (ttt180) REVERT: C 84 LYS cc_start: 0.8463 (mttt) cc_final: 0.8049 (tttt) REVERT: C 94 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7454 (tm-30) REVERT: C 160 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7383 (mmm-85) REVERT: C 238 MET cc_start: 0.8368 (ttm) cc_final: 0.8151 (ttp) REVERT: C 399 GLU cc_start: 0.6790 (tp30) cc_final: 0.6447 (tp30) REVERT: D 12 ARG cc_start: 0.7799 (ttm110) cc_final: 0.7398 (ttm110) REVERT: D 84 LYS cc_start: 0.8475 (mttt) cc_final: 0.7980 (tttt) REVERT: D 94 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7602 (tm-30) REVERT: D 157 ARG cc_start: 0.6815 (mtp180) cc_final: 0.6343 (mtp180) REVERT: D 160 ARG cc_start: 0.7802 (mmm-85) cc_final: 0.7583 (mmm-85) REVERT: D 189 MET cc_start: 0.8617 (mmm) cc_final: 0.8370 (mmm) REVERT: D 315 MET cc_start: 0.1090 (ttp) cc_final: 0.0820 (ttm) REVERT: D 371 MET cc_start: 0.8187 (mmm) cc_final: 0.7350 (mmt) REVERT: D 375 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6835 (mt-10) REVERT: D 379 ILE cc_start: 0.8917 (mt) cc_final: 0.8716 (mt) REVERT: D 399 GLU cc_start: 0.6856 (tp30) cc_final: 0.6553 (tp30) REVERT: E 34 ARG cc_start: 0.6055 (OUTLIER) cc_final: 0.5848 (pmm-80) REVERT: E 84 LYS cc_start: 0.8490 (mttt) cc_final: 0.8033 (tttt) REVERT: E 157 ARG cc_start: 0.7136 (mtp180) cc_final: 0.6747 (mtp180) REVERT: E 160 ARG cc_start: 0.7678 (mmm-85) cc_final: 0.7403 (mmm-85) REVERT: E 162 GLN cc_start: 0.7571 (tt0) cc_final: 0.7302 (tt0) REVERT: E 369 GLU cc_start: 0.6026 (mt-10) cc_final: 0.5177 (tt0) REVERT: E 378 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7670 (mt-10) REVERT: F 30 PHE cc_start: 0.7735 (m-80) cc_final: 0.7413 (m-10) REVERT: F 39 ARG cc_start: 0.7512 (ttm170) cc_final: 0.7305 (ttt180) REVERT: F 84 LYS cc_start: 0.8404 (mttt) cc_final: 0.7986 (tttt) REVERT: F 94 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7455 (tm-30) REVERT: F 160 ARG cc_start: 0.7801 (mmm-85) cc_final: 0.7386 (mmm-85) REVERT: F 238 MET cc_start: 0.8392 (ttm) cc_final: 0.8035 (ttp) REVERT: F 371 MET cc_start: 0.7873 (mmm) cc_final: 0.7510 (mmt) REVERT: F 399 GLU cc_start: 0.6696 (tp30) cc_final: 0.6322 (tp30) REVERT: G 12 ARG cc_start: 0.7797 (ttm110) cc_final: 0.7408 (ttm110) REVERT: G 84 LYS cc_start: 0.8469 (mttt) cc_final: 0.7981 (tttt) REVERT: G 94 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7610 (tm-30) REVERT: G 157 ARG cc_start: 0.6830 (mtp180) cc_final: 0.6349 (mtp180) REVERT: G 189 MET cc_start: 0.8613 (mmm) cc_final: 0.8379 (mmm) REVERT: G 315 MET cc_start: 0.1098 (ttp) cc_final: 0.0846 (ttm) REVERT: G 371 MET cc_start: 0.8114 (mmm) cc_final: 0.7375 (mmt) REVERT: G 375 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6840 (mt-10) REVERT: G 399 GLU cc_start: 0.6853 (tp30) cc_final: 0.6563 (tp30) REVERT: H 84 LYS cc_start: 0.8537 (mttt) cc_final: 0.8079 (tttt) REVERT: H 157 ARG cc_start: 0.7132 (mtp180) cc_final: 0.6746 (mtp180) REVERT: H 160 ARG cc_start: 0.7671 (mmm-85) cc_final: 0.7394 (mmm-85) REVERT: H 162 GLN cc_start: 0.7545 (tt0) cc_final: 0.7278 (tt0) REVERT: H 378 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7666 (mt-10) REVERT: I 30 PHE cc_start: 0.7753 (m-80) cc_final: 0.7434 (m-10) REVERT: I 39 ARG cc_start: 0.7505 (ttm170) cc_final: 0.7293 (ttt180) REVERT: I 84 LYS cc_start: 0.8420 (mttt) cc_final: 0.8019 (tttt) REVERT: I 94 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7450 (tm-30) REVERT: I 160 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7370 (mmm-85) REVERT: I 238 MET cc_start: 0.8359 (ttm) cc_final: 0.8143 (ttp) REVERT: I 371 MET cc_start: 0.7861 (mmm) cc_final: 0.7512 (mmt) REVERT: I 399 GLU cc_start: 0.6684 (tp30) cc_final: 0.6306 (tp30) REVERT: J 12 ARG cc_start: 0.7796 (ttm110) cc_final: 0.7402 (ttm110) REVERT: J 84 LYS cc_start: 0.8464 (mttt) cc_final: 0.7966 (tttt) REVERT: J 94 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7587 (tm-30) REVERT: J 157 ARG cc_start: 0.6807 (mtp180) cc_final: 0.6318 (mtp180) REVERT: J 160 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7555 (mmm-85) REVERT: J 189 MET cc_start: 0.8608 (mmm) cc_final: 0.8402 (mmm) REVERT: J 315 MET cc_start: 0.1035 (ttp) cc_final: 0.0760 (ttm) REVERT: J 371 MET cc_start: 0.8182 (mmm) cc_final: 0.7434 (mmt) REVERT: K 84 LYS cc_start: 0.8531 (mttt) cc_final: 0.8083 (tttt) REVERT: K 157 ARG cc_start: 0.7102 (mtp180) cc_final: 0.6709 (mtp180) REVERT: K 160 ARG cc_start: 0.7650 (mmm-85) cc_final: 0.7395 (mmm-85) REVERT: K 378 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7586 (mt-10) REVERT: L 30 PHE cc_start: 0.7749 (m-80) cc_final: 0.7423 (m-10) REVERT: L 39 ARG cc_start: 0.7475 (ttm170) cc_final: 0.7190 (ttt180) REVERT: L 84 LYS cc_start: 0.8417 (mttt) cc_final: 0.8010 (tttt) REVERT: L 94 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7441 (tm-30) REVERT: L 160 ARG cc_start: 0.7793 (mmm-85) cc_final: 0.7377 (mmm-85) REVERT: L 238 MET cc_start: 0.8380 (ttm) cc_final: 0.8154 (ttp) REVERT: L 371 MET cc_start: 0.7740 (mmm) cc_final: 0.7511 (mmt) REVERT: L 399 GLU cc_start: 0.6682 (tp30) cc_final: 0.6299 (tp30) REVERT: a 65 ARG cc_start: 0.6675 (ttm170) cc_final: 0.6233 (mtp85) REVERT: b 14 TYR cc_start: 0.8204 (m-80) cc_final: 0.7866 (m-80) REVERT: g 35 MET cc_start: 0.8357 (mmm) cc_final: 0.8062 (mmt) REVERT: h 14 TYR cc_start: 0.8193 (m-10) cc_final: 0.7881 (m-80) outliers start: 208 outliers final: 134 residues processed: 1485 average time/residue: 0.5770 time to fit residues: 1392.4808 Evaluate side-chains 1296 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1160 time to evaluate : 4.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 350 ILE Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 350 ILE Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 68 ASP Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain L residue 68 ASP Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 12 THR Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 67 THR Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 89 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 345 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 chunk 516 optimal weight: 10.0000 chunk 422 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 622 optimal weight: 4.9990 chunk 672 optimal weight: 3.9990 chunk 554 optimal weight: 10.0000 chunk 617 optimal weight: 8.9990 chunk 212 optimal weight: 1.9990 chunk 499 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN A 408 GLN B 325 ASN B 408 GLN C 325 ASN C 408 GLN ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 ASN D 408 GLN E 89 GLN E 325 ASN E 408 GLN F 291 GLN F 408 GLN ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 408 GLN H 89 GLN H 408 GLN ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 GLN ** J 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 408 GLN K 408 GLN ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 ASN L 408 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 54576 Z= 0.255 Angle : 0.666 9.046 74028 Z= 0.345 Chirality : 0.044 0.141 8196 Planarity : 0.005 0.047 9804 Dihedral : 5.818 27.172 7465 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 4.50 % Allowed : 14.01 % Favored : 81.50 % 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: -4.28 (0.08), residues: 6816 helix: -2.45 (0.08), residues: 2496 sheet: -2.71 (0.19), residues: 564 loop : -3.24 (0.08), residues: 3756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP f 40 HIS 0.006 0.002 HIS C 383 PHE 0.035 0.002 PHE G 30 TYR 0.013 0.001 TYR k 14 ARG 0.006 0.001 ARG g 122 *********************** 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 1512 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1255 time to evaluate : 4.419 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: A 12 ARG cc_start: 0.7869 (ttm110) cc_final: 0.7527 (ttm110) REVERT: A 84 LYS cc_start: 0.8403 (mttt) cc_final: 0.7954 (tttt) REVERT: A 157 ARG cc_start: 0.7217 (mtp180) cc_final: 0.6382 (mtp180) REVERT: A 371 MET cc_start: 0.8059 (mmm) cc_final: 0.7784 (mmt) REVERT: A 399 GLU cc_start: 0.6738 (tp30) cc_final: 0.6244 (tp30) REVERT: B 23 ARG cc_start: 0.8000 (tpt90) cc_final: 0.7360 (tpt-90) REVERT: B 84 LYS cc_start: 0.8432 (mttt) cc_final: 0.7953 (tttt) REVERT: B 157 ARG cc_start: 0.7310 (mtp180) cc_final: 0.6919 (mtp180) REVERT: B 378 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7457 (mt-10) REVERT: B 397 MET cc_start: 0.7441 (mmm) cc_final: 0.7090 (mmm) REVERT: C 84 LYS cc_start: 0.8421 (mttt) cc_final: 0.8032 (tttt) REVERT: C 157 ARG cc_start: 0.7722 (mtp180) cc_final: 0.7476 (mtp180) REVERT: C 160 ARG cc_start: 0.7510 (mmm-85) cc_final: 0.7276 (mmm-85) REVERT: C 238 MET cc_start: 0.8421 (ttm) cc_final: 0.8199 (ttp) REVERT: C 399 GLU cc_start: 0.6616 (tp30) cc_final: 0.5949 (tp30) REVERT: D 12 ARG cc_start: 0.7872 (ttm110) cc_final: 0.7520 (ttm110) REVERT: D 84 LYS cc_start: 0.8402 (mttt) cc_final: 0.7953 (tttt) REVERT: D 157 ARG cc_start: 0.7215 (mtp180) cc_final: 0.6387 (mtp180) REVERT: D 315 MET cc_start: 0.1517 (ttp) cc_final: 0.1229 (ttm) REVERT: D 371 MET cc_start: 0.8113 (mmm) cc_final: 0.7755 (mmt) REVERT: D 375 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6997 (mt-10) REVERT: D 399 GLU cc_start: 0.6768 (tp30) cc_final: 0.6250 (tp30) REVERT: E 23 ARG cc_start: 0.8002 (tpt90) cc_final: 0.7349 (tpt-90) REVERT: E 34 ARG cc_start: 0.6181 (OUTLIER) cc_final: 0.5944 (pmm-80) REVERT: E 84 LYS cc_start: 0.8448 (mttt) cc_final: 0.7956 (tttt) REVERT: E 157 ARG cc_start: 0.7302 (mtp180) cc_final: 0.6899 (mtp180) REVERT: E 160 ARG cc_start: 0.7525 (mmm-85) cc_final: 0.6993 (mmm-85) REVERT: E 162 GLN cc_start: 0.7761 (tt0) cc_final: 0.7538 (tt0) REVERT: E 369 GLU cc_start: 0.6008 (mt-10) cc_final: 0.5704 (tt0) REVERT: E 378 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7553 (mt-10) REVERT: F 84 LYS cc_start: 0.8408 (mttt) cc_final: 0.8005 (tttt) REVERT: F 160 ARG cc_start: 0.7515 (mmm-85) cc_final: 0.7277 (mmm-85) REVERT: F 238 MET cc_start: 0.8509 (ttm) cc_final: 0.8255 (ttp) REVERT: F 399 GLU cc_start: 0.6560 (tp30) cc_final: 0.5846 (tp30) REVERT: G 12 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7519 (ttm110) REVERT: G 84 LYS cc_start: 0.8398 (mttt) cc_final: 0.7958 (tttt) REVERT: G 157 ARG cc_start: 0.7226 (mtp180) cc_final: 0.6385 (mtp180) REVERT: G 315 MET cc_start: 0.1515 (ttp) cc_final: 0.1237 (ttm) REVERT: G 371 MET cc_start: 0.8064 (mmm) cc_final: 0.7783 (mmt) REVERT: G 399 GLU cc_start: 0.6766 (tp30) cc_final: 0.6255 (tp30) REVERT: H 23 ARG cc_start: 0.7999 (tpt90) cc_final: 0.7334 (tpt-90) REVERT: H 84 LYS cc_start: 0.8450 (mttt) cc_final: 0.7968 (tttt) REVERT: H 157 ARG cc_start: 0.7288 (mtp180) cc_final: 0.6890 (mtp180) REVERT: H 160 ARG cc_start: 0.7523 (mmm-85) cc_final: 0.6989 (mmm-85) REVERT: H 162 GLN cc_start: 0.7742 (tt0) cc_final: 0.7523 (tt0) REVERT: H 378 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7533 (mt-10) REVERT: H 420 ASP cc_start: 0.7049 (p0) cc_final: 0.6842 (p0) REVERT: I 84 LYS cc_start: 0.8420 (mttt) cc_final: 0.8032 (tttt) REVERT: I 157 ARG cc_start: 0.7683 (mtp180) cc_final: 0.7461 (mtp180) REVERT: I 160 ARG cc_start: 0.7506 (mmm-85) cc_final: 0.7287 (mmm-85) REVERT: I 238 MET cc_start: 0.8422 (ttm) cc_final: 0.8204 (ttp) REVERT: I 399 GLU cc_start: 0.6554 (tp30) cc_final: 0.5977 (tp30) REVERT: J 12 ARG cc_start: 0.7873 (ttm110) cc_final: 0.7518 (ttm110) REVERT: J 84 LYS cc_start: 0.8448 (mttt) cc_final: 0.8021 (tttt) REVERT: J 157 ARG cc_start: 0.7207 (mtp180) cc_final: 0.6370 (mtp180) REVERT: J 315 MET cc_start: 0.0976 (ttp) cc_final: 0.0708 (ttm) REVERT: J 378 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7162 (mt-10) REVERT: K 23 ARG cc_start: 0.7975 (tpt90) cc_final: 0.7340 (tpt-90) REVERT: K 84 LYS cc_start: 0.8426 (mttt) cc_final: 0.7948 (tttt) REVERT: K 157 ARG cc_start: 0.7307 (mtp180) cc_final: 0.6919 (mtp180) REVERT: K 378 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7456 (mt-10) REVERT: K 397 MET cc_start: 0.7446 (mmm) cc_final: 0.7092 (mmm) REVERT: K 420 ASP cc_start: 0.7092 (p0) cc_final: 0.6873 (p0) REVERT: L 39 ARG cc_start: 0.7521 (ttm170) cc_final: 0.7256 (ttt180) REVERT: L 84 LYS cc_start: 0.8408 (mttt) cc_final: 0.8000 (tttt) REVERT: L 160 ARG cc_start: 0.7479 (mmm-85) cc_final: 0.7244 (mmm-85) REVERT: L 238 MET cc_start: 0.8447 (ttm) cc_final: 0.8209 (ttp) REVERT: L 399 GLU cc_start: 0.6549 (tp30) cc_final: 0.5984 (tp30) REVERT: a 35 MET cc_start: 0.8483 (mmm) cc_final: 0.8201 (mmt) REVERT: c 16 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8166 (mp0) REVERT: f 65 ARG cc_start: 0.6965 (tmt170) cc_final: 0.6472 (tmm-80) REVERT: g 35 MET cc_start: 0.8355 (mmm) cc_final: 0.8117 (mmt) REVERT: h 14 TYR cc_start: 0.8252 (m-10) cc_final: 0.8039 (m-80) REVERT: i 16 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8166 (mp0) REVERT: l 16 GLU cc_start: 0.8148 (mp0) cc_final: 0.7676 (pm20) outliers start: 257 outliers final: 189 residues processed: 1373 average time/residue: 0.5694 time to fit residues: 1253.1271 Evaluate side-chains 1355 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1165 time to evaluate : 4.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 390 ILE Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 350 ILE Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 116 MET Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain K residue 424 GLN Chi-restraints excluded: chain L residue 34 ARG Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 116 MET Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 177 ILE Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 424 GLN Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 12 THR Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 42 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 67 THR Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 42 VAL Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 89 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 614 optimal weight: 7.9990 chunk 467 optimal weight: 7.9990 chunk 322 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 417 optimal weight: 1.9990 chunk 624 optimal weight: 7.9990 chunk 661 optimal weight: 6.9990 chunk 326 optimal weight: 5.9990 chunk 591 optimal weight: 8.9990 chunk 178 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 GLN B 70 GLN C 70 GLN D 70 GLN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN E 339 GLN F 70 GLN G 70 GLN ** G 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN H 325 ASN H 339 GLN ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN J 325 ASN K 70 GLN K 325 ASN ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 54576 Z= 0.312 Angle : 0.678 6.256 74028 Z= 0.352 Chirality : 0.045 0.145 8196 Planarity : 0.005 0.054 9804 Dihedral : 5.760 28.051 7465 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 5.30 % Allowed : 14.95 % Favored : 79.74 % 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: -3.91 (0.09), residues: 6816 helix: -1.99 (0.09), residues: 2520 sheet: -2.73 (0.19), residues: 588 loop : -3.10 (0.09), residues: 3708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 66 HIS 0.006 0.002 HIS I 383 PHE 0.043 0.003 PHE G 30 TYR 0.010 0.001 TYR A 155 ARG 0.008 0.001 ARG j 65 *********************** 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 1550 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 1247 time to evaluate : 4.451 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: A 12 ARG cc_start: 0.7980 (ttm110) cc_final: 0.7597 (ttm110) REVERT: A 160 ARG cc_start: 0.7831 (mmm-85) cc_final: 0.7592 (mmm-85) REVERT: B 23 ARG cc_start: 0.8021 (tpt90) cc_final: 0.7237 (tpt-90) REVERT: B 84 LYS cc_start: 0.8361 (mttt) cc_final: 0.7941 (tttt) REVERT: B 378 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7332 (mt-10) REVERT: C 84 LYS cc_start: 0.8411 (mttt) cc_final: 0.8078 (tttt) REVERT: C 129 ASP cc_start: 0.8222 (p0) cc_final: 0.7454 (p0) REVERT: C 238 MET cc_start: 0.8490 (ttm) cc_final: 0.8253 (ttp) REVERT: C 351 ARG cc_start: 0.8861 (tpp80) cc_final: 0.8653 (tpp-160) REVERT: C 399 GLU cc_start: 0.6707 (tp30) cc_final: 0.6151 (tp30) REVERT: D 12 ARG cc_start: 0.7985 (ttm110) cc_final: 0.7570 (ttm110) REVERT: D 84 LYS cc_start: 0.8398 (mttt) cc_final: 0.7989 (tttt) REVERT: D 160 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7580 (mmm-85) REVERT: E 23 ARG cc_start: 0.8007 (tpt90) cc_final: 0.7221 (tpt-90) REVERT: E 84 LYS cc_start: 0.8354 (mttt) cc_final: 0.7949 (tttt) REVERT: E 369 GLU cc_start: 0.5933 (mt-10) cc_final: 0.5655 (tt0) REVERT: E 378 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7344 (mt-10) REVERT: F 84 LYS cc_start: 0.8414 (mttt) cc_final: 0.8086 (tttt) REVERT: F 129 ASP cc_start: 0.8220 (p0) cc_final: 0.7480 (p0) REVERT: F 399 GLU cc_start: 0.6730 (tp30) cc_final: 0.6128 (tp30) REVERT: G 12 ARG cc_start: 0.7971 (ttm110) cc_final: 0.7558 (ttm110) REVERT: H 84 LYS cc_start: 0.8359 (mttt) cc_final: 0.7925 (tttt) REVERT: H 378 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7347 (mt-10) REVERT: I 84 LYS cc_start: 0.8414 (mttt) cc_final: 0.8086 (tttt) REVERT: I 129 ASP cc_start: 0.8218 (p0) cc_final: 0.7467 (p0) REVERT: I 238 MET cc_start: 0.8474 (ttm) cc_final: 0.8251 (ttp) REVERT: I 399 GLU cc_start: 0.6683 (tp30) cc_final: 0.6070 (tp30) REVERT: J 12 ARG cc_start: 0.7989 (ttm110) cc_final: 0.7578 (ttm110) REVERT: J 84 LYS cc_start: 0.8398 (mttt) cc_final: 0.7998 (tttt) REVERT: J 160 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7590 (mmm-85) REVERT: J 371 MET cc_start: 0.8019 (mmt) cc_final: 0.7803 (mmt) REVERT: J 373 GLU cc_start: 0.7795 (tp30) cc_final: 0.7559 (mm-30) REVERT: K 23 ARG cc_start: 0.8002 (tpt90) cc_final: 0.7208 (tpt-90) REVERT: K 84 LYS cc_start: 0.8353 (mttt) cc_final: 0.7932 (tttt) REVERT: K 378 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7336 (mt-10) REVERT: K 420 ASP cc_start: 0.7267 (p0) cc_final: 0.6993 (p0) REVERT: L 84 LYS cc_start: 0.8409 (mttt) cc_final: 0.8086 (tttt) REVERT: L 129 ASP cc_start: 0.8233 (p0) cc_final: 0.7488 (p0) REVERT: L 238 MET cc_start: 0.8471 (ttm) cc_final: 0.8250 (ttp) REVERT: L 399 GLU cc_start: 0.6680 (tp30) cc_final: 0.6127 (tp30) REVERT: f 65 ARG cc_start: 0.6819 (tmt170) cc_final: 0.6602 (ttp80) outliers start: 303 outliers final: 230 residues processed: 1393 average time/residue: 0.5516 time to fit residues: 1245.0138 Evaluate side-chains 1405 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1175 time to evaluate : 4.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 350 ILE Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 404 VAL Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 424 GLN Chi-restraints excluded: chain L residue 34 ARG Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 177 ILE Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 424 GLN Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain b residue 8 SER Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 12 THR Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 42 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 8 SER Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 67 THR Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 42 VAL Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 89 THR 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: 5.9990 chunk 9 optimal weight: 10.0000 chunk 492 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 564 optimal weight: 9.9990 chunk 457 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 337 optimal weight: 0.9980 chunk 593 optimal weight: 0.0970 chunk 166 optimal weight: 0.0670 overall best weight: 2.2320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 ASN ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 ASN ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 54576 Z= 0.202 Angle : 0.606 6.404 74028 Z= 0.312 Chirality : 0.042 0.135 8196 Planarity : 0.005 0.063 9804 Dihedral : 5.360 27.354 7465 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 4.64 % Allowed : 16.11 % Favored : 79.25 % 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: 2436 sheet: -2.58 (0.20), residues: 588 loop : -2.91 (0.09), residues: 3792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 49 HIS 0.004 0.001 HIS C 383 PHE 0.039 0.002 PHE L 30 TYR 0.014 0.001 TYR F 132 ARG 0.012 0.001 ARG l 65 *********************** 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 1497 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1232 time to evaluate : 4.693 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: A 12 ARG cc_start: 0.7983 (ttm110) cc_final: 0.7559 (ttm110) REVERT: A 84 LYS cc_start: 0.8265 (mttt) cc_final: 0.7950 (tttt) REVERT: A 373 GLU cc_start: 0.7737 (tp30) cc_final: 0.7418 (mm-30) REVERT: B 23 ARG cc_start: 0.7945 (tpt90) cc_final: 0.7224 (tpt-90) REVERT: B 84 LYS cc_start: 0.8331 (mttt) cc_final: 0.7932 (tttt) REVERT: B 160 ARG cc_start: 0.7430 (mmm-85) cc_final: 0.7105 (mmm-85) REVERT: B 378 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7272 (mt-10) REVERT: C 84 LYS cc_start: 0.8392 (mttt) cc_final: 0.8070 (tttt) REVERT: C 238 MET cc_start: 0.8444 (ttm) cc_final: 0.8242 (ttp) REVERT: C 375 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7657 (mt-10) REVERT: C 399 GLU cc_start: 0.6697 (tp30) cc_final: 0.6090 (tp30) REVERT: D 12 ARG cc_start: 0.7965 (ttm110) cc_final: 0.7545 (ttm110) REVERT: D 84 LYS cc_start: 0.8336 (mttt) cc_final: 0.7967 (tttt) REVERT: D 189 MET cc_start: 0.8553 (mmm) cc_final: 0.8278 (mmm) REVERT: D 373 GLU cc_start: 0.7728 (tp30) cc_final: 0.7389 (mm-30) REVERT: E 23 ARG cc_start: 0.7958 (tpt90) cc_final: 0.7247 (tpt-90) REVERT: E 84 LYS cc_start: 0.8292 (mttt) cc_final: 0.7912 (tttt) REVERT: E 378 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7231 (mt-10) REVERT: F 84 LYS cc_start: 0.8395 (mttt) cc_final: 0.8079 (tttt) REVERT: F 160 ARG cc_start: 0.7324 (mmm-85) cc_final: 0.6916 (mtp85) REVERT: F 357 ARG cc_start: 0.8002 (ttt-90) cc_final: 0.7712 (tmt170) REVERT: F 399 GLU cc_start: 0.6700 (tp30) cc_final: 0.6072 (tp30) REVERT: G 12 ARG cc_start: 0.7959 (ttm110) cc_final: 0.7540 (ttm110) REVERT: G 84 LYS cc_start: 0.8280 (mttt) cc_final: 0.7953 (tttt) REVERT: G 189 MET cc_start: 0.8568 (mmm) cc_final: 0.8291 (mmm) REVERT: G 239 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7814 (mp0) REVERT: H 84 LYS cc_start: 0.8335 (mttt) cc_final: 0.7978 (tttt) REVERT: H 378 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7235 (mt-10) REVERT: I 84 LYS cc_start: 0.8400 (mttt) cc_final: 0.8078 (tttt) REVERT: I 160 ARG cc_start: 0.7260 (mmm-85) cc_final: 0.6986 (mtp85) REVERT: I 357 ARG cc_start: 0.8001 (ttt-90) cc_final: 0.7726 (tmt170) REVERT: I 399 GLU cc_start: 0.6679 (tp30) cc_final: 0.6009 (tp30) REVERT: J 12 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7554 (ttm110) REVERT: J 84 LYS cc_start: 0.8360 (mttt) cc_final: 0.7969 (tttt) REVERT: K 23 ARG cc_start: 0.7929 (tpt90) cc_final: 0.7211 (tpt-90) REVERT: K 84 LYS cc_start: 0.8330 (mttt) cc_final: 0.7968 (tttt) REVERT: K 378 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7265 (mt-10) REVERT: K 420 ASP cc_start: 0.7388 (p0) cc_final: 0.7085 (p0) REVERT: L 84 LYS cc_start: 0.8393 (mttt) cc_final: 0.8075 (tttt) REVERT: L 160 ARG cc_start: 0.7323 (mmm-85) cc_final: 0.6911 (mtp85) REVERT: L 357 ARG cc_start: 0.8006 (ttt-90) cc_final: 0.7744 (tmt170) REVERT: L 399 GLU cc_start: 0.6706 (tp30) cc_final: 0.6085 (tp30) REVERT: a 16 GLU cc_start: 0.7835 (mp0) cc_final: 0.7474 (mp0) REVERT: a 62 TYR cc_start: 0.5938 (m-80) cc_final: 0.5702 (m-10) REVERT: d 16 GLU cc_start: 0.7762 (mp0) cc_final: 0.7417 (mp0) REVERT: e 16 GLU cc_start: 0.7846 (pm20) cc_final: 0.7375 (pm20) REVERT: f 16 GLU cc_start: 0.7855 (mp0) cc_final: 0.7508 (mp0) REVERT: f 65 ARG cc_start: 0.6799 (tmt170) cc_final: 0.6491 (ttp80) REVERT: g 16 GLU cc_start: 0.7729 (mp0) cc_final: 0.7392 (mp0) REVERT: h 16 GLU cc_start: 0.7697 (pm20) cc_final: 0.7391 (pm20) REVERT: j 16 GLU cc_start: 0.7830 (mp0) cc_final: 0.7481 (mp0) REVERT: j 62 TYR cc_start: 0.5836 (m-80) cc_final: 0.5619 (m-80) outliers start: 265 outliers final: 199 residues processed: 1351 average time/residue: 0.5530 time to fit residues: 1212.8631 Evaluate side-chains 1371 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1172 time to evaluate : 4.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 PHE Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 350 ILE Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 404 VAL Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 424 GLN Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 177 ILE Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 12 THR Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 8 SER Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 67 THR Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain g residue 8 SER Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 89 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 222 optimal weight: 3.9990 chunk 595 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 388 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 661 optimal weight: 1.9990 chunk 549 optimal weight: 4.9990 chunk 306 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 218 optimal weight: 8.9990 chunk 347 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 107 ASN e 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54576 Z= 0.210 Angle : 0.602 6.320 74028 Z= 0.310 Chirality : 0.042 0.138 8196 Planarity : 0.005 0.043 9804 Dihedral : 5.233 26.488 7465 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 4.99 % Allowed : 16.60 % Favored : 78.41 % 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: -3.10 (0.09), residues: 6816 helix: -0.94 (0.10), residues: 2436 sheet: -2.47 (0.20), residues: 588 loop : -2.86 (0.09), residues: 3792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 49 HIS 0.004 0.001 HIS I 383 PHE 0.032 0.002 PHE F 30 TYR 0.020 0.001 TYR F 132 ARG 0.008 0.001 ARG G 157 *********************** 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 1481 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1196 time to evaluate : 4.468 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: A 12 ARG cc_start: 0.8092 (ttm110) cc_final: 0.7654 (ttm110) REVERT: A 84 LYS cc_start: 0.8232 (mttt) cc_final: 0.7940 (tttt) REVERT: A 373 GLU cc_start: 0.7780 (tp30) cc_final: 0.7470 (mm-30) REVERT: B 23 ARG cc_start: 0.7964 (tpt90) cc_final: 0.7224 (tpt-90) REVERT: B 84 LYS cc_start: 0.8288 (mttt) cc_final: 0.7943 (tttt) REVERT: B 139 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8032 (mmm-85) REVERT: B 268 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7727 (mpp) REVERT: B 378 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7240 (mt-10) REVERT: C 84 LYS cc_start: 0.8355 (mttt) cc_final: 0.8051 (tttt) REVERT: C 399 GLU cc_start: 0.6688 (tp30) cc_final: 0.6304 (tp30) REVERT: D 12 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7623 (ttm110) REVERT: D 84 LYS cc_start: 0.8323 (mttt) cc_final: 0.7967 (tttt) REVERT: D 373 GLU cc_start: 0.7711 (tp30) cc_final: 0.7428 (mm-30) REVERT: E 23 ARG cc_start: 0.7977 (tpt90) cc_final: 0.7233 (tpt-90) REVERT: E 84 LYS cc_start: 0.8286 (mttt) cc_final: 0.7944 (tttt) REVERT: E 378 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7220 (mt-10) REVERT: F 84 LYS cc_start: 0.8349 (mttt) cc_final: 0.8058 (tttt) REVERT: F 160 ARG cc_start: 0.7353 (mmm-85) cc_final: 0.7020 (tpt-90) REVERT: F 357 ARG cc_start: 0.7957 (ttt-90) cc_final: 0.7713 (tmt170) REVERT: F 399 GLU cc_start: 0.6683 (tp30) cc_final: 0.6293 (tp30) REVERT: G 12 ARG cc_start: 0.8043 (ttm110) cc_final: 0.7619 (ttm110) REVERT: G 84 LYS cc_start: 0.8246 (mttt) cc_final: 0.7939 (tttt) REVERT: G 371 MET cc_start: 0.7941 (mmt) cc_final: 0.7658 (mmt) REVERT: G 373 GLU cc_start: 0.7751 (tp30) cc_final: 0.7434 (mm-30) REVERT: H 84 LYS cc_start: 0.8287 (mttt) cc_final: 0.7943 (tttt) REVERT: H 378 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7210 (mt-10) REVERT: I 84 LYS cc_start: 0.8350 (mttt) cc_final: 0.8061 (tttt) REVERT: I 357 ARG cc_start: 0.7969 (ttt-90) cc_final: 0.7743 (tmt170) REVERT: I 399 GLU cc_start: 0.6739 (tp30) cc_final: 0.6078 (tp30) REVERT: J 12 ARG cc_start: 0.8080 (ttm110) cc_final: 0.7636 (ttm110) REVERT: J 84 LYS cc_start: 0.8317 (mttt) cc_final: 0.7976 (tttt) REVERT: J 378 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7159 (mt-10) REVERT: K 23 ARG cc_start: 0.7962 (tpt90) cc_final: 0.7100 (tpt-90) REVERT: K 84 LYS cc_start: 0.8288 (mttt) cc_final: 0.7946 (tttt) REVERT: K 139 ARG cc_start: 0.8369 (mtp85) cc_final: 0.7982 (mmm-85) REVERT: K 160 ARG cc_start: 0.7197 (mmm-85) cc_final: 0.6979 (mtp85) REVERT: K 378 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7245 (mt-10) REVERT: K 420 ASP cc_start: 0.7385 (p0) cc_final: 0.7036 (p0) REVERT: L 84 LYS cc_start: 0.8343 (mttt) cc_final: 0.8055 (tttt) REVERT: L 160 ARG cc_start: 0.7343 (mmm-85) cc_final: 0.7100 (mtp85) REVERT: L 357 ARG cc_start: 0.7962 (ttt-90) cc_final: 0.7734 (tmt170) REVERT: L 371 MET cc_start: 0.7860 (mmt) cc_final: 0.7527 (mmt) REVERT: L 375 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7113 (mt-10) REVERT: L 399 GLU cc_start: 0.6686 (tp30) cc_final: 0.6303 (tp30) REVERT: d 62 TYR cc_start: 0.6072 (m-80) cc_final: 0.5654 (m-10) REVERT: e 16 GLU cc_start: 0.7896 (pm20) cc_final: 0.7545 (pm20) REVERT: f 16 GLU cc_start: 0.7786 (mp0) cc_final: 0.7473 (mp0) outliers start: 285 outliers final: 232 residues processed: 1325 average time/residue: 0.5484 time to fit residues: 1180.1886 Evaluate side-chains 1400 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1167 time to evaluate : 4.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 PHE Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 350 ILE Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 350 ILE Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 404 VAL Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 424 GLN Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 177 ILE Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain b residue 8 SER Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 12 THR Chi-restraints excluded: chain e residue 42 VAL Chi-restraints excluded: chain e residue 46 LYS Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 67 THR Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain g residue 8 SER Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 89 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 638 optimal weight: 0.0060 chunk 74 optimal weight: 20.0000 chunk 377 optimal weight: 10.0000 chunk 483 optimal weight: 7.9990 chunk 374 optimal weight: 4.9990 chunk 557 optimal weight: 0.0070 chunk 369 optimal weight: 20.0000 chunk 659 optimal weight: 3.9990 chunk 412 optimal weight: 4.9990 chunk 401 optimal weight: 10.0000 chunk 304 optimal weight: 0.2980 overall best weight: 1.8618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 54576 Z= 0.183 Angle : 0.580 6.631 74028 Z= 0.297 Chirality : 0.041 0.139 8196 Planarity : 0.004 0.041 9804 Dihedral : 5.062 25.903 7465 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 4.83 % Allowed : 17.30 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.09), residues: 6816 helix: -0.69 (0.11), residues: 2448 sheet: -2.34 (0.21), residues: 588 loop : -2.82 (0.09), residues: 3780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 49 HIS 0.004 0.001 HIS F 179 PHE 0.033 0.002 PHE C 30 TYR 0.017 0.001 TYR C 132 ARG 0.009 0.001 ARG C 160 *********************** 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 1482 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1206 time to evaluate : 4.453 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: A 12 ARG cc_start: 0.8079 (ttm110) cc_final: 0.7662 (ttm110) REVERT: A 84 LYS cc_start: 0.8224 (mttt) cc_final: 0.7912 (tttt) REVERT: A 373 GLU cc_start: 0.7746 (tp30) cc_final: 0.7462 (mm-30) REVERT: B 23 ARG cc_start: 0.7959 (tpt90) cc_final: 0.7099 (tpt-90) REVERT: B 84 LYS cc_start: 0.8269 (mttt) cc_final: 0.7939 (tttt) REVERT: B 268 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7770 (mpp) REVERT: B 378 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7235 (mt-10) REVERT: C 84 LYS cc_start: 0.8311 (mttt) cc_final: 0.8036 (tttt) REVERT: C 94 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8116 (tm-30) REVERT: C 399 GLU cc_start: 0.6697 (tp30) cc_final: 0.6300 (tp30) REVERT: D 12 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7616 (ttm110) REVERT: D 84 LYS cc_start: 0.8315 (mttt) cc_final: 0.7904 (tttt) REVERT: D 160 ARG cc_start: 0.7453 (mmm-85) cc_final: 0.6989 (mmm-85) REVERT: E 23 ARG cc_start: 0.8010 (tpt90) cc_final: 0.7255 (tpt-90) REVERT: E 84 LYS cc_start: 0.8248 (mttt) cc_final: 0.7922 (tttt) REVERT: E 378 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7199 (mt-10) REVERT: F 84 LYS cc_start: 0.8313 (mttt) cc_final: 0.8043 (tttt) REVERT: F 94 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8091 (tm-30) REVERT: F 357 ARG cc_start: 0.7922 (ttt-90) cc_final: 0.7667 (tmt170) REVERT: F 399 GLU cc_start: 0.6654 (tp30) cc_final: 0.6228 (tp30) REVERT: G 12 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7612 (ttm110) REVERT: G 84 LYS cc_start: 0.8227 (mttt) cc_final: 0.7901 (tttt) REVERT: G 189 MET cc_start: 0.8543 (mmm) cc_final: 0.8249 (mmm) REVERT: H 84 LYS cc_start: 0.8252 (mttt) cc_final: 0.7917 (tttt) REVERT: H 160 ARG cc_start: 0.7249 (mmm-85) cc_final: 0.6932 (mtp85) REVERT: H 378 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7193 (mt-10) REVERT: I 84 LYS cc_start: 0.8318 (mttt) cc_final: 0.8044 (tttt) REVERT: I 357 ARG cc_start: 0.7922 (ttt-90) cc_final: 0.7677 (tmt170) REVERT: I 399 GLU cc_start: 0.6779 (tp30) cc_final: 0.6099 (tp30) REVERT: J 12 ARG cc_start: 0.8077 (ttm110) cc_final: 0.7638 (ttm110) REVERT: J 84 LYS cc_start: 0.8299 (mttt) cc_final: 0.7940 (tttt) REVERT: J 315 MET cc_start: 0.1524 (ttp) cc_final: 0.1179 (ttm) REVERT: J 378 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7215 (mt-10) REVERT: K 23 ARG cc_start: 0.7969 (tpt90) cc_final: 0.7238 (tpt-90) REVERT: K 84 LYS cc_start: 0.8272 (mttt) cc_final: 0.7956 (tttt) REVERT: K 378 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7212 (mt-10) REVERT: K 420 ASP cc_start: 0.7335 (p0) cc_final: 0.7059 (p0) REVERT: L 84 LYS cc_start: 0.8307 (mttt) cc_final: 0.8066 (tttt) REVERT: L 94 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8096 (tm-30) REVERT: L 160 ARG cc_start: 0.7317 (mmm-85) cc_final: 0.7008 (tpt-90) REVERT: L 357 ARG cc_start: 0.7912 (ttt-90) cc_final: 0.7666 (tmt170) REVERT: L 399 GLU cc_start: 0.6657 (tp30) cc_final: 0.6238 (tp30) REVERT: a 16 GLU cc_start: 0.7827 (mp0) cc_final: 0.7486 (mp0) REVERT: a 62 TYR cc_start: 0.5944 (m-80) cc_final: 0.5658 (m-10) REVERT: d 62 TYR cc_start: 0.5937 (m-80) cc_final: 0.5605 (m-10) REVERT: f 16 GLU cc_start: 0.7818 (mp0) cc_final: 0.7516 (mp0) REVERT: j 16 GLU cc_start: 0.7828 (mp0) cc_final: 0.7486 (mp0) REVERT: j 62 TYR cc_start: 0.6087 (m-80) cc_final: 0.5806 (m-10) outliers start: 276 outliers final: 217 residues processed: 1324 average time/residue: 0.5478 time to fit residues: 1188.5448 Evaluate side-chains 1377 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1159 time to evaluate : 4.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 404 VAL Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 424 GLN Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 177 ILE Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain b residue 8 SER Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 12 THR Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 67 THR Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain g residue 8 SER Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain k residue 104 ASN Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 89 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 407 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 393 optimal weight: 8.9990 chunk 198 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 419 optimal weight: 10.0000 chunk 449 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 518 optimal weight: 10.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 54576 Z= 0.355 Angle : 0.688 7.930 74028 Z= 0.356 Chirality : 0.046 0.151 8196 Planarity : 0.005 0.060 9804 Dihedral : 5.535 29.235 7465 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.21 % Favored : 87.79 % Rotamer: Outliers : 5.44 % Allowed : 17.23 % Favored : 77.33 % 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: -3.03 (0.09), residues: 6816 helix: -0.87 (0.10), residues: 2436 sheet: -2.44 (0.20), residues: 588 loop : -2.83 (0.09), residues: 3792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 66 HIS 0.006 0.002 HIS C 173 PHE 0.042 0.003 PHE I 30 TYR 0.014 0.001 TYR I 132 ARG 0.011 0.001 ARG E 160 *********************** 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 1485 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1174 time to evaluate : 4.509 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: A 12 ARG cc_start: 0.8267 (ttm110) cc_final: 0.7924 (ttm110) REVERT: A 84 LYS cc_start: 0.8287 (mttt) cc_final: 0.7936 (tttt) REVERT: A 371 MET cc_start: 0.7872 (mmt) cc_final: 0.7649 (mmt) REVERT: A 378 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7224 (mt-10) REVERT: B 12 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7484 (ttm110) REVERT: B 23 ARG cc_start: 0.8159 (tpt90) cc_final: 0.7418 (tpt-90) REVERT: B 84 LYS cc_start: 0.8309 (mttt) cc_final: 0.7974 (tttt) REVERT: B 138 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7849 (ptt-90) REVERT: B 268 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7780 (mpp) REVERT: B 305 THR cc_start: 0.7464 (p) cc_final: 0.7246 (p) REVERT: B 378 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7282 (mt-10) REVERT: C 23 ARG cc_start: 0.7918 (tpt90) cc_final: 0.7238 (tpt-90) REVERT: C 84 LYS cc_start: 0.8347 (mttt) cc_final: 0.8084 (tttt) REVERT: D 12 ARG cc_start: 0.8256 (ttm110) cc_final: 0.7900 (ttm110) REVERT: E 23 ARG cc_start: 0.8166 (tpt90) cc_final: 0.7404 (tpt-90) REVERT: E 84 LYS cc_start: 0.8307 (mttt) cc_final: 0.7952 (tttt) REVERT: E 305 THR cc_start: 0.7455 (p) cc_final: 0.7250 (p) REVERT: E 378 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7273 (mt-10) REVERT: F 23 ARG cc_start: 0.7884 (tpt90) cc_final: 0.7229 (tpt-90) REVERT: F 84 LYS cc_start: 0.8349 (mttt) cc_final: 0.8082 (tttt) REVERT: G 12 ARG cc_start: 0.8256 (ttm110) cc_final: 0.7897 (ttm110) REVERT: G 84 LYS cc_start: 0.8293 (mttt) cc_final: 0.7944 (ttpp) REVERT: G 371 MET cc_start: 0.7981 (mmt) cc_final: 0.7742 (mmt) REVERT: G 378 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7265 (mt-10) REVERT: H 23 ARG cc_start: 0.8043 (tpt90) cc_final: 0.7340 (tpt-90) REVERT: H 84 LYS cc_start: 0.8302 (mttt) cc_final: 0.7955 (tttt) REVERT: H 305 THR cc_start: 0.7455 (p) cc_final: 0.7254 (p) REVERT: H 378 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7254 (mt-10) REVERT: I 23 ARG cc_start: 0.7900 (tpt90) cc_final: 0.7239 (tpt-90) REVERT: I 84 LYS cc_start: 0.8363 (mttt) cc_final: 0.8090 (tttt) REVERT: J 12 ARG cc_start: 0.8267 (ttm110) cc_final: 0.7919 (ttm110) REVERT: J 84 LYS cc_start: 0.8325 (mttt) cc_final: 0.8002 (tttt) REVERT: J 378 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7309 (mt-10) REVERT: K 12 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7508 (ttm110) REVERT: K 23 ARG cc_start: 0.8167 (tpt90) cc_final: 0.7408 (tpt-90) REVERT: K 84 LYS cc_start: 0.8273 (mttt) cc_final: 0.7955 (tttt) REVERT: K 138 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7877 (ptt-90) REVERT: K 305 THR cc_start: 0.7476 (p) cc_final: 0.7245 (p) REVERT: K 378 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7300 (mt-10) REVERT: K 420 ASP cc_start: 0.7475 (p0) cc_final: 0.7208 (p0) REVERT: L 23 ARG cc_start: 0.7902 (tpt90) cc_final: 0.7224 (tpt-90) REVERT: L 84 LYS cc_start: 0.8365 (mttt) cc_final: 0.8091 (tttt) REVERT: L 160 ARG cc_start: 0.7368 (mmm-85) cc_final: 0.7020 (tpt-90) REVERT: L 162 GLN cc_start: 0.7881 (tt0) cc_final: 0.7635 (tt0) REVERT: a 16 GLU cc_start: 0.7880 (mp0) cc_final: 0.7666 (mp0) REVERT: a 62 TYR cc_start: 0.6286 (m-80) cc_final: 0.5972 (m-10) REVERT: b 9 ASP cc_start: 0.7968 (t0) cc_final: 0.7727 (t0) REVERT: b 46 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8130 (tptm) REVERT: d 62 TYR cc_start: 0.6215 (m-80) cc_final: 0.5913 (m-10) REVERT: f 65 ARG cc_start: 0.7237 (tpp80) cc_final: 0.6385 (tpp80) REVERT: g 62 TYR cc_start: 0.6244 (m-10) cc_final: 0.5922 (m-10) REVERT: j 16 GLU cc_start: 0.7890 (mp0) cc_final: 0.7675 (mp0) REVERT: j 62 TYR cc_start: 0.6288 (m-80) cc_final: 0.6040 (m-10) REVERT: k 9 ASP cc_start: 0.7974 (t0) cc_final: 0.7744 (t0) REVERT: k 46 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8150 (tptm) outliers start: 311 outliers final: 239 residues processed: 1330 average time/residue: 0.5554 time to fit residues: 1193.2275 Evaluate side-chains 1380 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1134 time to evaluate : 4.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 349 ILE Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 350 ILE Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 404 VAL Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 138 ARG Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 424 GLN Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 177 ILE Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 238 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 424 GLN Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain b residue 8 SER Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 12 THR Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 67 THR Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain g residue 8 SER Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 28 ILE Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 84 VAL Chi-restraints excluded: chain i residue 88 SER Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain k residue 46 LYS Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 84 VAL Chi-restraints excluded: chain l residue 89 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 599 optimal weight: 10.0000 chunk 631 optimal weight: 4.9990 chunk 576 optimal weight: 30.0000 chunk 614 optimal weight: 0.9980 chunk 369 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 482 optimal weight: 4.9990 chunk 188 optimal weight: 8.9990 chunk 555 optimal weight: 0.2980 chunk 581 optimal weight: 10.0000 chunk 612 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 GLN ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 ASN ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 54576 Z= 0.229 Angle : 0.630 9.071 74028 Z= 0.323 Chirality : 0.043 0.193 8196 Planarity : 0.005 0.057 9804 Dihedral : 5.321 28.520 7465 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 4.92 % Allowed : 17.98 % Favored : 77.10 % 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: -2.89 (0.09), residues: 6816 helix: -0.60 (0.11), residues: 2448 sheet: -2.38 (0.20), residues: 588 loop : -2.87 (0.09), residues: 3780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 49 HIS 0.005 0.001 HIS I 173 PHE 0.034 0.002 PHE A 154 TYR 0.011 0.001 TYR L 132 ARG 0.009 0.001 ARG K 160 *********************** 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 1421 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1140 time to evaluate : 4.552 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: A 12 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7835 (ttm110) REVERT: A 23 ARG cc_start: 0.7890 (tpt90) cc_final: 0.7258 (tpt-90) REVERT: A 84 LYS cc_start: 0.8253 (mttt) cc_final: 0.7938 (tttt) REVERT: A 378 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7091 (mt-10) REVERT: B 12 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7458 (ttm110) REVERT: B 23 ARG cc_start: 0.8112 (tpt90) cc_final: 0.7336 (tpt-90) REVERT: B 84 LYS cc_start: 0.8300 (mttt) cc_final: 0.7988 (tttt) REVERT: B 268 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7728 (mpp) REVERT: B 305 THR cc_start: 0.7343 (p) cc_final: 0.7112 (p) REVERT: B 378 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7232 (mt-10) REVERT: C 84 LYS cc_start: 0.8320 (mttt) cc_final: 0.8073 (tttt) REVERT: D 12 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7753 (ttm110) REVERT: D 84 LYS cc_start: 0.8277 (mttt) cc_final: 0.7947 (tttt) REVERT: E 12 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7518 (ttm110) REVERT: E 23 ARG cc_start: 0.8120 (tpt90) cc_final: 0.7322 (tpt-90) REVERT: E 43 TYR cc_start: 0.8257 (m-80) cc_final: 0.8018 (m-80) REVERT: E 84 LYS cc_start: 0.8302 (mttt) cc_final: 0.7982 (tttt) REVERT: E 305 THR cc_start: 0.7336 (p) cc_final: 0.7092 (p) REVERT: E 378 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7231 (mt-10) REVERT: F 84 LYS cc_start: 0.8336 (mttt) cc_final: 0.8081 (tttt) REVERT: F 162 GLN cc_start: 0.7877 (tt0) cc_final: 0.7658 (tt0) REVERT: G 12 ARG cc_start: 0.8196 (ttm110) cc_final: 0.7747 (ttm110) REVERT: G 84 LYS cc_start: 0.8264 (mttt) cc_final: 0.7938 (tttt) REVERT: G 189 MET cc_start: 0.8473 (mmm) cc_final: 0.8177 (mmm) REVERT: G 378 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7130 (mt-10) REVERT: H 43 TYR cc_start: 0.8199 (m-80) cc_final: 0.7954 (m-80) REVERT: H 84 LYS cc_start: 0.8305 (mttt) cc_final: 0.7989 (tttt) REVERT: H 160 ARG cc_start: 0.7368 (mmm-85) cc_final: 0.7067 (mtp85) REVERT: H 176 ARG cc_start: 0.6658 (mtp180) cc_final: 0.6332 (mtm-85) REVERT: H 305 THR cc_start: 0.7356 (p) cc_final: 0.7118 (p) REVERT: H 378 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7218 (mt-10) REVERT: I 84 LYS cc_start: 0.8342 (mttt) cc_final: 0.8085 (tttt) REVERT: J 12 ARG cc_start: 0.8181 (ttm110) cc_final: 0.7827 (ttm110) REVERT: J 23 ARG cc_start: 0.7890 (tpt90) cc_final: 0.7252 (tpt-90) REVERT: J 84 LYS cc_start: 0.8322 (mttt) cc_final: 0.7949 (tttt) REVERT: J 378 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7216 (mt-10) REVERT: K 12 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7496 (ttm110) REVERT: K 23 ARG cc_start: 0.8077 (tpt90) cc_final: 0.7307 (tpt-90) REVERT: K 43 TYR cc_start: 0.8173 (m-80) cc_final: 0.7933 (m-80) REVERT: K 84 LYS cc_start: 0.8296 (mttt) cc_final: 0.7993 (tttt) REVERT: K 305 THR cc_start: 0.7331 (p) cc_final: 0.7104 (p) REVERT: K 378 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7247 (mt-10) REVERT: K 420 ASP cc_start: 0.7584 (p0) cc_final: 0.7289 (p0) REVERT: L 84 LYS cc_start: 0.8341 (mttt) cc_final: 0.8094 (tttt) REVERT: L 160 ARG cc_start: 0.7349 (mmm-85) cc_final: 0.7028 (tpt-90) REVERT: L 162 GLN cc_start: 0.7817 (tt0) cc_final: 0.7559 (tt0) REVERT: a 16 GLU cc_start: 0.7838 (mp0) cc_final: 0.7468 (mp0) REVERT: a 62 TYR cc_start: 0.6175 (m-80) cc_final: 0.5820 (m-10) REVERT: d 62 TYR cc_start: 0.6037 (m-80) cc_final: 0.5556 (m-10) REVERT: e 16 GLU cc_start: 0.7913 (pm20) cc_final: 0.7610 (pm20) REVERT: f 65 ARG cc_start: 0.7270 (tpp80) cc_final: 0.6334 (tpp80) REVERT: g 62 TYR cc_start: 0.6125 (m-10) cc_final: 0.5816 (m-10) REVERT: j 16 GLU cc_start: 0.7892 (mp0) cc_final: 0.7520 (mp0) REVERT: j 62 TYR cc_start: 0.6125 (m-80) cc_final: 0.5735 (m-10) outliers start: 281 outliers final: 234 residues processed: 1278 average time/residue: 0.5442 time to fit residues: 1130.0448 Evaluate side-chains 1365 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1127 time to evaluate : 4.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 411 GLU Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 411 GLU Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 350 ILE Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 404 VAL Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 424 GLN Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 PHE Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 177 ILE Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 349 ILE Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 62 TYR Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 12 THR Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 67 THR Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 84 VAL Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 28 ILE Chi-restraints excluded: chain h residue 62 TYR Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 84 VAL Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain k residue 46 LYS Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 84 VAL Chi-restraints excluded: chain l residue 88 SER Chi-restraints excluded: chain l residue 89 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 403 optimal weight: 9.9990 chunk 649 optimal weight: 3.9990 chunk 396 optimal weight: 10.0000 chunk 308 optimal weight: 8.9990 chunk 451 optimal weight: 9.9990 chunk 681 optimal weight: 9.9990 chunk 627 optimal weight: 0.9990 chunk 542 optimal weight: 0.0040 chunk 56 optimal weight: 9.9990 chunk 419 optimal weight: 9.9990 chunk 332 optimal weight: 10.0000 overall best weight: 4.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 HIS ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 54576 Z= 0.353 Angle : 0.705 10.162 74028 Z= 0.363 Chirality : 0.046 0.166 8196 Planarity : 0.005 0.048 9804 Dihedral : 5.611 29.853 7465 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.82 % Favored : 87.18 % Rotamer: Outliers : 4.59 % Allowed : 18.33 % Favored : 77.08 % 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: -3.04 (0.09), residues: 6816 helix: -0.81 (0.10), residues: 2520 sheet: -2.47 (0.20), residues: 588 loop : -2.93 (0.09), residues: 3708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 66 HIS 0.006 0.002 HIS F 173 PHE 0.038 0.002 PHE I 30 TYR 0.014 0.002 TYR I 155 ARG 0.017 0.001 ARG K 160 ********************** 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 1406 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1144 time to evaluate : 4.494 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: A 12 ARG cc_start: 0.8299 (ttm110) cc_final: 0.7946 (ttm110) REVERT: A 84 LYS cc_start: 0.8322 (mttt) cc_final: 0.8012 (ttpp) REVERT: B 12 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7525 (ttm110) REVERT: B 23 ARG cc_start: 0.8171 (tpt90) cc_final: 0.7424 (tpt-90) REVERT: B 84 LYS cc_start: 0.8301 (mttt) cc_final: 0.8005 (tttt) REVERT: B 268 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7755 (mpp) REVERT: B 305 THR cc_start: 0.7628 (p) cc_final: 0.7404 (p) REVERT: B 378 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7287 (mt-10) REVERT: C 23 ARG cc_start: 0.7888 (tpt90) cc_final: 0.7177 (tpt-90) REVERT: C 80 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7857 (mt-10) REVERT: C 84 LYS cc_start: 0.8344 (mttt) cc_final: 0.8102 (tttt) REVERT: D 12 ARG cc_start: 0.8284 (ttm110) cc_final: 0.7925 (ttm110) REVERT: D 84 LYS cc_start: 0.8323 (mttt) cc_final: 0.7979 (ttpp) REVERT: E 12 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7550 (ttm110) REVERT: E 23 ARG cc_start: 0.8166 (tpt90) cc_final: 0.7403 (tpt-90) REVERT: E 84 LYS cc_start: 0.8294 (mttt) cc_final: 0.7993 (tttt) REVERT: E 160 ARG cc_start: 0.7030 (mtp85) cc_final: 0.6777 (mmm160) REVERT: E 305 THR cc_start: 0.7580 (p) cc_final: 0.7371 (p) REVERT: E 378 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7281 (mt-10) REVERT: F 23 ARG cc_start: 0.7906 (tpt90) cc_final: 0.7244 (tpt-90) REVERT: F 80 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7855 (mt-10) REVERT: F 84 LYS cc_start: 0.8345 (mttt) cc_final: 0.8104 (tttt) REVERT: G 12 ARG cc_start: 0.8281 (ttm110) cc_final: 0.7915 (ttm110) REVERT: G 84 LYS cc_start: 0.8336 (mttt) cc_final: 0.7983 (tttt) REVERT: G 189 MET cc_start: 0.8505 (mmm) cc_final: 0.8186 (mmm) REVERT: G 378 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7270 (mt-10) REVERT: H 23 ARG cc_start: 0.8008 (tpt90) cc_final: 0.7189 (tpt-90) REVERT: H 84 LYS cc_start: 0.8296 (mttt) cc_final: 0.7992 (tttt) REVERT: H 160 ARG cc_start: 0.7480 (mmm-85) cc_final: 0.7192 (mtp85) REVERT: H 305 THR cc_start: 0.7569 (p) cc_final: 0.7361 (p) REVERT: H 378 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7265 (mt-10) REVERT: I 23 ARG cc_start: 0.7927 (tpt90) cc_final: 0.7250 (tpt-90) REVERT: I 80 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7847 (mt-10) REVERT: I 84 LYS cc_start: 0.8351 (mttt) cc_final: 0.8109 (tttt) REVERT: J 12 ARG cc_start: 0.8290 (ttm110) cc_final: 0.7928 (ttm110) REVERT: J 76 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.8029 (tt) REVERT: J 84 LYS cc_start: 0.8334 (mttt) cc_final: 0.7991 (ttpp) REVERT: J 378 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7254 (mt-10) REVERT: K 12 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7532 (ttm110) REVERT: K 23 ARG cc_start: 0.8151 (tpt90) cc_final: 0.7402 (tpt-90) REVERT: K 84 LYS cc_start: 0.8290 (mttt) cc_final: 0.7990 (tttt) REVERT: K 138 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7804 (ptt-90) REVERT: K 160 ARG cc_start: 0.8149 (mmm160) cc_final: 0.7896 (ttt90) REVERT: K 305 THR cc_start: 0.7619 (p) cc_final: 0.7396 (p) REVERT: K 378 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7280 (mt-10) REVERT: L 23 ARG cc_start: 0.7900 (tpt90) cc_final: 0.7178 (tpt-90) REVERT: L 80 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7851 (mt-10) REVERT: L 84 LYS cc_start: 0.8350 (mttt) cc_final: 0.8106 (tttt) REVERT: L 160 ARG cc_start: 0.7491 (mmm-85) cc_final: 0.7115 (tpt-90) REVERT: b 46 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8235 (tptm) REVERT: e 16 GLU cc_start: 0.7915 (pm20) cc_final: 0.7581 (pm20) REVERT: f 65 ARG cc_start: 0.7468 (tpp80) cc_final: 0.6551 (tpp80) REVERT: g 62 TYR cc_start: 0.6180 (m-10) cc_final: 0.5616 (m-10) outliers start: 262 outliers final: 237 residues processed: 1284 average time/residue: 0.5520 time to fit residues: 1149.1561 Evaluate side-chains 1368 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1124 time to evaluate : 4.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 411 GLU Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 411 GLU Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 350 ILE Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 404 VAL Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 138 ARG Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 424 GLN Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 120 PHE Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 177 ILE Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 349 ILE Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 411 GLU Chi-restraints excluded: chain L residue 424 GLN Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain b residue 8 SER Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 12 THR Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 67 THR Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 84 VAL Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 28 ILE Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 84 VAL Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 84 VAL Chi-restraints excluded: chain l residue 89 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 431 optimal weight: 8.9990 chunk 578 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 500 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 543 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 558 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.159451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.134670 restraints weight = 77498.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.138087 restraints weight = 44368.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.140295 restraints weight = 30700.124| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 54576 Z= 0.267 Angle : 0.664 10.116 74028 Z= 0.340 Chirality : 0.044 0.191 8196 Planarity : 0.005 0.051 9804 Dihedral : 5.435 29.035 7464 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 4.83 % Allowed : 18.21 % Favored : 76.96 % 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: -2.92 (0.09), residues: 6816 helix: -0.67 (0.11), residues: 2520 sheet: -2.46 (0.20), residues: 588 loop : -2.88 (0.09), residues: 3708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 49 HIS 0.004 0.002 HIS L 173 PHE 0.034 0.002 PHE L 30 TYR 0.012 0.001 TYR C 155 ARG 0.012 0.001 ARG K 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16355.59 seconds wall clock time: 284 minutes 14.07 seconds (17054.07 seconds total)