Starting phenix.real_space_refine on Tue Jan 14 21:22:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9imv_60695/01_2025/9imv_60695.cif Found real_map, /net/cci-nas-00/data/ceres_data/9imv_60695/01_2025/9imv_60695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9imv_60695/01_2025/9imv_60695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9imv_60695/01_2025/9imv_60695.map" model { file = "/net/cci-nas-00/data/ceres_data/9imv_60695/01_2025/9imv_60695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9imv_60695/01_2025/9imv_60695.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 sd= 1.238 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 252 5.16 5 C 32616 2.51 5 N 8628 2.21 5 O 9924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 51420 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2938 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain: "B" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2938 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain: "C" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2938 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain: "D" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2938 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain: "E" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2938 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain: "F" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2938 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain: "G" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2938 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain: "H" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2938 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain: "I" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2938 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain: "J" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2938 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain: "K" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2938 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain: "L" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2938 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain: "M" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "N" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "O" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "P" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "Q" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "R" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "S" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "T" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "U" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "V" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "W" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "X" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Time building chain proxies: 21.07, per 1000 atoms: 0.41 Number of scatterers: 51420 At special positions: 0 Unit cell: (152.1, 152.1, 159.9, 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 252 16.00 O 9924 8.00 N 8628 7.00 C 32616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.59 Conformation dependent library (CDL) restraints added in 5.0 seconds 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12216 Finding SS restraints... Secondary structure from input PDB file: 227 helices and 83 sheets defined 46.2% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 31 through 42 removed outlier: 3.692A pdb=" N THR A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 94 through 109 Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 180 through 201 removed outlier: 3.748A pdb=" N LYS A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 230 removed outlier: 3.573A pdb=" N TYR A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 278 removed outlier: 3.768A pdb=" N PHE A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 4.020A pdb=" N LEU A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 320 Proline residue: A 306 - end of helix Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.721A pdb=" N THR A 334 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'B' and resid 14 through 22 Processing helix chain 'B' and resid 31 through 42 removed outlier: 3.782A pdb=" N THR B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 56 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 94 through 109 removed outlier: 3.634A pdb=" N PHE B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 180 through 201 removed outlier: 3.791A pdb=" N LYS B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 230 Processing helix chain 'B' and resid 262 through 278 removed outlier: 3.520A pdb=" N ALA B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 4.006A pdb=" N LEU B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 320 removed outlier: 4.447A pdb=" N ARG B 293 " --> pdb=" O ASN B 289 " (cutoff:3.500A) Proline residue: B 294 - end of helix Proline residue: B 306 - end of helix removed outlier: 3.702A pdb=" N LEU B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.988A pdb=" N THR B 334 " --> pdb=" O ALA B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 350 Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 31 through 42 removed outlier: 3.677A pdb=" N THR C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 77 through 87 Processing helix chain 'C' and resid 94 through 109 removed outlier: 3.621A pdb=" N PHE C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 180 through 201 removed outlier: 3.711A pdb=" N LYS C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 230 removed outlier: 3.524A pdb=" N TYR C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 278 removed outlier: 3.821A pdb=" N PHE C 277 " --> pdb=" O ILE C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.980A pdb=" N LEU C 284 " --> pdb=" O PRO C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 319 removed outlier: 4.554A pdb=" N ARG C 293 " --> pdb=" O ASN C 289 " (cutoff:3.500A) Proline residue: C 294 - end of helix Proline residue: C 306 - end of helix removed outlier: 3.715A pdb=" N LEU C 311 " --> pdb=" O MET C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 removed outlier: 3.694A pdb=" N THR C 334 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 350 Processing helix chain 'C' and resid 354 through 362 Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 31 through 42 removed outlier: 3.609A pdb=" N THR D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 56 removed outlier: 3.536A pdb=" N ARG D 47 " --> pdb=" O GLU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 87 Processing helix chain 'D' and resid 94 through 109 removed outlier: 3.553A pdb=" N PHE D 98 " --> pdb=" O ASP D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 179 Processing helix chain 'D' and resid 180 through 201 removed outlier: 3.785A pdb=" N LYS D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 230 removed outlier: 3.515A pdb=" N TYR D 230 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 278 removed outlier: 3.807A pdb=" N PHE D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.997A pdb=" N LEU D 284 " --> pdb=" O PRO D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 320 removed outlier: 4.670A pdb=" N ARG D 293 " --> pdb=" O ASN D 289 " (cutoff:3.500A) Proline residue: D 294 - end of helix Proline residue: D 306 - end of helix removed outlier: 3.626A pdb=" N LEU D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 334 removed outlier: 3.907A pdb=" N THR D 334 " --> pdb=" O ALA D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 350 Processing helix chain 'D' and resid 354 through 362 Processing helix chain 'E' and resid 14 through 22 Processing helix chain 'E' and resid 31 through 42 removed outlier: 3.676A pdb=" N THR E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 56 Processing helix chain 'E' and resid 77 through 87 Processing helix chain 'E' and resid 94 through 109 removed outlier: 3.597A pdb=" N PHE E 98 " --> pdb=" O ASP E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 179 Processing helix chain 'E' and resid 180 through 201 removed outlier: 3.744A pdb=" N LYS E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU E 195 " --> pdb=" O LEU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 230 Processing helix chain 'E' and resid 262 through 278 removed outlier: 3.884A pdb=" N PHE E 277 " --> pdb=" O ILE E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 285 removed outlier: 4.013A pdb=" N LEU E 284 " --> pdb=" O PRO E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 320 Proline residue: E 306 - end of helix removed outlier: 3.723A pdb=" N LEU E 311 " --> pdb=" O MET E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 334 removed outlier: 3.744A pdb=" N THR E 334 " --> pdb=" O ALA E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 350 Processing helix chain 'E' and resid 354 through 362 Processing helix chain 'F' and resid 14 through 22 Processing helix chain 'F' and resid 31 through 42 removed outlier: 3.683A pdb=" N THR F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 56 Processing helix chain 'F' and resid 77 through 87 Processing helix chain 'F' and resid 94 through 109 Processing helix chain 'F' and resid 176 through 179 Processing helix chain 'F' and resid 180 through 201 removed outlier: 3.625A pdb=" N LYS F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU F 195 " --> pdb=" O LEU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 230 Processing helix chain 'F' and resid 256 through 260 Processing helix chain 'F' and resid 262 through 278 removed outlier: 4.179A pdb=" N PHE F 277 " --> pdb=" O ILE F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 285 removed outlier: 4.002A pdb=" N LEU F 284 " --> pdb=" O PRO F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 320 removed outlier: 4.312A pdb=" N ARG F 293 " --> pdb=" O ASN F 289 " (cutoff:3.500A) Proline residue: F 294 - end of helix Proline residue: F 306 - end of helix removed outlier: 3.611A pdb=" N LEU F 311 " --> pdb=" O MET F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 334 removed outlier: 3.762A pdb=" N THR F 334 " --> pdb=" O ALA F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 350 Processing helix chain 'F' and resid 354 through 362 Processing helix chain 'F' and resid 370 through 374 removed outlier: 3.565A pdb=" N ASN F 373 " --> pdb=" O GLU F 370 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS F 374 " --> pdb=" O GLN F 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 370 through 374' Processing helix chain 'G' and resid 14 through 22 Processing helix chain 'G' and resid 31 through 42 removed outlier: 3.688A pdb=" N THR G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 56 Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 94 through 109 removed outlier: 3.597A pdb=" N PHE G 98 " --> pdb=" O ASP G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 179 Processing helix chain 'G' and resid 180 through 201 removed outlier: 3.756A pdb=" N LYS G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU G 195 " --> pdb=" O LEU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 230 Processing helix chain 'G' and resid 262 through 278 removed outlier: 3.736A pdb=" N PHE G 277 " --> pdb=" O ILE G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 285 removed outlier: 4.038A pdb=" N LEU G 284 " --> pdb=" O PRO G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 320 removed outlier: 4.556A pdb=" N ARG G 293 " --> pdb=" O ASN G 289 " (cutoff:3.500A) Proline residue: G 294 - end of helix Proline residue: G 306 - end of helix removed outlier: 3.723A pdb=" N LEU G 311 " --> pdb=" O MET G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 334 removed outlier: 3.970A pdb=" N THR G 334 " --> pdb=" O ALA G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 350 Processing helix chain 'G' and resid 354 through 362 Processing helix chain 'H' and resid 14 through 22 Processing helix chain 'H' and resid 31 through 42 removed outlier: 3.724A pdb=" N THR H 35 " --> pdb=" O LYS H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 56 Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 94 through 109 removed outlier: 3.552A pdb=" N PHE H 98 " --> pdb=" O ASP H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 179 Processing helix chain 'H' and resid 180 through 201 removed outlier: 3.708A pdb=" N LYS H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU H 195 " --> pdb=" O LEU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 230 Processing helix chain 'H' and resid 262 through 278 removed outlier: 3.597A pdb=" N ALA H 276 " --> pdb=" O SER H 272 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE H 277 " --> pdb=" O ILE H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 285 removed outlier: 4.002A pdb=" N LEU H 284 " --> pdb=" O PRO H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 320 Proline residue: H 306 - end of helix removed outlier: 3.786A pdb=" N LEU H 311 " --> pdb=" O MET H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 334 removed outlier: 3.735A pdb=" N THR H 334 " --> pdb=" O ALA H 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 350 Processing helix chain 'H' and resid 354 through 362 Processing helix chain 'I' and resid 14 through 22 Processing helix chain 'I' and resid 31 through 42 removed outlier: 3.717A pdb=" N THR I 35 " --> pdb=" O LYS I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 56 Processing helix chain 'I' and resid 77 through 87 Processing helix chain 'I' and resid 94 through 109 removed outlier: 3.633A pdb=" N PHE I 98 " --> pdb=" O ASP I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 179 removed outlier: 3.597A pdb=" N THR I 179 " --> pdb=" O ARG I 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 176 through 179' Processing helix chain 'I' and resid 180 through 201 removed outlier: 3.747A pdb=" N LYS I 194 " --> pdb=" O MET I 190 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU I 195 " --> pdb=" O LEU I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 230 removed outlier: 3.552A pdb=" N TYR I 230 " --> pdb=" O LEU I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 278 removed outlier: 3.557A pdb=" N ALA I 276 " --> pdb=" O SER I 272 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE I 277 " --> pdb=" O ILE I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 285 removed outlier: 4.074A pdb=" N LEU I 284 " --> pdb=" O PRO I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 320 removed outlier: 4.254A pdb=" N ARG I 293 " --> pdb=" O ASN I 289 " (cutoff:3.500A) Proline residue: I 294 - end of helix Proline residue: I 306 - end of helix removed outlier: 3.755A pdb=" N LEU I 311 " --> pdb=" O MET I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 334 removed outlier: 3.808A pdb=" N THR I 334 " --> pdb=" O ALA I 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 350 Processing helix chain 'I' and resid 354 through 362 Processing helix chain 'J' and resid 14 through 22 Processing helix chain 'J' and resid 31 through 42 removed outlier: 3.690A pdb=" N THR J 35 " --> pdb=" O LYS J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 59 removed outlier: 3.749A pdb=" N ARG J 47 " --> pdb=" O GLU J 43 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N CYS J 59 " --> pdb=" O SER J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 87 Processing helix chain 'J' and resid 94 through 109 removed outlier: 3.687A pdb=" N PHE J 98 " --> pdb=" O ASP J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 179 Processing helix chain 'J' and resid 180 through 201 removed outlier: 3.698A pdb=" N LYS J 194 " --> pdb=" O MET J 190 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU J 195 " --> pdb=" O LEU J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 230 Processing helix chain 'J' and resid 262 through 278 removed outlier: 3.745A pdb=" N PHE J 277 " --> pdb=" O ILE J 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 285 removed outlier: 4.028A pdb=" N LEU J 284 " --> pdb=" O PRO J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 320 removed outlier: 4.480A pdb=" N ARG J 293 " --> pdb=" O ASN J 289 " (cutoff:3.500A) Proline residue: J 294 - end of helix Proline residue: J 306 - end of helix removed outlier: 3.651A pdb=" N LEU J 311 " --> pdb=" O MET J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 330 through 334 removed outlier: 3.756A pdb=" N THR J 334 " --> pdb=" O ALA J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 351 Processing helix chain 'J' and resid 354 through 362 Processing helix chain 'K' and resid 14 through 22 Processing helix chain 'K' and resid 31 through 42 removed outlier: 3.669A pdb=" N THR K 35 " --> pdb=" O LYS K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 59 removed outlier: 4.202A pdb=" N CYS K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 87 Processing helix chain 'K' and resid 94 through 109 removed outlier: 3.562A pdb=" N PHE K 98 " --> pdb=" O ASP K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 179 Processing helix chain 'K' and resid 180 through 201 removed outlier: 3.730A pdb=" N LYS K 194 " --> pdb=" O MET K 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU K 195 " --> pdb=" O LEU K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 230 removed outlier: 3.584A pdb=" N TYR K 230 " --> pdb=" O LEU K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 260 Processing helix chain 'K' and resid 262 through 278 removed outlier: 3.686A pdb=" N ALA K 276 " --> pdb=" O SER K 272 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE K 277 " --> pdb=" O ILE K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 285 removed outlier: 3.999A pdb=" N LEU K 284 " --> pdb=" O PRO K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 320 Proline residue: K 306 - end of helix removed outlier: 3.685A pdb=" N LEU K 311 " --> pdb=" O MET K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 330 through 334 removed outlier: 3.679A pdb=" N THR K 334 " --> pdb=" O ALA K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 350 Processing helix chain 'K' and resid 354 through 362 Processing helix chain 'L' and resid 14 through 22 Processing helix chain 'L' and resid 31 through 42 removed outlier: 3.683A pdb=" N THR L 35 " --> pdb=" O LYS L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 56 Processing helix chain 'L' and resid 77 through 87 Processing helix chain 'L' and resid 94 through 109 Processing helix chain 'L' and resid 176 through 179 removed outlier: 3.664A pdb=" N THR L 179 " --> pdb=" O ARG L 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 176 through 179' Processing helix chain 'L' and resid 180 through 201 removed outlier: 3.731A pdb=" N LYS L 194 " --> pdb=" O MET L 190 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU L 195 " --> pdb=" O LEU L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 230 removed outlier: 3.524A pdb=" N TYR L 230 " --> pdb=" O LEU L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 278 removed outlier: 3.869A pdb=" N PHE L 277 " --> pdb=" O ILE L 273 " (cutoff:3.500A) Processing helix chain 'L' and resid 280 through 285 removed outlier: 4.073A pdb=" N LEU L 284 " --> pdb=" O PRO L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 320 removed outlier: 4.296A pdb=" N ARG L 293 " --> pdb=" O ASN L 289 " (cutoff:3.500A) Proline residue: L 294 - end of helix Proline residue: L 306 - end of helix removed outlier: 3.750A pdb=" N LEU L 311 " --> pdb=" O MET L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 330 through 334 removed outlier: 3.718A pdb=" N THR L 334 " --> pdb=" O ALA L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 336 through 350 Processing helix chain 'L' and resid 354 through 362 Processing helix chain 'M' and resid 4 through 13 removed outlier: 3.626A pdb=" N ASP M 8 " --> pdb=" O ILE M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 39 removed outlier: 3.578A pdb=" N GLU M 25 " --> pdb=" O GLU M 21 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL M 26 " --> pdb=" O SER M 22 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR M 29 " --> pdb=" O GLU M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 83 No H-bonds generated for 'chain 'M' and resid 81 through 83' Processing helix chain 'M' and resid 117 through 133 Processing helix chain 'M' and resid 157 through 168 Processing helix chain 'N' and resid 4 through 13 removed outlier: 3.638A pdb=" N ASP N 8 " --> pdb=" O ILE N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 39 removed outlier: 3.660A pdb=" N GLU N 25 " --> pdb=" O GLU N 21 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL N 26 " --> pdb=" O SER N 22 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET N 27 " --> pdb=" O GLY N 23 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR N 29 " --> pdb=" O GLU N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 117 through 133 removed outlier: 3.512A pdb=" N LYS N 121 " --> pdb=" O PRO N 117 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS N 133 " --> pdb=" O ASP N 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 167 Processing helix chain 'O' and resid 4 through 13 removed outlier: 3.616A pdb=" N ASP O 8 " --> pdb=" O ILE O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 39 removed outlier: 3.571A pdb=" N GLU O 25 " --> pdb=" O GLU O 21 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL O 26 " --> pdb=" O SER O 22 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR O 29 " --> pdb=" O GLU O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 83 No H-bonds generated for 'chain 'O' and resid 81 through 83' Processing helix chain 'O' and resid 117 through 133 removed outlier: 3.605A pdb=" N LYS O 121 " --> pdb=" O PRO O 117 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS O 133 " --> pdb=" O ASP O 129 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 167 Processing helix chain 'P' and resid 4 through 13 removed outlier: 3.564A pdb=" N ASP P 8 " --> pdb=" O ILE P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 39 removed outlier: 3.570A pdb=" N GLU P 25 " --> pdb=" O GLU P 21 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL P 26 " --> pdb=" O SER P 22 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR P 29 " --> pdb=" O GLU P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 83 No H-bonds generated for 'chain 'P' and resid 81 through 83' Processing helix chain 'P' and resid 117 through 133 Processing helix chain 'P' and resid 157 through 167 Processing helix chain 'Q' and resid 4 through 13 removed outlier: 3.640A pdb=" N ASP Q 8 " --> pdb=" O ILE Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 39 removed outlier: 3.568A pdb=" N GLU Q 25 " --> pdb=" O GLU Q 21 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL Q 26 " --> pdb=" O SER Q 22 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET Q 27 " --> pdb=" O GLY Q 23 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR Q 29 " --> pdb=" O GLU Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 83 No H-bonds generated for 'chain 'Q' and resid 81 through 83' Processing helix chain 'Q' and resid 117 through 133 removed outlier: 3.551A pdb=" N LYS Q 121 " --> pdb=" O PRO Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 158 through 167 Processing helix chain 'R' and resid 4 through 13 removed outlier: 3.590A pdb=" N ASP R 8 " --> pdb=" O ILE R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 39 removed outlier: 3.639A pdb=" N GLU R 25 " --> pdb=" O GLU R 21 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL R 26 " --> pdb=" O SER R 22 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR R 29 " --> pdb=" O GLU R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 83 No H-bonds generated for 'chain 'R' and resid 81 through 83' Processing helix chain 'R' and resid 117 through 133 removed outlier: 3.523A pdb=" N LYS R 121 " --> pdb=" O PRO R 117 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS R 133 " --> pdb=" O ASP R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 167 Processing helix chain 'S' and resid 4 through 13 removed outlier: 3.554A pdb=" N ASP S 8 " --> pdb=" O ILE S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 39 removed outlier: 3.571A pdb=" N GLU S 25 " --> pdb=" O GLU S 21 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL S 26 " --> pdb=" O SER S 22 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 83 No H-bonds generated for 'chain 'S' and resid 81 through 83' Processing helix chain 'S' and resid 117 through 134 removed outlier: 3.543A pdb=" N GLN S 134 " --> pdb=" O HIS S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 157 through 167 Processing helix chain 'T' and resid 4 through 13 removed outlier: 3.640A pdb=" N ASP T 8 " --> pdb=" O ILE T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 21 through 39 removed outlier: 3.556A pdb=" N GLU T 25 " --> pdb=" O GLU T 21 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL T 26 " --> pdb=" O SER T 22 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET T 27 " --> pdb=" O GLY T 23 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR T 29 " --> pdb=" O GLU T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 117 through 133 removed outlier: 3.576A pdb=" N LYS T 121 " --> pdb=" O PRO T 117 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS T 133 " --> pdb=" O ASP T 129 " (cutoff:3.500A) Processing helix chain 'T' and resid 158 through 167 Processing helix chain 'U' and resid 4 through 13 removed outlier: 3.618A pdb=" N ASP U 8 " --> pdb=" O ILE U 4 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 39 removed outlier: 3.548A pdb=" N GLU U 25 " --> pdb=" O GLU U 21 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL U 26 " --> pdb=" O SER U 22 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR U 29 " --> pdb=" O GLU U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 83 No H-bonds generated for 'chain 'U' and resid 81 through 83' Processing helix chain 'U' and resid 117 through 133 removed outlier: 3.577A pdb=" N LYS U 121 " --> pdb=" O PRO U 117 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS U 133 " --> pdb=" O ASP U 129 " (cutoff:3.500A) Processing helix chain 'U' and resid 158 through 167 Processing helix chain 'V' and resid 4 through 13 removed outlier: 3.648A pdb=" N ASP V 8 " --> pdb=" O ILE V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 21 through 39 removed outlier: 3.592A pdb=" N GLU V 25 " --> pdb=" O GLU V 21 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL V 26 " --> pdb=" O SER V 22 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR V 29 " --> pdb=" O GLU V 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 117 through 134 removed outlier: 3.504A pdb=" N LYS V 121 " --> pdb=" O PRO V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 157 through 168 Processing helix chain 'W' and resid 4 through 13 removed outlier: 3.599A pdb=" N ASP W 8 " --> pdb=" O ILE W 4 " (cutoff:3.500A) Processing helix chain 'W' and resid 21 through 39 removed outlier: 3.722A pdb=" N GLU W 25 " --> pdb=" O GLU W 21 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL W 26 " --> pdb=" O SER W 22 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET W 27 " --> pdb=" O GLY W 23 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 133 removed outlier: 3.545A pdb=" N LYS W 121 " --> pdb=" O PRO W 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 167 Processing helix chain 'X' and resid 4 through 13 removed outlier: 3.616A pdb=" N ASP X 8 " --> pdb=" O ILE X 4 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 39 removed outlier: 4.176A pdb=" N VAL X 26 " --> pdb=" O SER X 22 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR X 29 " --> pdb=" O GLU X 25 " (cutoff:3.500A) Processing helix chain 'X' and resid 81 through 83 No H-bonds generated for 'chain 'X' and resid 81 through 83' Processing helix chain 'X' and resid 117 through 133 removed outlier: 3.584A pdb=" N LYS X 121 " --> pdb=" O PRO X 117 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 168 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 66 removed outlier: 5.094A pdb=" N LYS A 322 " --> pdb=" O GLY A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.598A pdb=" N VAL A 124 " --> pdb=" O TYR A 113 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR A 113 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 133 removed outlier: 3.696A pdb=" N LYS A 141 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 248 Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA6, first strand: chain 'B' and resid 61 through 66 removed outlier: 3.579A pdb=" N THR B 62 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR B 324 " --> pdb=" O THR B 62 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS B 322 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 123 through 124 removed outlier: 3.517A pdb=" N VAL B 124 " --> pdb=" O TYR B 113 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR B 113 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 129 through 133 Processing sheet with id=AA9, first strand: chain 'B' and resid 247 through 248 Processing sheet with id=AB1, first strand: chain 'C' and resid 61 through 66 removed outlier: 3.593A pdb=" N THR C 62 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LYS C 322 " --> pdb=" O GLY C 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 123 through 124 removed outlier: 3.618A pdb=" N VAL C 124 " --> pdb=" O TYR C 113 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR C 113 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 129 through 133 removed outlier: 3.523A pdb=" N LYS C 141 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 239 through 242 removed outlier: 6.079A pdb=" N LEU C 240 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 61 through 66 removed outlier: 3.561A pdb=" N THR D 62 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR D 324 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LYS D 322 " --> pdb=" O GLY D 64 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 121 through 124 removed outlier: 3.536A pdb=" N VAL D 124 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR D 113 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 129 through 132 removed outlier: 3.515A pdb=" N LYS D 141 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 239 through 242 removed outlier: 5.990A pdb=" N LEU D 240 " --> pdb=" O LEU L 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 61 through 66 removed outlier: 3.503A pdb=" N THR E 62 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LYS E 322 " --> pdb=" O GLY E 64 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 123 through 124 removed outlier: 3.773A pdb=" N VAL E 124 " --> pdb=" O TYR E 113 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR E 113 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE E 114 " --> pdb=" O ILE E 156 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 129 through 133 removed outlier: 3.653A pdb=" N LYS E 141 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 247 through 248 removed outlier: 6.227A pdb=" N LEU E 206 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU F 242 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU E 208 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 61 through 66 removed outlier: 5.082A pdb=" N LYS F 322 " --> pdb=" O GLY F 64 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 123 through 124 removed outlier: 4.165A pdb=" N TYR F 113 " --> pdb=" O VAL F 124 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 129 through 133 removed outlier: 3.915A pdb=" N LYS F 141 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 247 through 248 Processing sheet with id=AC8, first strand: chain 'G' and resid 61 through 66 removed outlier: 3.510A pdb=" N THR G 62 " --> pdb=" O THR G 324 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR G 324 " --> pdb=" O THR G 62 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LYS G 322 " --> pdb=" O GLY G 64 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 123 through 124 removed outlier: 4.010A pdb=" N TYR G 113 " --> pdb=" O VAL G 124 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 129 through 132 Processing sheet with id=AD2, first strand: chain 'G' and resid 247 through 248 Processing sheet with id=AD3, first strand: chain 'H' and resid 61 through 66 removed outlier: 5.243A pdb=" N LYS H 322 " --> pdb=" O GLY H 64 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 123 through 124 removed outlier: 3.652A pdb=" N VAL H 124 " --> pdb=" O TYR H 113 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR H 113 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE H 114 " --> pdb=" O ILE H 156 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.642A pdb=" N LYS H 141 " --> pdb=" O GLU H 132 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 247 through 248 removed outlier: 6.088A pdb=" N LEU H 206 " --> pdb=" O LEU I 240 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU I 242 " --> pdb=" O LEU H 206 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU H 208 " --> pdb=" O LEU I 242 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 61 through 66 removed outlier: 3.559A pdb=" N THR I 62 " --> pdb=" O THR I 324 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR I 324 " --> pdb=" O THR I 62 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LYS I 322 " --> pdb=" O GLY I 64 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 121 through 124 removed outlier: 4.161A pdb=" N TYR I 113 " --> pdb=" O VAL I 124 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 129 through 132 Processing sheet with id=AE1, first strand: chain 'I' and resid 247 through 248 Processing sheet with id=AE2, first strand: chain 'J' and resid 61 through 66 removed outlier: 3.547A pdb=" N THR J 62 " --> pdb=" O THR J 324 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR J 324 " --> pdb=" O THR J 62 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LYS J 322 " --> pdb=" O GLY J 64 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 123 through 124 removed outlier: 4.113A pdb=" N TYR J 113 " --> pdb=" O VAL J 124 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 129 through 132 Processing sheet with id=AE5, first strand: chain 'J' and resid 247 through 248 removed outlier: 6.863A pdb=" N LEU J 206 " --> pdb=" O LEU K 240 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU K 242 " --> pdb=" O LEU J 206 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU J 208 " --> pdb=" O LEU K 242 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 61 through 66 removed outlier: 3.501A pdb=" N THR K 62 " --> pdb=" O THR K 324 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS K 322 " --> pdb=" O GLY K 64 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 123 through 124 removed outlier: 3.596A pdb=" N VAL K 124 " --> pdb=" O TYR K 113 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR K 113 " --> pdb=" O VAL K 124 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 129 through 133 removed outlier: 3.539A pdb=" N LYS K 141 " --> pdb=" O GLU K 132 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 247 through 248 removed outlier: 6.181A pdb=" N LEU K 206 " --> pdb=" O LEU L 240 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU L 242 " --> pdb=" O LEU K 206 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU K 208 " --> pdb=" O LEU L 242 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 61 through 66 removed outlier: 5.127A pdb=" N LYS L 322 " --> pdb=" O GLY L 64 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 123 through 124 removed outlier: 3.653A pdb=" N VAL L 124 " --> pdb=" O TYR L 113 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR L 113 " --> pdb=" O VAL L 124 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 129 through 133 Processing sheet with id=AF4, first strand: chain 'M' and resid 46 through 53 removed outlier: 3.529A pdb=" N VAL M 106 " --> pdb=" O GLN M 49 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR M 53 " --> pdb=" O GLY M 102 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY M 102 " --> pdb=" O THR M 53 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR M 103 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE M 75 " --> pdb=" O TYR M 103 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP M 105 " --> pdb=" O MET M 73 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET M 73 " --> pdb=" O ASP M 105 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU M 107 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER M 69 " --> pdb=" O THR M 109 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 59 through 61 Processing sheet with id=AF6, first strand: chain 'M' and resid 139 through 142 removed outlier: 3.782A pdb=" N THR M 146 " --> pdb=" O THR X 141 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA X 139 " --> pdb=" O THR M 148 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE X 142 " --> pdb=" O GLU X 145 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU X 145 " --> pdb=" O ILE X 142 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR X 146 " --> pdb=" O THR W 141 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE W 142 " --> pdb=" O GLU W 145 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU W 145 " --> pdb=" O ILE W 142 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE U 142 " --> pdb=" O GLU U 145 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU U 145 " --> pdb=" O ILE U 142 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE S 142 " --> pdb=" O GLU S 145 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU S 145 " --> pdb=" O ILE S 142 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR S 146 " --> pdb=" O THR R 141 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE R 142 " --> pdb=" O GLU R 145 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU R 145 " --> pdb=" O ILE R 142 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR R 146 " --> pdb=" O THR Q 141 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE Q 142 " --> pdb=" O GLU Q 145 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU Q 145 " --> pdb=" O ILE Q 142 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR Q 146 " --> pdb=" O THR P 141 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE P 142 " --> pdb=" O GLU P 145 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU P 145 " --> pdb=" O ILE P 142 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR P 146 " --> pdb=" O THR O 141 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE O 142 " --> pdb=" O GLU O 145 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU O 145 " --> pdb=" O ILE O 142 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR O 146 " --> pdb=" O THR N 141 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA M 139 " --> pdb=" O THR N 148 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 46 through 53 removed outlier: 3.514A pdb=" N VAL N 106 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS N 72 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR N 109 " --> pdb=" O VAL N 70 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL N 70 " --> pdb=" O THR N 109 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 59 through 61 Processing sheet with id=AF9, first strand: chain 'N' and resid 152 through 153 Processing sheet with id=AG1, first strand: chain 'O' and resid 46 through 53 removed outlier: 3.505A pdb=" N GLY O 102 " --> pdb=" O THR O 53 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR O 103 " --> pdb=" O ILE O 75 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE O 75 " --> pdb=" O TYR O 103 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP O 105 " --> pdb=" O MET O 73 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET O 73 " --> pdb=" O ASP O 105 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU O 107 " --> pdb=" O THR O 71 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER O 69 " --> pdb=" O THR O 109 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 59 through 61 Processing sheet with id=AG3, first strand: chain 'O' and resid 152 through 153 Processing sheet with id=AG4, first strand: chain 'P' and resid 46 through 53 removed outlier: 3.522A pdb=" N TYR P 108 " --> pdb=" O VAL P 47 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL P 106 " --> pdb=" O GLN P 49 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE P 51 " --> pdb=" O MET P 104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY P 102 " --> pdb=" O THR P 53 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLU P 107 " --> pdb=" O THR P 71 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER P 69 " --> pdb=" O THR P 109 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 59 through 61 Processing sheet with id=AG6, first strand: chain 'Q' and resid 46 through 53 removed outlier: 3.547A pdb=" N THR Q 53 " --> pdb=" O GLY Q 102 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY Q 102 " --> pdb=" O THR Q 53 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR Q 103 " --> pdb=" O THR Q 74 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR Q 74 " --> pdb=" O TYR Q 103 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASP Q 105 " --> pdb=" O LYS Q 72 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS Q 72 " --> pdb=" O ASP Q 105 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU Q 107 " --> pdb=" O VAL Q 70 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL Q 70 " --> pdb=" O GLU Q 107 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR Q 109 " --> pdb=" O THR Q 68 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 59 through 61 Processing sheet with id=AG8, first strand: chain 'Q' and resid 152 through 153 Processing sheet with id=AG9, first strand: chain 'R' and resid 46 through 53 removed outlier: 3.510A pdb=" N VAL R 106 " --> pdb=" O GLN R 49 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR R 53 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY R 102 " --> pdb=" O THR R 53 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR R 103 " --> pdb=" O ILE R 75 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE R 75 " --> pdb=" O TYR R 103 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASP R 105 " --> pdb=" O MET R 73 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N MET R 73 " --> pdb=" O ASP R 105 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU R 107 " --> pdb=" O THR R 71 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER R 69 " --> pdb=" O THR R 109 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'R' and resid 59 through 61 Processing sheet with id=AH2, first strand: chain 'R' and resid 152 through 153 Processing sheet with id=AH3, first strand: chain 'S' and resid 46 through 49 removed outlier: 3.514A pdb=" N GLN S 49 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL S 106 " --> pdb=" O GLN S 49 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY S 102 " --> pdb=" O THR S 53 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'S' and resid 46 through 49 removed outlier: 3.514A pdb=" N GLN S 49 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL S 106 " --> pdb=" O GLN S 49 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR S 103 " --> pdb=" O ILE S 75 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE S 75 " --> pdb=" O TYR S 103 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASP S 105 " --> pdb=" O MET S 73 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N MET S 73 " --> pdb=" O ASP S 105 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU S 107 " --> pdb=" O THR S 71 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER S 69 " --> pdb=" O THR S 109 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N MET S 73 " --> pdb=" O ILE S 80 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'S' and resid 59 through 61 Processing sheet with id=AH6, first strand: chain 'T' and resid 46 through 53 removed outlier: 3.549A pdb=" N VAL T 106 " --> pdb=" O GLN T 49 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR T 53 " --> pdb=" O GLY T 102 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY T 102 " --> pdb=" O THR T 53 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS T 72 " --> pdb=" O GLU T 107 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR T 109 " --> pdb=" O VAL T 70 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL T 70 " --> pdb=" O THR T 109 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'T' and resid 59 through 61 Processing sheet with id=AH8, first strand: chain 'T' and resid 152 through 153 Processing sheet with id=AH9, first strand: chain 'U' and resid 46 through 53 removed outlier: 3.547A pdb=" N GLY U 102 " --> pdb=" O THR U 53 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS U 72 " --> pdb=" O GLU U 107 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR U 109 " --> pdb=" O VAL U 70 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL U 70 " --> pdb=" O THR U 109 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'U' and resid 59 through 61 Processing sheet with id=AI2, first strand: chain 'U' and resid 152 through 153 Processing sheet with id=AI3, first strand: chain 'V' and resid 46 through 49 removed outlier: 3.617A pdb=" N VAL V 106 " --> pdb=" O GLN V 49 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU V 107 " --> pdb=" O THR V 71 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER V 69 " --> pdb=" O THR V 109 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'V' and resid 52 through 53 Processing sheet with id=AI5, first strand: chain 'V' and resid 59 through 61 Processing sheet with id=AI6, first strand: chain 'W' and resid 46 through 53 removed outlier: 3.673A pdb=" N THR W 53 " --> pdb=" O GLY W 102 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY W 102 " --> pdb=" O THR W 53 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR W 109 " --> pdb=" O VAL W 70 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL W 70 " --> pdb=" O THR W 109 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'W' and resid 59 through 61 Processing sheet with id=AI8, first strand: chain 'W' and resid 152 through 153 Processing sheet with id=AI9, first strand: chain 'X' and resid 46 through 53 removed outlier: 3.559A pdb=" N GLY X 102 " --> pdb=" O THR X 53 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR X 103 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE X 75 " --> pdb=" O TYR X 103 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP X 105 " --> pdb=" O MET X 73 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET X 73 " --> pdb=" O ASP X 105 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLU X 107 " --> pdb=" O THR X 71 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER X 69 " --> pdb=" O THR X 109 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'X' and resid 59 through 61 Processing sheet with id=AJ2, first strand: chain 'X' and resid 152 through 153 2260 hydrogen bonds defined for protein. 6585 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.73 Time building geometry restraints manager: 11.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 8830 1.30 - 1.43: 12441 1.43 - 1.56: 30626 1.56 - 1.68: 3 1.68 - 1.81: 444 Bond restraints: 52344 Sorted by residual: bond pdb=" N GLU F 43 " pdb=" CA GLU F 43 " ideal model delta sigma weight residual 1.457 1.542 -0.085 1.17e-02 7.31e+03 5.29e+01 bond pdb=" CA SER B 169 " pdb=" C SER B 169 " ideal model delta sigma weight residual 1.521 1.432 0.089 1.24e-02 6.50e+03 5.14e+01 bond pdb=" CA SER D 169 " pdb=" C SER D 169 " ideal model delta sigma weight residual 1.521 1.434 0.087 1.24e-02 6.50e+03 4.96e+01 bond pdb=" CA SER J 169 " pdb=" C SER J 169 " ideal model delta sigma weight residual 1.521 1.434 0.087 1.24e-02 6.50e+03 4.89e+01 bond pdb=" CA GLU D 43 " pdb=" C GLU D 43 " ideal model delta sigma weight residual 1.522 1.432 0.090 1.37e-02 5.33e+03 4.35e+01 ... (remaining 52339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 69405 2.31 - 4.62: 1201 4.62 - 6.93: 175 6.93 - 9.24: 33 9.24 - 11.55: 10 Bond angle restraints: 70824 Sorted by residual: angle pdb=" N ILE F 42 " pdb=" CA ILE F 42 " pdb=" C ILE F 42 " ideal model delta sigma weight residual 107.28 118.83 -11.55 1.59e+00 3.96e-01 5.28e+01 angle pdb=" N GLU J 43 " pdb=" CA GLU J 43 " pdb=" C GLU J 43 " ideal model delta sigma weight residual 113.20 121.36 -8.16 1.21e+00 6.83e-01 4.54e+01 angle pdb=" C ILE F 42 " pdb=" N GLU F 43 " pdb=" CA GLU F 43 " ideal model delta sigma weight residual 121.19 131.89 -10.70 1.59e+00 3.96e-01 4.53e+01 angle pdb=" C ILE F 42 " pdb=" CA ILE F 42 " pdb=" CB ILE F 42 " ideal model delta sigma weight residual 110.99 102.55 8.44 1.30e+00 5.92e-01 4.22e+01 angle pdb=" CA GLU F 43 " pdb=" C GLU F 43 " pdb=" N ILE F 44 " ideal model delta sigma weight residual 116.69 126.59 -9.90 1.58e+00 4.01e-01 3.93e+01 ... (remaining 70819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 28683 17.99 - 35.99: 2778 35.99 - 53.98: 459 53.98 - 71.98: 70 71.98 - 89.97: 74 Dihedral angle restraints: 32064 sinusoidal: 13116 harmonic: 18948 Sorted by residual: dihedral pdb=" CA ASN F 291 " pdb=" C ASN F 291 " pdb=" N ILE F 292 " pdb=" CA ILE F 292 " ideal model delta harmonic sigma weight residual -180.00 -151.78 -28.22 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA ASN L 291 " pdb=" C ASN L 291 " pdb=" N ILE L 292 " pdb=" CA ILE L 292 " ideal model delta harmonic sigma weight residual -180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ASN I 291 " pdb=" C ASN I 291 " pdb=" N ILE I 292 " pdb=" CA ILE I 292 " ideal model delta harmonic sigma weight residual -180.00 -156.30 -23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 32061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 7736 0.100 - 0.200: 317 0.200 - 0.300: 8 0.300 - 0.400: 10 0.400 - 0.500: 5 Chirality restraints: 8076 Sorted by residual: chirality pdb=" CA GLN V 134 " pdb=" N GLN V 134 " pdb=" C GLN V 134 " pdb=" CB GLN V 134 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.25e+00 chirality pdb=" CA GLN S 134 " pdb=" N GLN S 134 " pdb=" C GLN S 134 " pdb=" CB GLN S 134 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.91e+00 chirality pdb=" CA LYS S 133 " pdb=" N LYS S 133 " pdb=" C LYS S 133 " pdb=" CB LYS S 133 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.17e+00 ... (remaining 8073 not shown) Planarity restraints: 9156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN K 12 " -0.092 5.00e-02 4.00e+02 1.36e-01 2.98e+01 pdb=" N PRO K 13 " 0.236 5.00e-02 4.00e+02 pdb=" CA PRO K 13 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO K 13 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 12 " -0.089 5.00e-02 4.00e+02 1.36e-01 2.94e+01 pdb=" N PRO A 13 " 0.235 5.00e-02 4.00e+02 pdb=" CA PRO A 13 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 13 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN I 12 " 0.085 5.00e-02 4.00e+02 1.27e-01 2.58e+01 pdb=" N PRO I 13 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO I 13 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO I 13 " 0.067 5.00e-02 4.00e+02 ... (remaining 9153 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4533 2.74 - 3.28: 53259 3.28 - 3.82: 85300 3.82 - 4.36: 102543 4.36 - 4.90: 178091 Nonbonded interactions: 423726 Sorted by model distance: nonbonded pdb=" O ASP A 211 " pdb=" OG SER O 154 " model vdw 2.195 3.040 nonbonded pdb=" NE2 GLN A 223 " pdb=" OH TYR B 230 " model vdw 2.203 3.120 nonbonded pdb=" OH TYR C 230 " pdb=" OE1 GLN D 223 " model vdw 2.204 3.040 nonbonded pdb=" NZ LYS J 141 " pdb=" OD1 ASN J 149 " model vdw 2.211 3.120 nonbonded pdb=" NZ LYS T 133 " pdb=" OD2 ASP T 135 " model vdw 2.212 3.120 ... (remaining 423721 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 1.700 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: 0.040 Extract box with map and model: 1.370 Check model and map are aligned: 0.280 Set scattering table: 0.340 Process input model: 83.840 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.340 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:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 52344 Z= 0.325 Angle : 0.757 11.550 70824 Z= 0.422 Chirality : 0.048 0.500 8076 Planarity : 0.006 0.136 9156 Dihedral : 14.710 89.971 19848 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.88 % Favored : 91.43 % Rotamer: Outliers : 0.38 % Allowed : 0.42 % Favored : 99.20 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.10), residues: 6432 helix: 0.39 (0.10), residues: 2616 sheet: -0.45 (0.19), residues: 768 loop : -1.82 (0.11), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP U 131 HIS 0.010 0.002 HIS Q 130 PHE 0.023 0.002 PHE C 92 TYR 0.047 0.002 TYR I 300 ARG 0.007 0.001 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 1120 time to evaluate : 4.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 SER cc_start: 0.9036 (p) cc_final: 0.8496 (t) REVERT: A 371 GLN cc_start: 0.6911 (tp40) cc_final: 0.6546 (tp-100) REVERT: B 128 LEU cc_start: 0.8824 (mt) cc_final: 0.8579 (mt) REVERT: B 374 LYS cc_start: 0.7832 (pttt) cc_final: 0.6836 (ptmt) REVERT: C 203 VAL cc_start: 0.9594 (t) cc_final: 0.9211 (m) REVERT: D 128 LEU cc_start: 0.8880 (mt) cc_final: 0.8579 (mt) REVERT: D 148 ILE cc_start: 0.7982 (mp) cc_final: 0.7703 (mp) REVERT: D 374 LYS cc_start: 0.8151 (pttt) cc_final: 0.7060 (ptmt) REVERT: E 93 MET cc_start: 0.9003 (ttt) cc_final: 0.8523 (ttp) REVERT: E 224 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7310 (mt-10) REVERT: E 317 PHE cc_start: 0.8477 (t80) cc_final: 0.8151 (t80) REVERT: E 370 GLU cc_start: 0.6307 (mt-10) cc_final: 0.5998 (mt-10) REVERT: E 374 LYS cc_start: 0.7984 (ptpp) cc_final: 0.7689 (pttt) REVERT: G 93 MET cc_start: 0.9281 (ttt) cc_final: 0.8881 (ttm) REVERT: G 128 LEU cc_start: 0.8589 (mt) cc_final: 0.8309 (mt) REVERT: G 149 ASN cc_start: 0.8352 (m-40) cc_final: 0.8095 (m-40) REVERT: G 212 GLU cc_start: 0.8201 (mp0) cc_final: 0.7993 (mp0) REVERT: G 317 PHE cc_start: 0.8629 (t80) cc_final: 0.8213 (t80) REVERT: G 374 LYS cc_start: 0.7793 (mmtp) cc_final: 0.7034 (ptpt) REVERT: H 41 LYS cc_start: 0.7937 (mttt) cc_final: 0.7699 (ttpp) REVERT: I 353 ILE cc_start: 0.9331 (mm) cc_final: 0.9078 (tt) REVERT: J 22 GLU cc_start: 0.7504 (tt0) cc_final: 0.7070 (tt0) REVERT: J 43 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8181 (pt0) REVERT: J 92 PHE cc_start: 0.8083 (m-10) cc_final: 0.7222 (m-10) REVERT: J 93 MET cc_start: 0.9020 (ttt) cc_final: 0.8472 (ttm) REVERT: J 212 GLU cc_start: 0.8341 (mp0) cc_final: 0.8066 (mp0) REVERT: J 307 MET cc_start: 0.8882 (ttm) cc_final: 0.8594 (ttm) REVERT: J 372 MET cc_start: 0.8560 (tpp) cc_final: 0.8122 (tpp) REVERT: J 374 LYS cc_start: 0.7770 (pttt) cc_final: 0.6664 (ptmt) REVERT: K 374 LYS cc_start: 0.7650 (pttm) cc_final: 0.6558 (ptmt) REVERT: L 353 ILE cc_start: 0.9216 (mm) cc_final: 0.8918 (tt) REVERT: L 374 LYS cc_start: 0.7728 (ptmt) cc_final: 0.7342 (pttt) REVERT: M 19 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6456 (tm-30) REVERT: N 1 MET cc_start: 0.8695 (mpp) cc_final: 0.8340 (mpp) REVERT: N 21 GLU cc_start: 0.6337 (mt-10) cc_final: 0.6058 (mp0) REVERT: N 73 MET cc_start: 0.9305 (ttt) cc_final: 0.8608 (ttt) REVERT: N 76 ASN cc_start: 0.9004 (m110) cc_final: 0.8788 (m-40) REVERT: N 85 TYR cc_start: 0.8909 (p90) cc_final: 0.8227 (p90) REVERT: N 98 ASN cc_start: 0.9136 (t0) cc_final: 0.8789 (m-40) REVERT: N 145 GLU cc_start: 0.7531 (pm20) cc_final: 0.7110 (pm20) REVERT: O 42 ASP cc_start: 0.7433 (m-30) cc_final: 0.7156 (p0) REVERT: O 73 MET cc_start: 0.8906 (ttt) cc_final: 0.8616 (ttt) REVERT: P 1 MET cc_start: 0.8319 (mpp) cc_final: 0.7835 (mpp) REVERT: P 73 MET cc_start: 0.9031 (ttm) cc_final: 0.8600 (ttp) REVERT: Q 149 PHE cc_start: 0.8261 (m-80) cc_final: 0.7977 (m-80) REVERT: T 49 GLN cc_start: 0.8637 (tt0) cc_final: 0.8272 (tt0) REVERT: T 98 ASN cc_start: 0.9082 (t0) cc_final: 0.8852 (m-40) REVERT: U 134 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8129 (mm-40) REVERT: U 154 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8338 (p) REVERT: V 1 MET cc_start: 0.8036 (mpp) cc_final: 0.7836 (mpp) REVERT: W 8 ASP cc_start: 0.7150 (m-30) cc_final: 0.6830 (m-30) REVERT: W 41 MET cc_start: 0.7999 (mmm) cc_final: 0.7002 (mmm) REVERT: W 133 LYS cc_start: 0.8383 (mtmt) cc_final: 0.8169 (mtmt) REVERT: X 64 SER cc_start: 0.9507 (t) cc_final: 0.9278 (m) REVERT: X 121 LYS cc_start: 0.8691 (mttt) cc_final: 0.8473 (mttt) REVERT: X 133 LYS cc_start: 0.8083 (mtmp) cc_final: 0.7755 (mtmt) REVERT: X 134 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8245 (mm-40) REVERT: X 153 LYS cc_start: 0.8506 (mttm) cc_final: 0.8271 (mttm) outliers start: 22 outliers final: 3 residues processed: 1139 average time/residue: 0.4748 time to fit residues: 942.9154 Evaluate side-chains 885 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 878 time to evaluate : 4.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 141 LYS Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain I residue 211 ASP Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain U residue 134 GLN Chi-restraints excluded: chain U residue 154 SER Chi-restraints excluded: chain X residue 134 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 547 optimal weight: 3.9990 chunk 491 optimal weight: 5.9990 chunk 272 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 331 optimal weight: 0.9990 chunk 262 optimal weight: 1.9990 chunk 507 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 378 optimal weight: 5.9990 chunk 588 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 GLN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 ASN D 170 GLN D 291 ASN ** D 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 GLN E 291 ASN F 161 ASN F 289 ASN F 350 ASN G 26 HIS G 288 ASN G 363 ASN H 46 ASN I 253 GLN J 26 HIS ** J 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 161 ASN ** J 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 ASN K 373 ASN ** L 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN ** S 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 GLN ** U 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 32 ASN W 32 ASN X 110 GLN X 151 ASN ** X 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.104514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.096891 restraints weight = 68713.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.096458 restraints weight = 73371.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.096913 restraints weight = 70241.731| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 52344 Z= 0.297 Angle : 0.679 10.704 70824 Z= 0.352 Chirality : 0.045 0.181 8076 Planarity : 0.005 0.086 9156 Dihedral : 5.598 87.847 7039 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.40 % Favored : 91.17 % Rotamer: Outliers : 1.79 % Allowed : 9.38 % Favored : 88.83 % 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: -0.88 (0.10), residues: 6432 helix: 0.56 (0.10), residues: 2652 sheet: -0.26 (0.19), residues: 780 loop : -1.75 (0.11), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 116 HIS 0.009 0.002 HIS V 130 PHE 0.020 0.002 PHE D 92 TYR 0.031 0.002 TYR I 300 ARG 0.006 0.001 ARG D 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 986 time to evaluate : 4.449 Fit side-chains REVERT: A 114 ILE cc_start: 0.9603 (mt) cc_final: 0.9221 (mt) REVERT: A 317 PHE cc_start: 0.8740 (t80) cc_final: 0.8194 (t80) REVERT: B 128 LEU cc_start: 0.8967 (mt) cc_final: 0.8706 (mt) REVERT: B 374 LYS cc_start: 0.7836 (pttt) cc_final: 0.6828 (ptmt) REVERT: C 117 ASP cc_start: 0.7957 (t0) cc_final: 0.7750 (t0) REVERT: C 203 VAL cc_start: 0.9430 (t) cc_final: 0.9004 (m) REVERT: C 317 PHE cc_start: 0.8715 (t80) cc_final: 0.8264 (t80) REVERT: D 128 LEU cc_start: 0.8950 (mt) cc_final: 0.8746 (mt) REVERT: D 374 LYS cc_start: 0.8075 (pttt) cc_final: 0.7081 (ptmt) REVERT: E 93 MET cc_start: 0.9090 (ttt) cc_final: 0.8727 (ttm) REVERT: F 371 GLN cc_start: 0.7096 (tp40) cc_final: 0.6562 (tp-100) REVERT: F 374 LYS cc_start: 0.7862 (pttt) cc_final: 0.7111 (ptmt) REVERT: G 93 MET cc_start: 0.9284 (ttt) cc_final: 0.8923 (ttm) REVERT: G 128 LEU cc_start: 0.8774 (mt) cc_final: 0.8480 (mt) REVERT: G 175 SER cc_start: 0.8752 (t) cc_final: 0.8426 (t) REVERT: G 317 PHE cc_start: 0.8685 (t80) cc_final: 0.8390 (t80) REVERT: G 374 LYS cc_start: 0.7788 (mmtp) cc_final: 0.7143 (pttt) REVERT: H 43 GLU cc_start: 0.8346 (pt0) cc_final: 0.8140 (pm20) REVERT: H 122 TYR cc_start: 0.7312 (m-80) cc_final: 0.7013 (m-80) REVERT: I 82 ASP cc_start: 0.7637 (t70) cc_final: 0.7425 (t0) REVERT: I 128 LEU cc_start: 0.9153 (mt) cc_final: 0.8936 (mt) REVERT: I 371 GLN cc_start: 0.6979 (tp40) cc_final: 0.6753 (tm-30) REVERT: J 93 MET cc_start: 0.9051 (ttt) cc_final: 0.8587 (ttm) REVERT: J 212 GLU cc_start: 0.8261 (mp0) cc_final: 0.8053 (mp0) REVERT: J 302 MET cc_start: 0.8360 (ttp) cc_final: 0.8146 (ttt) REVERT: J 317 PHE cc_start: 0.8908 (t80) cc_final: 0.8417 (t80) REVERT: J 321 TYR cc_start: 0.9041 (m-80) cc_final: 0.8836 (m-10) REVERT: J 371 GLN cc_start: 0.6797 (tp40) cc_final: 0.6444 (tp40) REVERT: J 372 MET cc_start: 0.8777 (tpp) cc_final: 0.8367 (tpp) REVERT: K 113 TYR cc_start: 0.9223 (m-80) cc_final: 0.9008 (m-80) REVERT: K 122 TYR cc_start: 0.7696 (m-10) cc_final: 0.7163 (m-80) REVERT: K 374 LYS cc_start: 0.7529 (pttm) cc_final: 0.6526 (ptmt) REVERT: L 113 TYR cc_start: 0.8801 (m-10) cc_final: 0.8552 (m-10) REVERT: L 209 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8023 (mt-10) REVERT: L 353 ILE cc_start: 0.9273 (mm) cc_final: 0.8999 (tt) REVERT: L 374 LYS cc_start: 0.7524 (ptmt) cc_final: 0.7217 (pttt) REVERT: M 27 MET cc_start: 0.8502 (mtt) cc_final: 0.8288 (mtt) REVERT: M 78 LYS cc_start: 0.8419 (pttp) cc_final: 0.8167 (pttt) REVERT: N 73 MET cc_start: 0.9353 (ttt) cc_final: 0.8793 (ttt) REVERT: N 85 TYR cc_start: 0.8884 (p90) cc_final: 0.8160 (p90) REVERT: N 98 ASN cc_start: 0.9057 (t0) cc_final: 0.8780 (m-40) REVERT: N 122 LEU cc_start: 0.9341 (tp) cc_final: 0.9122 (tp) REVERT: O 7 GLU cc_start: 0.6795 (tp30) cc_final: 0.6427 (tp30) REVERT: O 41 MET cc_start: 0.8105 (mmm) cc_final: 0.7362 (mmm) REVERT: O 42 ASP cc_start: 0.7284 (m-30) cc_final: 0.7065 (p0) REVERT: O 73 MET cc_start: 0.9141 (ttt) cc_final: 0.8658 (ttt) REVERT: O 104 MET cc_start: 0.8755 (ttp) cc_final: 0.8477 (ttm) REVERT: P 41 MET cc_start: 0.8526 (mmm) cc_final: 0.7699 (mmm) REVERT: P 50 LEU cc_start: 0.9161 (tp) cc_final: 0.8802 (tt) REVERT: P 60 TYR cc_start: 0.9171 (m-80) cc_final: 0.8891 (m-80) REVERT: P 77 ASP cc_start: 0.7188 (m-30) cc_final: 0.6920 (t0) REVERT: P 135 ASP cc_start: 0.8105 (m-30) cc_final: 0.7623 (t0) REVERT: Q 98 ASN cc_start: 0.9176 (t0) cc_final: 0.8867 (m-40) REVERT: R 32 ASN cc_start: 0.8604 (m-40) cc_final: 0.8327 (m110) REVERT: R 41 MET cc_start: 0.7974 (mmm) cc_final: 0.7391 (mmm) REVERT: T 49 GLN cc_start: 0.8755 (tt0) cc_final: 0.8489 (tt0) REVERT: T 86 LYS cc_start: 0.8445 (ttmm) cc_final: 0.7959 (ttmm) REVERT: T 98 ASN cc_start: 0.9132 (t0) cc_final: 0.8911 (m-40) REVERT: U 32 ASN cc_start: 0.8480 (m-40) cc_final: 0.8190 (m110) REVERT: U 134 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8212 (mm-40) REVERT: V 27 MET cc_start: 0.8637 (ttm) cc_final: 0.8395 (mtt) REVERT: V 50 LEU cc_start: 0.9149 (tp) cc_final: 0.8901 (tt) REVERT: V 108 TYR cc_start: 0.8938 (p90) cc_final: 0.8710 (p90) REVERT: W 41 MET cc_start: 0.7802 (mmm) cc_final: 0.7344 (mmm) REVERT: W 101 GLU cc_start: 0.8383 (tt0) cc_final: 0.8103 (tt0) REVERT: W 105 ASP cc_start: 0.8652 (t0) cc_final: 0.8306 (t0) REVERT: X 41 MET cc_start: 0.8214 (mmm) cc_final: 0.7780 (mmm) REVERT: X 134 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8546 (mm-40) REVERT: X 153 LYS cc_start: 0.8536 (mttm) cc_final: 0.8331 (mttm) outliers start: 103 outliers final: 73 residues processed: 1055 average time/residue: 0.4555 time to fit residues: 835.9211 Evaluate side-chains 960 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 885 time to evaluate : 4.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 289 ASN Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 223 GLN Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 51 MET Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 51 MET Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain K residue 155 ILE Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain L residue 143 ILE Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain O residue 27 MET Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 19 GLU Chi-restraints excluded: chain P residue 156 ILE Chi-restraints excluded: chain Q residue 166 VAL Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 134 GLN Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain X residue 134 GLN Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 166 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 19 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 211 optimal weight: 0.6980 chunk 228 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 528 optimal weight: 0.9990 chunk 608 optimal weight: 10.0000 chunk 422 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 15 optimal weight: 0.0970 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN D 161 ASN E 161 ASN ** E 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN G 295 ASN H 174 GLN I 200 ASN J 26 HIS ** J 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 ASN M 32 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 110 GLN O 134 GLN P 32 ASN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN ** S 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 32 ASN ** T 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 32 ASN ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 32 ASN ** W 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 151 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.107984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.100028 restraints weight = 68046.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.099933 restraints weight = 65980.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.100434 restraints weight = 59314.921| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 52344 Z= 0.199 Angle : 0.607 17.436 70824 Z= 0.313 Chirality : 0.043 0.153 8076 Planarity : 0.005 0.078 9156 Dihedral : 5.101 83.075 7026 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.71 % Favored : 91.93 % Rotamer: Outliers : 1.83 % Allowed : 13.10 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.11), residues: 6432 helix: 0.76 (0.10), residues: 2652 sheet: -0.14 (0.19), residues: 852 loop : -1.75 (0.11), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 116 HIS 0.012 0.002 HIS G 26 PHE 0.019 0.001 PHE K 317 TYR 0.020 0.001 TYR G 150 ARG 0.006 0.000 ARG J 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 1014 time to evaluate : 4.455 Fit side-chains revert: symmetry clash REVERT: A 114 ILE cc_start: 0.9566 (mt) cc_final: 0.9204 (mt) REVERT: A 317 PHE cc_start: 0.8720 (t80) cc_final: 0.8354 (t80) REVERT: B 317 PHE cc_start: 0.8857 (t80) cc_final: 0.8355 (t80) REVERT: B 374 LYS cc_start: 0.7877 (pttt) cc_final: 0.6854 (ptmt) REVERT: C 203 VAL cc_start: 0.9419 (t) cc_final: 0.9065 (m) REVERT: C 291 ASN cc_start: 0.8533 (m-40) cc_final: 0.8124 (m-40) REVERT: D 143 ILE cc_start: 0.8646 (mm) cc_final: 0.8415 (mm) REVERT: D 374 LYS cc_start: 0.8058 (pttt) cc_final: 0.7076 (ptmt) REVERT: E 84 LEU cc_start: 0.8732 (mt) cc_final: 0.8477 (tt) REVERT: E 93 MET cc_start: 0.9034 (ttt) cc_final: 0.8547 (ttp) REVERT: E 109 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7327 (mp0) REVERT: E 291 ASN cc_start: 0.8718 (m-40) cc_final: 0.8353 (m-40) REVERT: E 374 LYS cc_start: 0.7839 (pttt) cc_final: 0.6853 (ptmt) REVERT: F 371 GLN cc_start: 0.7074 (tp40) cc_final: 0.6722 (tp-100) REVERT: G 93 MET cc_start: 0.9258 (ttt) cc_final: 0.8943 (ttm) REVERT: G 128 LEU cc_start: 0.8815 (mt) cc_final: 0.8549 (mt) REVERT: G 317 PHE cc_start: 0.8768 (t80) cc_final: 0.8417 (t80) REVERT: G 374 LYS cc_start: 0.7577 (mmtp) cc_final: 0.6998 (pttt) REVERT: H 11 LEU cc_start: 0.8329 (mp) cc_final: 0.8099 (mp) REVERT: H 109 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7233 (mp0) REVERT: H 122 TYR cc_start: 0.7318 (m-80) cc_final: 0.7029 (m-80) REVERT: I 109 GLU cc_start: 0.7168 (mp0) cc_final: 0.6946 (mp0) REVERT: J 93 MET cc_start: 0.9012 (ttt) cc_final: 0.8609 (ttm) REVERT: J 265 ASP cc_start: 0.6829 (m-30) cc_final: 0.6581 (m-30) REVERT: J 317 PHE cc_start: 0.8940 (t80) cc_final: 0.8487 (t80) REVERT: J 371 GLN cc_start: 0.6798 (tp40) cc_final: 0.6504 (tp40) REVERT: J 372 MET cc_start: 0.8776 (tpp) cc_final: 0.8400 (tpp) REVERT: J 374 LYS cc_start: 0.7707 (pttt) cc_final: 0.6989 (ptmt) REVERT: K 122 TYR cc_start: 0.7609 (m-10) cc_final: 0.7112 (m-80) REVERT: K 374 LYS cc_start: 0.7380 (pttm) cc_final: 0.6365 (ptmt) REVERT: L 209 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8133 (mt-10) REVERT: L 353 ILE cc_start: 0.9217 (mm) cc_final: 0.8993 (tt) REVERT: L 374 LYS cc_start: 0.7561 (ptmt) cc_final: 0.7089 (pttt) REVERT: M 19 GLU cc_start: 0.6744 (tm-30) cc_final: 0.6350 (tm-30) REVERT: M 78 LYS cc_start: 0.8357 (pttp) cc_final: 0.8125 (pttt) REVERT: M 145 GLU cc_start: 0.6110 (pm20) cc_final: 0.5846 (pm20) REVERT: N 21 GLU cc_start: 0.6598 (mt-10) cc_final: 0.6262 (mp0) REVERT: N 73 MET cc_start: 0.9313 (ttt) cc_final: 0.8876 (ttt) REVERT: N 105 ASP cc_start: 0.8239 (t0) cc_final: 0.7947 (t0) REVERT: N 145 GLU cc_start: 0.7221 (pm20) cc_final: 0.6865 (pm20) REVERT: O 7 GLU cc_start: 0.6980 (tp30) cc_final: 0.6659 (tp30) REVERT: O 41 MET cc_start: 0.7963 (mmm) cc_final: 0.7214 (mmm) REVERT: O 73 MET cc_start: 0.9054 (ttt) cc_final: 0.8541 (ttt) REVERT: O 104 MET cc_start: 0.8681 (ttp) cc_final: 0.8458 (ttm) REVERT: P 50 LEU cc_start: 0.9169 (tp) cc_final: 0.8828 (tt) REVERT: P 60 TYR cc_start: 0.9188 (m-80) cc_final: 0.8876 (m-80) REVERT: P 134 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8600 (mm-40) REVERT: R 32 ASN cc_start: 0.8532 (m-40) cc_final: 0.8198 (m110) REVERT: R 58 LYS cc_start: 0.8495 (mttp) cc_final: 0.7891 (mtmm) REVERT: R 121 LYS cc_start: 0.8864 (mttt) cc_final: 0.8617 (mttt) REVERT: S 27 MET cc_start: 0.8701 (ttm) cc_final: 0.8346 (mtt) REVERT: S 133 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8132 (mtpp) REVERT: T 49 GLN cc_start: 0.8831 (tt0) cc_final: 0.8502 (tt0) REVERT: U 7 GLU cc_start: 0.7243 (tp30) cc_final: 0.6912 (tp30) REVERT: U 32 ASN cc_start: 0.8379 (m-40) cc_final: 0.7998 (m110) REVERT: V 27 MET cc_start: 0.8669 (ttm) cc_final: 0.8435 (mtt) REVERT: V 50 LEU cc_start: 0.9069 (tp) cc_final: 0.8820 (tt) REVERT: V 108 TYR cc_start: 0.8860 (p90) cc_final: 0.8549 (p90) REVERT: W 11 LEU cc_start: 0.7999 (tp) cc_final: 0.7772 (tp) REVERT: W 41 MET cc_start: 0.7680 (mmm) cc_final: 0.7367 (mmm) REVERT: W 101 GLU cc_start: 0.8273 (tt0) cc_final: 0.8020 (tt0) REVERT: W 105 ASP cc_start: 0.8731 (t0) cc_final: 0.8330 (t0) REVERT: W 134 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8554 (mm-40) REVERT: X 41 MET cc_start: 0.8212 (mmm) cc_final: 0.7911 (mmm) REVERT: X 134 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8415 (mm-40) outliers start: 105 outliers final: 65 residues processed: 1073 average time/residue: 0.4767 time to fit residues: 882.0610 Evaluate side-chains 931 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 865 time to evaluate : 4.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 288 ASN Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 51 MET Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain K residue 155 ILE Chi-restraints excluded: chain K residue 288 ASN Chi-restraints excluded: chain L residue 143 ILE Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain O residue 27 MET Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain Q residue 166 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain V residue 142 ILE Chi-restraints excluded: chain X residue 134 GLN Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 166 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 628 optimal weight: 3.9990 chunk 579 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 580 optimal weight: 0.9980 chunk 564 optimal weight: 4.9990 chunk 522 optimal weight: 1.9990 chunk 388 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 367 optimal weight: 5.9990 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 295 ASN ** B 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 ASN ** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 223 GLN G 26 HIS G 37 GLN ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 HIS J 37 GLN J 90 ASN ** J 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 170 GLN L 161 ASN ** L 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN N 32 ASN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 GLN ** O 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN Q 32 ASN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN ** S 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 32 ASN ** T 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 32 ASN W 32 ASN ** W 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 32 ASN X 151 ASN ** X 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.099566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.091851 restraints weight = 70273.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.091371 restraints weight = 74139.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.091714 restraints weight = 71494.204| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 52344 Z= 0.395 Angle : 0.711 8.333 70824 Z= 0.366 Chirality : 0.047 0.156 8076 Planarity : 0.005 0.082 9156 Dihedral : 5.346 76.648 7023 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.91 % Favored : 90.83 % Rotamer: Outliers : 3.10 % Allowed : 15.12 % Favored : 81.78 % 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: -0.88 (0.10), residues: 6432 helix: 0.62 (0.10), residues: 2652 sheet: 0.00 (0.21), residues: 708 loop : -1.86 (0.11), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 116 HIS 0.010 0.002 HIS O 130 PHE 0.031 0.002 PHE K 317 TYR 0.031 0.002 TYR A 113 ARG 0.007 0.001 ARG F 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 943 time to evaluate : 4.488 Fit side-chains revert: symmetry clash REVERT: A 114 ILE cc_start: 0.9555 (mt) cc_final: 0.9217 (mt) REVERT: A 317 PHE cc_start: 0.8811 (t80) cc_final: 0.8563 (t80) REVERT: B 71 THR cc_start: 0.9220 (p) cc_final: 0.8723 (t) REVERT: B 224 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6648 (mt-10) REVERT: B 317 PHE cc_start: 0.8782 (t80) cc_final: 0.8163 (t80) REVERT: B 374 LYS cc_start: 0.7954 (pttt) cc_final: 0.6868 (ptmt) REVERT: D 71 THR cc_start: 0.9245 (p) cc_final: 0.8750 (t) REVERT: D 79 LYS cc_start: 0.8106 (tppt) cc_final: 0.7477 (tmtt) REVERT: D 143 ILE cc_start: 0.8781 (mm) cc_final: 0.8559 (mm) REVERT: D 317 PHE cc_start: 0.8952 (t80) cc_final: 0.8266 (t80) REVERT: D 374 LYS cc_start: 0.7895 (pttt) cc_final: 0.7001 (ptmt) REVERT: E 93 MET cc_start: 0.9249 (ttt) cc_final: 0.8737 (ttm) REVERT: E 129 MET cc_start: 0.8890 (ttm) cc_final: 0.8486 (mtp) REVERT: E 291 ASN cc_start: 0.8692 (m-40) cc_final: 0.8178 (m-40) REVERT: E 374 LYS cc_start: 0.8054 (pttt) cc_final: 0.6979 (ptmt) REVERT: F 371 GLN cc_start: 0.7423 (tp40) cc_final: 0.6897 (tp-100) REVERT: G 71 THR cc_start: 0.9285 (p) cc_final: 0.8794 (t) REVERT: G 93 MET cc_start: 0.9266 (ttt) cc_final: 0.8928 (ttm) REVERT: G 141 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8588 (pttt) REVERT: G 317 PHE cc_start: 0.8869 (t80) cc_final: 0.8421 (t80) REVERT: G 374 LYS cc_start: 0.7647 (mmtp) cc_final: 0.7128 (pttt) REVERT: H 41 LYS cc_start: 0.8433 (mttt) cc_final: 0.7826 (mtmt) REVERT: H 109 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7312 (mp0) REVERT: H 122 TYR cc_start: 0.7696 (m-80) cc_final: 0.7342 (m-80) REVERT: I 109 GLU cc_start: 0.7529 (mp0) cc_final: 0.7265 (mp0) REVERT: J 71 THR cc_start: 0.9237 (p) cc_final: 0.8778 (t) REVERT: J 93 MET cc_start: 0.9093 (ttt) cc_final: 0.8703 (ttm) REVERT: J 265 ASP cc_start: 0.7048 (m-30) cc_final: 0.6804 (m-30) REVERT: J 317 PHE cc_start: 0.8957 (t80) cc_final: 0.8395 (t80) REVERT: J 374 LYS cc_start: 0.7861 (pttt) cc_final: 0.7588 (ptpt) REVERT: K 41 LYS cc_start: 0.8214 (mttt) cc_final: 0.7719 (mtmt) REVERT: K 66 LYS cc_start: 0.8768 (tptm) cc_final: 0.8522 (tptm) REVERT: K 122 TYR cc_start: 0.7800 (m-10) cc_final: 0.7229 (m-80) REVERT: K 374 LYS cc_start: 0.7522 (pttm) cc_final: 0.7318 (pttm) REVERT: L 93 MET cc_start: 0.9314 (ptp) cc_final: 0.8903 (ptp) REVERT: M 76 ASN cc_start: 0.8812 (m110) cc_final: 0.8490 (m110) REVERT: M 134 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7902 (mm-40) REVERT: N 21 GLU cc_start: 0.6571 (mt-10) cc_final: 0.6236 (mp0) REVERT: N 32 ASN cc_start: 0.8794 (m-40) cc_final: 0.8505 (m110) REVERT: N 73 MET cc_start: 0.9281 (ttt) cc_final: 0.8840 (ttt) REVERT: N 85 TYR cc_start: 0.8939 (p90) cc_final: 0.8370 (p90) REVERT: N 105 ASP cc_start: 0.8318 (t0) cc_final: 0.8017 (t0) REVERT: O 72 LYS cc_start: 0.8786 (ttmt) cc_final: 0.8581 (ttmt) REVERT: O 79 GLU cc_start: 0.7161 (tt0) cc_final: 0.6923 (tt0) REVERT: O 135 ASP cc_start: 0.7029 (t0) cc_final: 0.6766 (t0) REVERT: P 50 LEU cc_start: 0.9199 (tp) cc_final: 0.8910 (tt) REVERT: P 60 TYR cc_start: 0.9194 (m-80) cc_final: 0.8852 (m-80) REVERT: P 134 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8497 (mm-40) REVERT: Q 98 ASN cc_start: 0.9273 (t0) cc_final: 0.8983 (t0) REVERT: R 32 ASN cc_start: 0.8555 (m-40) cc_final: 0.8231 (m110) REVERT: R 135 ASP cc_start: 0.7659 (t0) cc_final: 0.7046 (t0) REVERT: S 27 MET cc_start: 0.8870 (ttm) cc_final: 0.8459 (mtt) REVERT: S 50 LEU cc_start: 0.9180 (tp) cc_final: 0.8910 (tt) REVERT: T 49 GLN cc_start: 0.8767 (tt0) cc_final: 0.8463 (tt0) REVERT: U 7 GLU cc_start: 0.7408 (tp30) cc_final: 0.7032 (tp30) REVERT: U 32 ASN cc_start: 0.8586 (m-40) cc_final: 0.8224 (m110) REVERT: V 27 MET cc_start: 0.8720 (ttm) cc_final: 0.8459 (mtt) REVERT: V 50 LEU cc_start: 0.9137 (tp) cc_final: 0.8903 (tt) REVERT: V 77 ASP cc_start: 0.7552 (m-30) cc_final: 0.6988 (t0) REVERT: W 41 MET cc_start: 0.7734 (mmm) cc_final: 0.7177 (mmm) REVERT: W 85 TYR cc_start: 0.8980 (p90) cc_final: 0.8458 (p90) REVERT: W 101 GLU cc_start: 0.8320 (tt0) cc_final: 0.8044 (tt0) REVERT: W 105 ASP cc_start: 0.8719 (t0) cc_final: 0.8336 (t0) REVERT: X 41 MET cc_start: 0.8181 (mmm) cc_final: 0.7448 (mmm) REVERT: X 73 MET cc_start: 0.8607 (tpp) cc_final: 0.8369 (ttt) REVERT: X 104 MET cc_start: 0.9121 (ttt) cc_final: 0.8913 (ttt) REVERT: X 134 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8450 (mm-40) outliers start: 178 outliers final: 119 residues processed: 1064 average time/residue: 0.4453 time to fit residues: 828.7153 Evaluate side-chains 1008 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 885 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 141 LYS Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 288 ASN Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 51 MET Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 343 HIS Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 51 MET Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain K residue 155 ILE Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain L residue 143 ILE Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain L residue 161 ASN Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 279 VAL Chi-restraints excluded: chain L residue 305 ILE Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 134 GLN Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain O residue 27 MET Chi-restraints excluded: chain O residue 43 ASP Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 156 ILE Chi-restraints excluded: chain Q residue 166 VAL Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain S residue 72 LYS Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain V residue 19 GLU Chi-restraints excluded: chain V residue 142 ILE Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain X residue 43 ASP Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 134 GLN Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 166 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 405 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 190 optimal weight: 0.9990 chunk 585 optimal weight: 5.9990 chunk 315 optimal weight: 0.9980 chunk 225 optimal weight: 0.7980 chunk 573 optimal weight: 0.9980 chunk 466 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 527 optimal weight: 3.9990 chunk 456 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 ASN G 26 HIS G 363 ASN J 161 ASN M 32 ASN M 110 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN Q 32 ASN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN ** S 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 ASN T 32 ASN ** U 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 32 ASN ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 32 ASN ** W 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.103782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.096076 restraints weight = 68905.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.095795 restraints weight = 67953.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.095948 restraints weight = 67202.977| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 52344 Z= 0.218 Angle : 0.614 9.841 70824 Z= 0.316 Chirality : 0.044 0.160 8076 Planarity : 0.004 0.078 9156 Dihedral : 5.037 71.005 7023 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.98 % Favored : 91.81 % Rotamer: Outliers : 2.63 % Allowed : 16.89 % Favored : 80.48 % 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: -0.68 (0.10), residues: 6432 helix: 0.82 (0.10), residues: 2628 sheet: -0.13 (0.20), residues: 744 loop : -1.72 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.011 0.002 HIS O 130 PHE 0.022 0.001 PHE H 92 TYR 0.016 0.001 TYR G 150 ARG 0.005 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 937 time to evaluate : 4.636 Fit side-chains REVERT: A 114 ILE cc_start: 0.9560 (mt) cc_final: 0.9202 (mt) REVERT: A 317 PHE cc_start: 0.8853 (t80) cc_final: 0.8648 (t80) REVERT: B 71 THR cc_start: 0.9215 (p) cc_final: 0.8721 (t) REVERT: B 224 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6627 (mt-10) REVERT: B 317 PHE cc_start: 0.8810 (t80) cc_final: 0.8216 (t80) REVERT: C 141 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8886 (pttt) REVERT: C 203 VAL cc_start: 0.9368 (t) cc_final: 0.9008 (m) REVERT: C 291 ASN cc_start: 0.8493 (m-40) cc_final: 0.8127 (m-40) REVERT: D 71 THR cc_start: 0.9242 (p) cc_final: 0.8731 (t) REVERT: D 143 ILE cc_start: 0.8745 (mm) cc_final: 0.8515 (mm) REVERT: D 317 PHE cc_start: 0.8957 (t80) cc_final: 0.8304 (t80) REVERT: D 374 LYS cc_start: 0.8002 (pttt) cc_final: 0.6967 (ptmt) REVERT: E 84 LEU cc_start: 0.8872 (mt) cc_final: 0.8536 (tt) REVERT: E 93 MET cc_start: 0.9182 (ttt) cc_final: 0.8646 (ttp) REVERT: E 109 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7269 (mp0) REVERT: E 122 TYR cc_start: 0.7788 (m-80) cc_final: 0.7584 (m-80) REVERT: E 129 MET cc_start: 0.8880 (ttm) cc_final: 0.8524 (mtp) REVERT: E 291 ASN cc_start: 0.8757 (m-40) cc_final: 0.8345 (m-40) REVERT: E 317 PHE cc_start: 0.8752 (t80) cc_final: 0.8538 (t80) REVERT: E 374 LYS cc_start: 0.7968 (pttt) cc_final: 0.6934 (ptmt) REVERT: F 109 GLU cc_start: 0.7387 (mp0) cc_final: 0.6944 (mp0) REVERT: F 371 GLN cc_start: 0.7165 (tp40) cc_final: 0.6745 (tp-100) REVERT: F 374 LYS cc_start: 0.7865 (pttt) cc_final: 0.6865 (ptmt) REVERT: G 93 MET cc_start: 0.9265 (ttt) cc_final: 0.8919 (ttm) REVERT: G 230 TYR cc_start: 0.8575 (m-80) cc_final: 0.8353 (m-80) REVERT: G 317 PHE cc_start: 0.8855 (t80) cc_final: 0.8629 (t80) REVERT: G 374 LYS cc_start: 0.7667 (mmtp) cc_final: 0.7038 (pttt) REVERT: H 41 LYS cc_start: 0.8355 (mttt) cc_final: 0.7821 (mtmt) REVERT: H 109 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7208 (mp0) REVERT: H 122 TYR cc_start: 0.7651 (m-80) cc_final: 0.7194 (m-80) REVERT: I 92 PHE cc_start: 0.5045 (m-80) cc_final: 0.4755 (m-80) REVERT: I 300 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.7794 (t80) REVERT: I 372 MET cc_start: 0.9396 (mmm) cc_final: 0.9159 (mmm) REVERT: I 374 LYS cc_start: 0.7861 (pttt) cc_final: 0.6649 (ptmt) REVERT: J 93 MET cc_start: 0.9099 (ttt) cc_final: 0.8853 (ttt) REVERT: J 224 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6483 (mt-10) REVERT: J 228 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8642 (mm) REVERT: J 265 ASP cc_start: 0.6954 (m-30) cc_final: 0.6711 (m-30) REVERT: J 302 MET cc_start: 0.8513 (ttt) cc_final: 0.8130 (ttt) REVERT: J 317 PHE cc_start: 0.8972 (t80) cc_final: 0.8616 (t80) REVERT: J 372 MET cc_start: 0.8652 (tpp) cc_final: 0.7948 (tpp) REVERT: J 374 LYS cc_start: 0.7821 (pttt) cc_final: 0.7466 (ptpt) REVERT: K 41 LYS cc_start: 0.8159 (mttt) cc_final: 0.7689 (mtmt) REVERT: K 66 LYS cc_start: 0.8771 (tptm) cc_final: 0.8552 (tptm) REVERT: K 122 TYR cc_start: 0.7612 (m-10) cc_final: 0.7162 (m-80) REVERT: L 93 MET cc_start: 0.9195 (ptp) cc_final: 0.8864 (ptp) REVERT: L 163 TYR cc_start: 0.8440 (t80) cc_final: 0.8192 (t80) REVERT: M 1 MET cc_start: 0.8598 (mpp) cc_final: 0.8387 (mpp) REVERT: M 7 GLU cc_start: 0.7957 (tp30) cc_final: 0.7527 (tp30) REVERT: N 21 GLU cc_start: 0.6567 (mt-10) cc_final: 0.6197 (mp0) REVERT: N 32 ASN cc_start: 0.8733 (m-40) cc_final: 0.8257 (m110) REVERT: N 73 MET cc_start: 0.9271 (ttt) cc_final: 0.8765 (ttt) REVERT: N 85 TYR cc_start: 0.8836 (p90) cc_final: 0.8195 (p90) REVERT: N 86 LYS cc_start: 0.8407 (ttmm) cc_final: 0.8042 (tttp) REVERT: N 105 ASP cc_start: 0.8310 (t0) cc_final: 0.7954 (t0) REVERT: N 145 GLU cc_start: 0.7165 (pm20) cc_final: 0.6893 (pm20) REVERT: O 121 LYS cc_start: 0.8856 (mttt) cc_final: 0.8615 (mttt) REVERT: O 135 ASP cc_start: 0.7114 (t0) cc_final: 0.6640 (t70) REVERT: P 1 MET cc_start: 0.8820 (mpp) cc_final: 0.8535 (mpp) REVERT: P 50 LEU cc_start: 0.9162 (tp) cc_final: 0.8881 (tt) REVERT: P 134 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8566 (mm-40) REVERT: P 170 VAL cc_start: 0.8104 (t) cc_final: 0.7550 (m) REVERT: Q 21 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6272 (mp0) REVERT: Q 25 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7302 (mt-10) REVERT: Q 98 ASN cc_start: 0.9220 (t0) cc_final: 0.8853 (m-40) REVERT: Q 153 LYS cc_start: 0.8861 (mttm) cc_final: 0.8512 (mttp) REVERT: R 32 ASN cc_start: 0.8381 (m-40) cc_final: 0.8050 (m110) REVERT: R 58 LYS cc_start: 0.8484 (mttp) cc_final: 0.7821 (mtmm) REVERT: R 135 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7043 (t0) REVERT: R 142 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8027 (mt) REVERT: S 27 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8377 (mtt) REVERT: S 50 LEU cc_start: 0.9134 (tp) cc_final: 0.8843 (tt) REVERT: T 49 GLN cc_start: 0.8788 (tt0) cc_final: 0.8492 (tt0) REVERT: U 7 GLU cc_start: 0.7425 (tp30) cc_final: 0.7020 (tp30) REVERT: U 32 ASN cc_start: 0.8463 (m-40) cc_final: 0.8059 (m110) REVERT: V 27 MET cc_start: 0.8690 (ttm) cc_final: 0.8466 (mtt) REVERT: V 50 LEU cc_start: 0.9087 (tp) cc_final: 0.8841 (tt) REVERT: W 101 GLU cc_start: 0.8270 (tt0) cc_final: 0.8011 (tt0) REVERT: W 105 ASP cc_start: 0.8674 (t0) cc_final: 0.8276 (t0) REVERT: X 41 MET cc_start: 0.8136 (mmm) cc_final: 0.7793 (mtp) REVERT: X 104 MET cc_start: 0.9137 (ttt) cc_final: 0.8922 (ttp) REVERT: X 134 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8530 (mm-40) REVERT: X 142 ILE cc_start: 0.8555 (pt) cc_final: 0.8191 (pt) outliers start: 151 outliers final: 106 residues processed: 1043 average time/residue: 0.4531 time to fit residues: 823.4357 Evaluate side-chains 983 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 868 time to evaluate : 4.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 343 HIS Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 343 HIS Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 288 ASN Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain J residue 51 MET Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 343 HIS Chi-restraints excluded: chain K residue 51 MET Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 288 ASN Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 343 HIS Chi-restraints excluded: chain L residue 26 HIS Chi-restraints excluded: chain L residue 143 ILE Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 279 VAL Chi-restraints excluded: chain L residue 288 ASN Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 343 HIS Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain O residue 27 MET Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P residue 156 ILE Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 166 VAL Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 135 ASP Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain V residue 142 ILE Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain V residue 170 VAL Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 134 GLN Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 166 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 325 optimal weight: 0.7980 chunk 438 optimal weight: 0.0970 chunk 367 optimal weight: 5.9990 chunk 455 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 639 optimal weight: 0.7980 chunk 282 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 486 optimal weight: 2.9990 chunk 295 optimal weight: 0.4980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 HIS ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 GLN J 26 HIS J 161 ASN ** K 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 151 ASN ** O 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN P 110 GLN Q 32 ASN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 GLN ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN S 134 GLN T 32 ASN ** T 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 32 ASN ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 32 ASN ** W 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.106388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.098862 restraints weight = 68146.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.098534 restraints weight = 66508.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.098858 restraints weight = 62720.430| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 52344 Z= 0.185 Angle : 0.593 10.266 70824 Z= 0.303 Chirality : 0.043 0.153 8076 Planarity : 0.004 0.069 9156 Dihedral : 4.797 68.325 7023 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.18 % Favored : 91.60 % Rotamer: Outliers : 2.75 % Allowed : 17.62 % Favored : 79.63 % 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: -0.56 (0.11), residues: 6432 helix: 0.91 (0.10), residues: 2652 sheet: -0.33 (0.18), residues: 912 loop : -1.64 (0.11), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 116 HIS 0.012 0.001 HIS O 130 PHE 0.032 0.001 PHE C 317 TYR 0.016 0.001 TYR E 150 ARG 0.006 0.000 ARG I 376 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1106 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 948 time to evaluate : 4.466 Fit side-chains REVERT: A 114 ILE cc_start: 0.9527 (mt) cc_final: 0.9176 (mt) REVERT: A 317 PHE cc_start: 0.8884 (t80) cc_final: 0.8661 (t80) REVERT: B 170 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8264 (mt0) REVERT: B 317 PHE cc_start: 0.8807 (t80) cc_final: 0.8488 (t80) REVERT: C 43 GLU cc_start: 0.8086 (pm20) cc_final: 0.7860 (pm20) REVERT: C 141 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8848 (pttt) REVERT: C 203 VAL cc_start: 0.9361 (t) cc_final: 0.9012 (m) REVERT: C 291 ASN cc_start: 0.8550 (m-40) cc_final: 0.8220 (m-40) REVERT: C 317 PHE cc_start: 0.8496 (t80) cc_final: 0.8173 (t80) REVERT: D 71 THR cc_start: 0.9194 (p) cc_final: 0.8693 (t) REVERT: D 79 LYS cc_start: 0.8056 (tppt) cc_final: 0.7323 (tmtt) REVERT: D 143 ILE cc_start: 0.8648 (mm) cc_final: 0.8229 (mt) REVERT: D 272 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8780 (t) REVERT: D 317 PHE cc_start: 0.8960 (t80) cc_final: 0.8318 (t80) REVERT: D 374 LYS cc_start: 0.8071 (pttt) cc_final: 0.6993 (ptmt) REVERT: E 84 LEU cc_start: 0.8757 (mt) cc_final: 0.8533 (tt) REVERT: E 109 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7375 (mp0) REVERT: E 138 PHE cc_start: 0.8381 (t80) cc_final: 0.8135 (t80) REVERT: E 209 GLU cc_start: 0.8710 (pm20) cc_final: 0.8384 (pt0) REVERT: E 291 ASN cc_start: 0.8789 (m-40) cc_final: 0.8401 (m-40) REVERT: E 317 PHE cc_start: 0.8801 (t80) cc_final: 0.8592 (t80) REVERT: E 374 LYS cc_start: 0.7952 (pttt) cc_final: 0.6937 (ptmt) REVERT: F 68 ASN cc_start: 0.8297 (p0) cc_final: 0.7860 (t0) REVERT: F 109 GLU cc_start: 0.7368 (mp0) cc_final: 0.6877 (mp0) REVERT: F 371 GLN cc_start: 0.7225 (tp40) cc_final: 0.6769 (tp-100) REVERT: F 374 LYS cc_start: 0.7813 (pttt) cc_final: 0.6903 (ptmt) REVERT: G 93 MET cc_start: 0.9233 (ttt) cc_final: 0.8874 (ttm) REVERT: G 230 TYR cc_start: 0.8442 (m-80) cc_final: 0.8216 (m-80) REVERT: G 317 PHE cc_start: 0.8898 (t80) cc_final: 0.8683 (t80) REVERT: G 374 LYS cc_start: 0.7523 (mmtp) cc_final: 0.6863 (pttt) REVERT: H 41 LYS cc_start: 0.8345 (mttt) cc_final: 0.7785 (mtmt) REVERT: H 61 TYR cc_start: 0.8767 (m-80) cc_final: 0.8417 (m-80) REVERT: H 66 LYS cc_start: 0.8728 (tptm) cc_final: 0.8305 (tptm) REVERT: H 109 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7208 (mp0) REVERT: H 122 TYR cc_start: 0.7641 (m-80) cc_final: 0.7172 (m-80) REVERT: H 374 LYS cc_start: 0.7465 (pttm) cc_final: 0.6713 (ptmt) REVERT: I 92 PHE cc_start: 0.5001 (m-80) cc_final: 0.4736 (m-80) REVERT: I 109 GLU cc_start: 0.7322 (mp0) cc_final: 0.7042 (mp0) REVERT: I 300 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.7607 (t80) REVERT: I 374 LYS cc_start: 0.7482 (pttt) cc_final: 0.6351 (ptmt) REVERT: J 93 MET cc_start: 0.9116 (ttt) cc_final: 0.8723 (ttm) REVERT: J 224 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6622 (mt-10) REVERT: J 265 ASP cc_start: 0.6903 (m-30) cc_final: 0.6680 (m-30) REVERT: J 317 PHE cc_start: 0.8968 (t80) cc_final: 0.8580 (t80) REVERT: J 374 LYS cc_start: 0.7805 (pttt) cc_final: 0.7465 (ptpt) REVERT: K 41 LYS cc_start: 0.8109 (mttt) cc_final: 0.7669 (mtmt) REVERT: K 122 TYR cc_start: 0.7608 (m-10) cc_final: 0.7208 (m-80) REVERT: L 93 MET cc_start: 0.9123 (ptp) cc_final: 0.8802 (ptp) REVERT: L 374 LYS cc_start: 0.7521 (ptmt) cc_final: 0.7271 (pttt) REVERT: M 1 MET cc_start: 0.8601 (mpp) cc_final: 0.8394 (mpp) REVERT: M 7 GLU cc_start: 0.7923 (tp30) cc_final: 0.7521 (tp30) REVERT: M 21 GLU cc_start: 0.5698 (mp0) cc_final: 0.5349 (mp0) REVERT: M 101 GLU cc_start: 0.8230 (tt0) cc_final: 0.7989 (tt0) REVERT: N 21 GLU cc_start: 0.6592 (mt-10) cc_final: 0.6259 (mp0) REVERT: N 73 MET cc_start: 0.9265 (ttt) cc_final: 0.8740 (ttt) REVERT: N 85 TYR cc_start: 0.8797 (p90) cc_final: 0.8103 (p90) REVERT: N 86 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8046 (tttp) REVERT: N 105 ASP cc_start: 0.8271 (t0) cc_final: 0.7923 (t0) REVERT: O 73 MET cc_start: 0.8398 (ttt) cc_final: 0.7862 (ttt) REVERT: O 135 ASP cc_start: 0.7257 (t0) cc_final: 0.6844 (t0) REVERT: O 142 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8517 (pt) REVERT: P 1 MET cc_start: 0.8856 (mpp) cc_final: 0.8315 (mpp) REVERT: Q 11 LEU cc_start: 0.8001 (tp) cc_final: 0.7798 (tp) REVERT: Q 98 ASN cc_start: 0.9153 (t0) cc_final: 0.8820 (m-40) REVERT: Q 153 LYS cc_start: 0.8776 (mttm) cc_final: 0.8542 (mttm) REVERT: R 32 ASN cc_start: 0.8309 (m-40) cc_final: 0.7888 (m110) REVERT: R 58 LYS cc_start: 0.8465 (mttp) cc_final: 0.7851 (mtmm) REVERT: R 98 ASN cc_start: 0.9033 (m-40) cc_final: 0.8732 (m-40) REVERT: R 118 GLU cc_start: 0.8622 (mp0) cc_final: 0.8336 (mp0) REVERT: R 135 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.6971 (t0) REVERT: S 27 MET cc_start: 0.8777 (ttm) cc_final: 0.8373 (mtt) REVERT: S 50 LEU cc_start: 0.9129 (tp) cc_final: 0.8846 (tt) REVERT: T 49 GLN cc_start: 0.8837 (tt0) cc_final: 0.8429 (tt0) REVERT: T 86 LYS cc_start: 0.8253 (ttmm) cc_final: 0.7920 (ptmm) REVERT: U 7 GLU cc_start: 0.7434 (tp30) cc_final: 0.7037 (tp30) REVERT: U 32 ASN cc_start: 0.8501 (m-40) cc_final: 0.8085 (m110) REVERT: V 7 GLU cc_start: 0.7836 (tp30) cc_final: 0.7413 (tp30) REVERT: V 27 MET cc_start: 0.8670 (ttm) cc_final: 0.8392 (mtt) REVERT: V 50 LEU cc_start: 0.9055 (tp) cc_final: 0.8796 (tt) REVERT: W 101 GLU cc_start: 0.8297 (tt0) cc_final: 0.8020 (tt0) REVERT: W 105 ASP cc_start: 0.8727 (t0) cc_final: 0.8462 (t0) REVERT: X 1 MET cc_start: 0.8940 (mpp) cc_final: 0.8540 (mpp) REVERT: X 134 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8451 (mm-40) REVERT: X 142 ILE cc_start: 0.8456 (pt) cc_final: 0.8140 (pt) outliers start: 158 outliers final: 109 residues processed: 1053 average time/residue: 0.4929 time to fit residues: 907.6365 Evaluate side-chains 1006 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 889 time to evaluate : 4.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 343 HIS Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 343 HIS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 343 HIS Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 343 HIS Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 288 ASN Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain J residue 51 MET Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain J residue 343 HIS Chi-restraints excluded: chain K residue 51 MET Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain K residue 155 ILE Chi-restraints excluded: chain K residue 288 ASN Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 343 HIS Chi-restraints excluded: chain L residue 26 HIS Chi-restraints excluded: chain L residue 143 ILE Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 279 VAL Chi-restraints excluded: chain L residue 288 ASN Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 343 HIS Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain O residue 27 MET Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P residue 156 ILE Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 72 LYS Chi-restraints excluded: chain Q residue 166 VAL Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 135 ASP Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain V residue 142 ILE Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain X residue 43 ASP Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 134 GLN Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 166 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 473 optimal weight: 0.6980 chunk 455 optimal weight: 7.9990 chunk 309 optimal weight: 3.9990 chunk 609 optimal weight: 0.7980 chunk 540 optimal weight: 0.0270 chunk 5 optimal weight: 0.9980 chunk 586 optimal weight: 0.0670 chunk 626 optimal weight: 0.6980 chunk 348 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 ASN D 295 ASN F 90 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN N 32 ASN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 151 ASN ** O 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN Q 32 ASN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN ** S 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 32 ASN ** T 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 32 ASN ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 32 ASN ** W 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.108632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.100951 restraints weight = 67768.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.100978 restraints weight = 65088.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.101435 restraints weight = 61663.186| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 52344 Z= 0.171 Angle : 0.590 10.626 70824 Z= 0.301 Chirality : 0.043 0.167 8076 Planarity : 0.004 0.063 9156 Dihedral : 4.668 67.066 7023 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.66 % Favored : 92.18 % Rotamer: Outliers : 2.70 % Allowed : 18.37 % Favored : 78.93 % 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: -0.44 (0.11), residues: 6432 helix: 1.06 (0.10), residues: 2640 sheet: -0.29 (0.19), residues: 888 loop : -1.59 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 116 HIS 0.010 0.001 HIS O 130 PHE 0.031 0.001 PHE K 317 TYR 0.017 0.001 TYR C 150 ARG 0.005 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 970 time to evaluate : 4.529 Fit side-chains revert: symmetry clash REVERT: A 114 ILE cc_start: 0.9482 (mt) cc_final: 0.9089 (mt) REVERT: A 317 PHE cc_start: 0.8864 (t80) cc_final: 0.8605 (t80) REVERT: B 170 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8364 (mt0) REVERT: B 218 LEU cc_start: 0.9089 (mm) cc_final: 0.8889 (mt) REVERT: B 317 PHE cc_start: 0.8804 (t80) cc_final: 0.8439 (t80) REVERT: C 141 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8838 (pttt) REVERT: C 203 VAL cc_start: 0.9352 (t) cc_final: 0.9028 (m) REVERT: C 291 ASN cc_start: 0.8497 (m-40) cc_final: 0.8191 (m-40) REVERT: D 71 THR cc_start: 0.9130 (p) cc_final: 0.8641 (t) REVERT: D 79 LYS cc_start: 0.7799 (tppt) cc_final: 0.7358 (tmtt) REVERT: D 143 ILE cc_start: 0.8634 (mm) cc_final: 0.8200 (mt) REVERT: D 272 SER cc_start: 0.9047 (OUTLIER) cc_final: 0.8819 (t) REVERT: D 291 ASN cc_start: 0.8647 (m110) cc_final: 0.8157 (m110) REVERT: D 317 PHE cc_start: 0.8931 (t80) cc_final: 0.8278 (t80) REVERT: D 374 LYS cc_start: 0.8047 (pttt) cc_final: 0.6952 (ptmt) REVERT: E 93 MET cc_start: 0.9235 (ttp) cc_final: 0.8968 (ttp) REVERT: E 129 MET cc_start: 0.8822 (ttm) cc_final: 0.8259 (mtp) REVERT: E 209 GLU cc_start: 0.8652 (pm20) cc_final: 0.8367 (pt0) REVERT: E 291 ASN cc_start: 0.8790 (m-40) cc_final: 0.8404 (m-40) REVERT: E 317 PHE cc_start: 0.8758 (t80) cc_final: 0.8170 (t80) REVERT: E 374 LYS cc_start: 0.7915 (pttt) cc_final: 0.6903 (ptmt) REVERT: F 68 ASN cc_start: 0.8256 (p0) cc_final: 0.7883 (t0) REVERT: F 109 GLU cc_start: 0.7316 (mp0) cc_final: 0.6870 (mp0) REVERT: F 371 GLN cc_start: 0.7182 (tp40) cc_final: 0.6444 (tm-30) REVERT: F 374 LYS cc_start: 0.7838 (pttt) cc_final: 0.7129 (ptmt) REVERT: G 93 MET cc_start: 0.9175 (ttt) cc_final: 0.8873 (ttm) REVERT: G 230 TYR cc_start: 0.8401 (m-80) cc_final: 0.8144 (m-80) REVERT: G 291 ASN cc_start: 0.8933 (m110) cc_final: 0.8568 (m110) REVERT: G 317 PHE cc_start: 0.8865 (t80) cc_final: 0.8585 (t80) REVERT: H 41 LYS cc_start: 0.8314 (mttt) cc_final: 0.7792 (mtmt) REVERT: H 61 TYR cc_start: 0.8760 (m-80) cc_final: 0.8388 (m-80) REVERT: H 109 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7154 (mp0) REVERT: H 122 TYR cc_start: 0.7581 (m-80) cc_final: 0.7205 (m-80) REVERT: H 138 PHE cc_start: 0.8521 (t80) cc_final: 0.8320 (t80) REVERT: H 326 ASN cc_start: 0.6430 (t0) cc_final: 0.6092 (m-40) REVERT: H 374 LYS cc_start: 0.7424 (pttm) cc_final: 0.6718 (ptmt) REVERT: I 43 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: I 109 GLU cc_start: 0.7344 (mp0) cc_final: 0.7048 (mp0) REVERT: I 141 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8530 (ptmm) REVERT: I 233 SER cc_start: 0.8716 (p) cc_final: 0.8341 (t) REVERT: I 300 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.7595 (t80) REVERT: I 374 LYS cc_start: 0.7372 (pttt) cc_final: 0.6259 (ptmt) REVERT: J 93 MET cc_start: 0.9120 (ttt) cc_final: 0.8750 (ttm) REVERT: J 224 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6609 (mt-10) REVERT: J 228 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8672 (mm) REVERT: J 317 PHE cc_start: 0.8935 (t80) cc_final: 0.8563 (t80) REVERT: J 374 LYS cc_start: 0.7702 (pttt) cc_final: 0.7339 (ptpt) REVERT: K 41 LYS cc_start: 0.8085 (mttt) cc_final: 0.7559 (mtmt) REVERT: K 122 TYR cc_start: 0.7596 (m-10) cc_final: 0.7185 (m-80) REVERT: K 150 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7688 (m-10) REVERT: K 300 TYR cc_start: 0.8737 (OUTLIER) cc_final: 0.7172 (t80) REVERT: K 317 PHE cc_start: 0.8449 (t80) cc_final: 0.8220 (t80) REVERT: K 326 ASN cc_start: 0.6275 (t0) cc_final: 0.6059 (m-40) REVERT: K 374 LYS cc_start: 0.6985 (pttm) cc_final: 0.6187 (ptmt) REVERT: L 300 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.7763 (t80) REVERT: L 374 LYS cc_start: 0.7598 (ptmt) cc_final: 0.7223 (pttt) REVERT: M 1 MET cc_start: 0.8585 (mpp) cc_final: 0.8372 (mpp) REVERT: M 7 GLU cc_start: 0.7859 (tp30) cc_final: 0.7485 (tp30) REVERT: M 101 GLU cc_start: 0.8229 (tt0) cc_final: 0.7969 (tt0) REVERT: N 8 ASP cc_start: 0.7373 (m-30) cc_final: 0.7118 (m-30) REVERT: N 21 GLU cc_start: 0.6568 (mt-10) cc_final: 0.6273 (mp0) REVERT: N 73 MET cc_start: 0.9266 (ttt) cc_final: 0.8767 (ttt) REVERT: N 85 TYR cc_start: 0.8784 (p90) cc_final: 0.8090 (p90) REVERT: N 86 LYS cc_start: 0.8356 (ttmm) cc_final: 0.7988 (tttp) REVERT: N 105 ASP cc_start: 0.8359 (t0) cc_final: 0.8003 (t0) REVERT: O 121 LYS cc_start: 0.8826 (mttt) cc_final: 0.8535 (mttp) REVERT: O 135 ASP cc_start: 0.7449 (t0) cc_final: 0.6915 (t0) REVERT: O 153 LYS cc_start: 0.8420 (mttm) cc_final: 0.8124 (mttm) REVERT: P 1 MET cc_start: 0.8839 (mpp) cc_final: 0.8534 (mpp) REVERT: P 73 MET cc_start: 0.8896 (ttm) cc_final: 0.8643 (ttm) REVERT: Q 7 GLU cc_start: 0.7658 (tp30) cc_final: 0.7316 (tp30) REVERT: Q 21 GLU cc_start: 0.6498 (mt-10) cc_final: 0.6255 (mp0) REVERT: Q 25 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7161 (mt-10) REVERT: Q 86 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7895 (ptmm) REVERT: Q 98 ASN cc_start: 0.9149 (t0) cc_final: 0.8824 (m-40) REVERT: Q 107 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7195 (mt-10) REVERT: Q 153 LYS cc_start: 0.8683 (mttm) cc_final: 0.8345 (mttm) REVERT: R 32 ASN cc_start: 0.8453 (m-40) cc_final: 0.7976 (m110) REVERT: R 58 LYS cc_start: 0.8494 (mttp) cc_final: 0.7955 (mtmm) REVERT: R 98 ASN cc_start: 0.9020 (m-40) cc_final: 0.8745 (m-40) REVERT: R 135 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.6984 (t0) REVERT: R 142 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8394 (pt) REVERT: S 27 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8337 (mtt) REVERT: S 134 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8791 (mm-40) REVERT: T 41 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7999 (mmm) REVERT: T 49 GLN cc_start: 0.8878 (tt0) cc_final: 0.8480 (tt0) REVERT: U 7 GLU cc_start: 0.7520 (tp30) cc_final: 0.7039 (tp30) REVERT: V 7 GLU cc_start: 0.7902 (tp30) cc_final: 0.7507 (tp30) REVERT: V 27 MET cc_start: 0.8678 (ttm) cc_final: 0.8367 (mtt) REVERT: V 50 LEU cc_start: 0.9020 (tp) cc_final: 0.8780 (tt) REVERT: W 21 GLU cc_start: 0.5402 (mp0) cc_final: 0.5181 (mp0) REVERT: W 86 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7933 (tttp) REVERT: W 101 GLU cc_start: 0.8308 (tt0) cc_final: 0.8009 (tt0) REVERT: W 105 ASP cc_start: 0.8715 (t0) cc_final: 0.8486 (t0) REVERT: X 73 MET cc_start: 0.8276 (tpp) cc_final: 0.7839 (ttt) REVERT: X 84 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8433 (tp40) REVERT: X 104 MET cc_start: 0.8652 (ttm) cc_final: 0.8127 (ttt) REVERT: X 134 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8294 (mm-40) REVERT: X 142 ILE cc_start: 0.8389 (pt) cc_final: 0.8115 (pt) outliers start: 155 outliers final: 110 residues processed: 1070 average time/residue: 0.4581 time to fit residues: 848.9356 Evaluate side-chains 1024 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 897 time to evaluate : 4.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 343 HIS Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 343 HIS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 343 HIS Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 343 HIS Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 141 LYS Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 51 MET Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain J residue 343 HIS Chi-restraints excluded: chain K residue 51 MET Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain K residue 150 TYR Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 343 HIS Chi-restraints excluded: chain L residue 26 HIS Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 288 ASN Chi-restraints excluded: chain L residue 300 TYR Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 343 HIS Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain O residue 27 MET Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 166 VAL Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 135 ASP Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain T residue 41 MET Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain V residue 142 ILE Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 84 GLN Chi-restraints excluded: chain X residue 134 GLN Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 166 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 18 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 391 optimal weight: 2.9990 chunk 453 optimal weight: 4.9990 chunk 642 optimal weight: 0.0370 chunk 191 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 368 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 212 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 295 ASN ** J 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 ASN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 151 ASN ** O 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN Q 32 ASN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN T 32 ASN ** T 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 32 ASN ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 32 ASN ** W 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.107874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.100102 restraints weight = 68025.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.100363 restraints weight = 62400.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.100452 restraints weight = 55656.866| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 52344 Z= 0.190 Angle : 0.604 10.371 70824 Z= 0.306 Chirality : 0.043 0.174 8076 Planarity : 0.004 0.060 9156 Dihedral : 4.663 67.038 7023 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.26 % Favored : 91.64 % Rotamer: Outliers : 2.73 % Allowed : 18.79 % Favored : 78.48 % 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: -0.41 (0.11), residues: 6432 helix: 1.12 (0.10), residues: 2628 sheet: -0.25 (0.18), residues: 912 loop : -1.63 (0.11), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 116 HIS 0.016 0.002 HIS Q 130 PHE 0.033 0.001 PHE C 317 TYR 0.020 0.001 TYR C 113 ARG 0.004 0.000 ARG M 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 935 time to evaluate : 4.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ILE cc_start: 0.9466 (mt) cc_final: 0.9092 (mt) REVERT: A 317 PHE cc_start: 0.8828 (t80) cc_final: 0.8619 (t80) REVERT: B 170 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8327 (mt0) REVERT: B 317 PHE cc_start: 0.8809 (t80) cc_final: 0.8452 (t80) REVERT: C 141 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8814 (pttt) REVERT: C 203 VAL cc_start: 0.9352 (t) cc_final: 0.9029 (m) REVERT: C 291 ASN cc_start: 0.8493 (m-40) cc_final: 0.8164 (m-40) REVERT: C 317 PHE cc_start: 0.8512 (t80) cc_final: 0.8150 (t80) REVERT: D 79 LYS cc_start: 0.7578 (tppt) cc_final: 0.7312 (tmtt) REVERT: D 117 ASP cc_start: 0.7669 (t0) cc_final: 0.7430 (t70) REVERT: D 143 ILE cc_start: 0.8727 (mm) cc_final: 0.8488 (mm) REVERT: D 317 PHE cc_start: 0.8869 (t80) cc_final: 0.8470 (t80) REVERT: E 129 MET cc_start: 0.8850 (ttm) cc_final: 0.8305 (mtp) REVERT: E 209 GLU cc_start: 0.8663 (pm20) cc_final: 0.8377 (pt0) REVERT: E 291 ASN cc_start: 0.8799 (m-40) cc_final: 0.8414 (m-40) REVERT: E 317 PHE cc_start: 0.8480 (t80) cc_final: 0.8165 (t80) REVERT: E 374 LYS cc_start: 0.7947 (pttt) cc_final: 0.6938 (ptmt) REVERT: F 68 ASN cc_start: 0.8246 (p0) cc_final: 0.7910 (t0) REVERT: F 109 GLU cc_start: 0.7355 (mp0) cc_final: 0.6895 (mp0) REVERT: F 371 GLN cc_start: 0.7336 (tp40) cc_final: 0.6577 (tm-30) REVERT: F 374 LYS cc_start: 0.7886 (pttt) cc_final: 0.7178 (ptmt) REVERT: G 28 THR cc_start: 0.8995 (t) cc_final: 0.8789 (t) REVERT: G 93 MET cc_start: 0.9196 (ttt) cc_final: 0.8902 (ttm) REVERT: G 230 TYR cc_start: 0.8371 (m-80) cc_final: 0.8120 (m-80) REVERT: G 291 ASN cc_start: 0.8956 (m110) cc_final: 0.8559 (m110) REVERT: G 317 PHE cc_start: 0.8879 (t80) cc_final: 0.8594 (t80) REVERT: H 41 LYS cc_start: 0.8294 (mttt) cc_final: 0.7770 (mtmt) REVERT: H 61 TYR cc_start: 0.8801 (m-80) cc_final: 0.8408 (m-80) REVERT: H 122 TYR cc_start: 0.7677 (m-80) cc_final: 0.7213 (m-80) REVERT: H 374 LYS cc_start: 0.7421 (pttm) cc_final: 0.6730 (ptmt) REVERT: I 43 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: I 109 GLU cc_start: 0.7343 (mp0) cc_final: 0.7078 (mp0) REVERT: I 141 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8513 (ptmt) REVERT: I 233 SER cc_start: 0.8691 (p) cc_final: 0.8326 (t) REVERT: I 300 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.7606 (t80) REVERT: I 374 LYS cc_start: 0.7041 (pttt) cc_final: 0.6059 (ptmt) REVERT: J 43 GLU cc_start: 0.7861 (pm20) cc_final: 0.7609 (pm20) REVERT: J 93 MET cc_start: 0.9123 (ttt) cc_final: 0.8769 (ttm) REVERT: J 224 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6596 (mt-10) REVERT: J 228 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8706 (mm) REVERT: J 317 PHE cc_start: 0.8975 (t80) cc_final: 0.8539 (t80) REVERT: J 374 LYS cc_start: 0.7568 (pttt) cc_final: 0.7109 (ptpt) REVERT: K 41 LYS cc_start: 0.8093 (mttt) cc_final: 0.7554 (mtmt) REVERT: K 122 TYR cc_start: 0.7664 (m-10) cc_final: 0.7228 (m-80) REVERT: K 141 LYS cc_start: 0.9135 (ptmt) cc_final: 0.8852 (pttp) REVERT: K 150 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.7849 (m-10) REVERT: K 317 PHE cc_start: 0.8510 (t80) cc_final: 0.8227 (t80) REVERT: K 374 LYS cc_start: 0.7002 (pttm) cc_final: 0.6211 (ptmt) REVERT: L 300 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.7749 (t80) REVERT: M 1 MET cc_start: 0.8545 (mpp) cc_final: 0.8319 (mpp) REVERT: M 7 GLU cc_start: 0.7859 (tp30) cc_final: 0.7493 (tp30) REVERT: M 101 GLU cc_start: 0.8220 (tt0) cc_final: 0.7990 (tt0) REVERT: N 8 ASP cc_start: 0.7382 (m-30) cc_final: 0.7169 (m-30) REVERT: N 73 MET cc_start: 0.9250 (ttt) cc_final: 0.8764 (ttt) REVERT: N 85 TYR cc_start: 0.8798 (p90) cc_final: 0.8088 (p90) REVERT: N 86 LYS cc_start: 0.8373 (ttmm) cc_final: 0.8050 (tttp) REVERT: O 41 MET cc_start: 0.8148 (mtp) cc_final: 0.7856 (mtp) REVERT: O 121 LYS cc_start: 0.8798 (mttt) cc_final: 0.8485 (mttp) REVERT: O 135 ASP cc_start: 0.7410 (t0) cc_final: 0.6930 (t0) REVERT: O 153 LYS cc_start: 0.8430 (mttm) cc_final: 0.8130 (mttm) REVERT: P 50 LEU cc_start: 0.9060 (tp) cc_final: 0.8734 (tt) REVERT: Q 11 LEU cc_start: 0.7849 (tp) cc_final: 0.7503 (tp) REVERT: Q 98 ASN cc_start: 0.9169 (t0) cc_final: 0.8820 (m-40) REVERT: Q 153 LYS cc_start: 0.8688 (mttm) cc_final: 0.8352 (mttp) REVERT: R 32 ASN cc_start: 0.8602 (m-40) cc_final: 0.8127 (m110) REVERT: R 58 LYS cc_start: 0.8551 (mttp) cc_final: 0.7982 (mtmm) REVERT: R 98 ASN cc_start: 0.8981 (m-40) cc_final: 0.8693 (m-40) REVERT: R 135 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.6989 (t0) REVERT: S 27 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8321 (mtt) REVERT: S 134 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8588 (mm-40) REVERT: T 41 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8078 (mpp) REVERT: T 49 GLN cc_start: 0.8881 (tt0) cc_final: 0.8505 (tt0) REVERT: T 86 LYS cc_start: 0.8346 (ttmm) cc_final: 0.7966 (ptmm) REVERT: T 170 VAL cc_start: 0.8154 (m) cc_final: 0.7869 (m) REVERT: U 7 GLU cc_start: 0.7502 (tp30) cc_final: 0.7033 (tp30) REVERT: V 27 MET cc_start: 0.8678 (ttm) cc_final: 0.8379 (mtt) REVERT: V 50 LEU cc_start: 0.9029 (tp) cc_final: 0.8790 (tt) REVERT: W 10 ARG cc_start: 0.7706 (ttm-80) cc_final: 0.7493 (mtt90) REVERT: W 104 MET cc_start: 0.8844 (ttt) cc_final: 0.7963 (ttt) REVERT: W 105 ASP cc_start: 0.8739 (t0) cc_final: 0.8482 (t0) REVERT: X 84 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8497 (tp40) REVERT: X 134 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8278 (mm-40) outliers start: 157 outliers final: 122 residues processed: 1038 average time/residue: 0.4649 time to fit residues: 833.9491 Evaluate side-chains 1032 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 896 time to evaluate : 4.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 343 HIS Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 343 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 343 HIS Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 343 HIS Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 141 LYS Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 51 MET Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 204 ILE Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain J residue 343 HIS Chi-restraints excluded: chain K residue 51 MET Chi-restraints excluded: chain K residue 150 TYR Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 343 HIS Chi-restraints excluded: chain L residue 26 HIS Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 279 VAL Chi-restraints excluded: chain L residue 288 ASN Chi-restraints excluded: chain L residue 300 TYR Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 343 HIS Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain O residue 27 MET Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 166 VAL Chi-restraints excluded: chain R residue 27 MET Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 135 ASP Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain T residue 41 MET Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 142 ILE Chi-restraints excluded: chain V residue 142 ILE Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 84 GLN Chi-restraints excluded: chain X residue 134 GLN Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 166 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 445 optimal weight: 0.1980 chunk 216 optimal weight: 0.0050 chunk 468 optimal weight: 2.9990 chunk 441 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 582 optimal weight: 2.9990 chunk 641 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 413 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 389 optimal weight: 3.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 ASN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS M 32 ASN N 32 ASN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 151 ASN ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN Q 32 ASN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN ** S 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 32 ASN ** T 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 32 ASN ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 32 ASN ** W 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 32 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.109975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.102263 restraints weight = 67681.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.102839 restraints weight = 59519.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.103034 restraints weight = 52598.882| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 52344 Z= 0.172 Angle : 0.600 10.894 70824 Z= 0.303 Chirality : 0.043 0.175 8076 Planarity : 0.004 0.059 9156 Dihedral : 4.601 66.535 7023 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.90 % Favored : 92.01 % Rotamer: Outliers : 2.68 % Allowed : 18.93 % Favored : 78.39 % 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: -0.39 (0.11), residues: 6432 helix: 1.13 (0.10), residues: 2640 sheet: -0.22 (0.19), residues: 888 loop : -1.62 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 116 HIS 0.015 0.001 HIS Q 130 PHE 0.032 0.001 PHE H 92 TYR 0.017 0.001 TYR L 113 ARG 0.004 0.000 ARG G 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 931 time to evaluate : 4.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.7956 (p-80) REVERT: A 114 ILE cc_start: 0.9436 (mt) cc_final: 0.9092 (mt) REVERT: A 317 PHE cc_start: 0.8830 (t80) cc_final: 0.8625 (t80) REVERT: B 138 PHE cc_start: 0.8878 (t80) cc_final: 0.8596 (t80) REVERT: B 170 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8385 (mt0) REVERT: B 300 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.7365 (t80) REVERT: B 317 PHE cc_start: 0.8780 (t80) cc_final: 0.8393 (t80) REVERT: C 141 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8811 (pttt) REVERT: C 203 VAL cc_start: 0.9316 (t) cc_final: 0.8999 (m) REVERT: C 291 ASN cc_start: 0.8444 (m-40) cc_final: 0.8152 (m-40) REVERT: C 317 PHE cc_start: 0.8519 (t80) cc_final: 0.8102 (t80) REVERT: D 71 THR cc_start: 0.9075 (p) cc_final: 0.8584 (t) REVERT: D 117 ASP cc_start: 0.7580 (t0) cc_final: 0.7280 (t70) REVERT: D 204 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8422 (mm) REVERT: D 291 ASN cc_start: 0.8686 (m110) cc_final: 0.8217 (m110) REVERT: D 317 PHE cc_start: 0.8893 (t80) cc_final: 0.8187 (t80) REVERT: D 374 LYS cc_start: 0.7810 (ptpt) cc_final: 0.6669 (ptmt) REVERT: E 129 MET cc_start: 0.8816 (ttm) cc_final: 0.8328 (mtp) REVERT: E 209 GLU cc_start: 0.8687 (pm20) cc_final: 0.8323 (pt0) REVERT: E 291 ASN cc_start: 0.8950 (m-40) cc_final: 0.8427 (m-40) REVERT: E 317 PHE cc_start: 0.8469 (t80) cc_final: 0.8222 (t80) REVERT: E 374 LYS cc_start: 0.8059 (pttt) cc_final: 0.6961 (ptmt) REVERT: F 68 ASN cc_start: 0.8250 (p0) cc_final: 0.7902 (t0) REVERT: F 109 GLU cc_start: 0.7364 (mp0) cc_final: 0.6881 (mp0) REVERT: F 371 GLN cc_start: 0.7233 (tp40) cc_final: 0.6564 (tm-30) REVERT: F 374 LYS cc_start: 0.7928 (pttt) cc_final: 0.7215 (ptmt) REVERT: G 93 MET cc_start: 0.9172 (ttt) cc_final: 0.8867 (ttm) REVERT: G 230 TYR cc_start: 0.8347 (m-80) cc_final: 0.8097 (m-80) REVERT: G 265 ASP cc_start: 0.7190 (m-30) cc_final: 0.6879 (m-30) REVERT: G 291 ASN cc_start: 0.8942 (m110) cc_final: 0.8309 (m110) REVERT: G 317 PHE cc_start: 0.8878 (t80) cc_final: 0.8585 (t80) REVERT: H 41 LYS cc_start: 0.8249 (mttt) cc_final: 0.7741 (mtmt) REVERT: H 61 TYR cc_start: 0.8794 (m-80) cc_final: 0.8432 (m-80) REVERT: H 122 TYR cc_start: 0.7624 (m-80) cc_final: 0.7207 (m-80) REVERT: H 374 LYS cc_start: 0.7239 (pttm) cc_final: 0.6524 (ptmt) REVERT: I 109 GLU cc_start: 0.7287 (mp0) cc_final: 0.7042 (mp0) REVERT: I 141 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8523 (ptmt) REVERT: I 233 SER cc_start: 0.8660 (p) cc_final: 0.8340 (t) REVERT: I 300 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.7639 (t80) REVERT: I 370 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7333 (mt-10) REVERT: I 374 LYS cc_start: 0.7582 (pttt) cc_final: 0.6554 (ptmt) REVERT: J 51 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8235 (ttp) REVERT: J 141 LYS cc_start: 0.8850 (pttp) cc_final: 0.8643 (ptpt) REVERT: J 228 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8599 (mm) REVERT: J 317 PHE cc_start: 0.8962 (t80) cc_final: 0.8517 (t80) REVERT: J 374 LYS cc_start: 0.7881 (pttt) cc_final: 0.7512 (ptpt) REVERT: K 41 LYS cc_start: 0.8085 (mttt) cc_final: 0.7567 (mtmt) REVERT: K 122 TYR cc_start: 0.7595 (m-10) cc_final: 0.7195 (m-80) REVERT: K 150 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7796 (m-10) REVERT: K 300 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.7050 (t80) REVERT: K 317 PHE cc_start: 0.8528 (t80) cc_final: 0.8185 (t80) REVERT: K 374 LYS cc_start: 0.6971 (pttm) cc_final: 0.6181 (ptmt) REVERT: L 68 ASN cc_start: 0.8347 (p0) cc_final: 0.8010 (t0) REVERT: L 300 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.7729 (t80) REVERT: L 374 LYS cc_start: 0.7551 (ptmt) cc_final: 0.7100 (pttt) REVERT: M 1 MET cc_start: 0.8528 (mpp) cc_final: 0.8316 (mpp) REVERT: M 7 GLU cc_start: 0.7845 (tp30) cc_final: 0.7467 (tp30) REVERT: N 73 MET cc_start: 0.9240 (ttt) cc_final: 0.8742 (ttt) REVERT: N 85 TYR cc_start: 0.8830 (p90) cc_final: 0.8055 (p90) REVERT: N 86 LYS cc_start: 0.8358 (ttmm) cc_final: 0.7965 (tttp) REVERT: N 122 LEU cc_start: 0.9402 (tp) cc_final: 0.9178 (tp) REVERT: O 73 MET cc_start: 0.8508 (tpp) cc_final: 0.8150 (ttt) REVERT: O 135 ASP cc_start: 0.7541 (t0) cc_final: 0.7066 (t0) REVERT: Q 7 GLU cc_start: 0.7529 (tp30) cc_final: 0.7245 (tp30) REVERT: Q 21 GLU cc_start: 0.6550 (mt-10) cc_final: 0.6275 (mp0) REVERT: Q 25 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7122 (mt-10) REVERT: Q 86 LYS cc_start: 0.8260 (ttmm) cc_final: 0.7873 (ptmm) REVERT: Q 107 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7233 (mt-10) REVERT: R 58 LYS cc_start: 0.8587 (mttp) cc_final: 0.8059 (mtmm) REVERT: R 135 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.6913 (t0) REVERT: R 142 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8314 (pt) REVERT: S 8 ASP cc_start: 0.7331 (m-30) cc_final: 0.7118 (m-30) REVERT: S 27 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8317 (mtt) REVERT: S 134 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8592 (mm-40) REVERT: T 8 ASP cc_start: 0.7004 (m-30) cc_final: 0.6735 (m-30) REVERT: T 41 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8099 (mpp) REVERT: T 49 GLN cc_start: 0.8873 (tt0) cc_final: 0.8560 (tt0) REVERT: T 86 LYS cc_start: 0.8366 (ttmm) cc_final: 0.7945 (ptmm) REVERT: U 7 GLU cc_start: 0.7506 (tp30) cc_final: 0.7064 (tp30) REVERT: U 32 ASN cc_start: 0.8395 (m110) cc_final: 0.8048 (m110) REVERT: V 27 MET cc_start: 0.8673 (ttm) cc_final: 0.8359 (mtt) REVERT: W 8 ASP cc_start: 0.7271 (m-30) cc_final: 0.7019 (m-30) REVERT: W 86 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7970 (tttp) REVERT: W 104 MET cc_start: 0.8871 (ttt) cc_final: 0.7973 (ttt) REVERT: W 105 ASP cc_start: 0.8675 (t0) cc_final: 0.8438 (t0) REVERT: X 73 MET cc_start: 0.8076 (tpp) cc_final: 0.7728 (ttt) REVERT: X 84 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8411 (tp40) REVERT: X 105 ASP cc_start: 0.8375 (t70) cc_final: 0.8124 (t0) REVERT: X 134 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8262 (mm-40) outliers start: 154 outliers final: 118 residues processed: 1030 average time/residue: 0.4658 time to fit residues: 829.1677 Evaluate side-chains 1020 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 884 time to evaluate : 4.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 343 HIS Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 343 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 161 ASN Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 343 HIS Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 343 HIS Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 141 LYS Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 51 MET Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain J residue 343 HIS Chi-restraints excluded: chain K residue 51 MET Chi-restraints excluded: chain K residue 150 TYR Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 343 HIS Chi-restraints excluded: chain L residue 26 HIS Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 279 VAL Chi-restraints excluded: chain L residue 288 ASN Chi-restraints excluded: chain L residue 300 TYR Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 343 HIS Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain O residue 27 MET Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P residue 156 ILE Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 166 VAL Chi-restraints excluded: chain R residue 27 MET Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 84 GLN Chi-restraints excluded: chain R residue 135 ASP Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain T residue 41 MET Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 142 ILE Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 35 ILE Chi-restraints excluded: chain V residue 142 ILE Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 84 GLN Chi-restraints excluded: chain X residue 134 GLN Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 166 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 80 optimal weight: 9.9990 chunk 597 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 591 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 320 optimal weight: 2.9990 chunk 581 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN C 223 GLN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 ASN E 295 ASN ** E 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN F 295 ASN G 26 HIS ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 161 ASN ** J 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 170 GLN J 291 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 161 ASN L 295 ASN M 32 ASN N 32 ASN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 151 ASN O 134 GLN P 32 ASN Q 32 ASN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN ** S 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 32 ASN ** T 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 GLN ** U 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 32 ASN ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 32 ASN ** W 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 32 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.102431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.094454 restraints weight = 69476.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.094464 restraints weight = 60788.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.095304 restraints weight = 59744.151| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 52344 Z= 0.306 Angle : 0.686 11.523 70824 Z= 0.347 Chirality : 0.045 0.174 8076 Planarity : 0.004 0.059 9156 Dihedral : 4.898 66.885 7023 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.50 % Favored : 91.40 % Rotamer: Outliers : 2.54 % Allowed : 19.40 % Favored : 78.06 % 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: -0.54 (0.11), residues: 6432 helix: 1.01 (0.10), residues: 2628 sheet: -0.33 (0.18), residues: 912 loop : -1.68 (0.11), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 116 HIS 0.015 0.002 HIS Q 130 PHE 0.035 0.002 PHE C 317 TYR 0.022 0.002 TYR C 113 ARG 0.007 0.001 ARG I 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 925 time to evaluate : 4.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.8139 (p-80) REVERT: A 114 ILE cc_start: 0.9471 (mt) cc_final: 0.9121 (mt) REVERT: A 317 PHE cc_start: 0.8856 (t80) cc_final: 0.8650 (t80) REVERT: A 371 GLN cc_start: 0.7286 (tp40) cc_final: 0.6680 (tm-30) REVERT: B 71 THR cc_start: 0.9164 (p) cc_final: 0.8735 (t) REVERT: B 170 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8346 (mt0) REVERT: B 317 PHE cc_start: 0.8822 (t80) cc_final: 0.8199 (t80) REVERT: C 141 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8848 (pttt) REVERT: C 203 VAL cc_start: 0.9375 (t) cc_final: 0.9030 (m) REVERT: C 291 ASN cc_start: 0.8424 (m-40) cc_final: 0.8091 (m-40) REVERT: D 71 THR cc_start: 0.9171 (p) cc_final: 0.8693 (t) REVERT: D 317 PHE cc_start: 0.8921 (t80) cc_final: 0.8292 (t80) REVERT: E 129 MET cc_start: 0.8878 (ttm) cc_final: 0.8521 (mtp) REVERT: E 209 GLU cc_start: 0.8690 (pm20) cc_final: 0.8342 (pt0) REVERT: E 291 ASN cc_start: 0.8713 (m-40) cc_final: 0.8250 (m-40) REVERT: E 317 PHE cc_start: 0.8509 (t80) cc_final: 0.8302 (t80) REVERT: E 374 LYS cc_start: 0.7976 (pttt) cc_final: 0.6942 (ptmt) REVERT: F 68 ASN cc_start: 0.8355 (p0) cc_final: 0.7983 (t0) REVERT: F 371 GLN cc_start: 0.7210 (tp40) cc_final: 0.6645 (tm-30) REVERT: G 71 THR cc_start: 0.9214 (p) cc_final: 0.8758 (t) REVERT: G 317 PHE cc_start: 0.9047 (t80) cc_final: 0.8648 (t80) REVERT: H 41 LYS cc_start: 0.8346 (mttt) cc_final: 0.7770 (mtmt) REVERT: H 122 TYR cc_start: 0.7903 (m-80) cc_final: 0.7472 (m-80) REVERT: H 374 LYS cc_start: 0.7414 (pttm) cc_final: 0.6609 (ptmt) REVERT: I 141 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8579 (ptmt) REVERT: I 370 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7452 (mt-10) REVERT: I 374 LYS cc_start: 0.7339 (pttt) cc_final: 0.6259 (ptmt) REVERT: J 92 PHE cc_start: 0.8087 (m-10) cc_final: 0.7816 (m-10) REVERT: J 228 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8496 (mm) REVERT: J 317 PHE cc_start: 0.8997 (t80) cc_final: 0.8634 (t80) REVERT: J 374 LYS cc_start: 0.7886 (pttt) cc_final: 0.7546 (ptpt) REVERT: K 41 LYS cc_start: 0.8133 (mttt) cc_final: 0.7580 (mtmt) REVERT: K 122 TYR cc_start: 0.7736 (m-10) cc_final: 0.7236 (m-80) REVERT: K 150 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8044 (m-10) REVERT: L 374 LYS cc_start: 0.7622 (ptmt) cc_final: 0.7163 (pttt) REVERT: M 7 GLU cc_start: 0.7959 (tp30) cc_final: 0.7561 (tp30) REVERT: M 27 MET cc_start: 0.8490 (ttm) cc_final: 0.8200 (mtt) REVERT: M 145 GLU cc_start: 0.6360 (pm20) cc_final: 0.5962 (pm20) REVERT: N 73 MET cc_start: 0.9290 (ttt) cc_final: 0.8869 (ttt) REVERT: N 85 TYR cc_start: 0.8853 (p90) cc_final: 0.8171 (p90) REVERT: N 105 ASP cc_start: 0.8330 (t0) cc_final: 0.7944 (t0) REVERT: O 32 ASN cc_start: 0.8414 (m-40) cc_final: 0.8090 (m110) REVERT: O 135 ASP cc_start: 0.7572 (t0) cc_final: 0.7111 (t0) REVERT: P 50 LEU cc_start: 0.9201 (tp) cc_final: 0.8917 (tt) REVERT: Q 21 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6336 (mp0) REVERT: Q 25 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7252 (mt-10) REVERT: Q 98 ASN cc_start: 0.9325 (t0) cc_final: 0.8959 (m-40) REVERT: Q 107 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7355 (mt-10) REVERT: Q 153 LYS cc_start: 0.8656 (mttm) cc_final: 0.8342 (mttm) REVERT: R 58 LYS cc_start: 0.8557 (mttp) cc_final: 0.7861 (mtmm) REVERT: S 27 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8450 (mtt) REVERT: S 134 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8572 (mm-40) REVERT: T 41 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.7762 (mpp) REVERT: T 49 GLN cc_start: 0.8873 (tt0) cc_final: 0.8609 (tt0) REVERT: T 86 LYS cc_start: 0.8309 (ttmm) cc_final: 0.7992 (ptmm) REVERT: T 104 MET cc_start: 0.8687 (ttt) cc_final: 0.7880 (ttt) REVERT: U 7 GLU cc_start: 0.7560 (tp30) cc_final: 0.7050 (tp30) REVERT: V 27 MET cc_start: 0.8790 (ttm) cc_final: 0.8497 (mtt) REVERT: W 86 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7925 (tttp) REVERT: W 98 ASN cc_start: 0.9217 (t0) cc_final: 0.8746 (m-40) REVERT: W 105 ASP cc_start: 0.8689 (t0) cc_final: 0.8464 (t0) REVERT: X 84 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8450 (tp40) REVERT: X 105 ASP cc_start: 0.8386 (t70) cc_final: 0.8163 (t0) REVERT: X 134 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8455 (mm-40) REVERT: X 142 ILE cc_start: 0.8405 (pt) cc_final: 0.8083 (pt) outliers start: 146 outliers final: 123 residues processed: 1019 average time/residue: 0.4539 time to fit residues: 803.1860 Evaluate side-chains 1017 residues out of total 5748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 884 time to evaluate : 4.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 343 HIS Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 343 HIS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 343 HIS Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 343 HIS Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 141 LYS Chi-restraints excluded: chain I residue 161 ASN Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 51 MET Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain J residue 343 HIS Chi-restraints excluded: chain K residue 51 MET Chi-restraints excluded: chain K residue 150 TYR Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 343 HIS Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 161 ASN Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 279 VAL Chi-restraints excluded: chain L residue 288 ASN Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 343 HIS Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain O residue 27 MET Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P residue 156 ILE Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 166 VAL Chi-restraints excluded: chain R residue 21 GLU Chi-restraints excluded: chain R residue 27 MET Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 84 GLN Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain T residue 41 MET Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain V residue 35 ILE Chi-restraints excluded: chain V residue 142 ILE Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain X residue 41 MET Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 84 GLN Chi-restraints excluded: chain X residue 134 GLN Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 166 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 502 optimal weight: 2.9990 chunk 295 optimal weight: 0.5980 chunk 286 optimal weight: 0.0980 chunk 636 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 157 optimal weight: 0.7980 chunk 638 optimal weight: 3.9990 chunk 643 optimal weight: 1.9990 chunk 352 optimal weight: 0.8980 chunk 472 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS C 46 ASN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 161 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 ASN K 373 ASN L 161 ASN ** L 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN N 32 ASN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 151 ASN P 32 ASN Q 32 ASN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN ** S 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 32 ASN ** T 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 32 ASN ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 32 ASN ** W 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 32 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.102524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.094917 restraints weight = 69464.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.094707 restraints weight = 65558.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.094944 restraints weight = 65056.822| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.220 52344 Z= 0.313 Angle : 0.895 59.196 70824 Z= 0.519 Chirality : 0.052 1.423 8076 Planarity : 0.005 0.114 9156 Dihedral : 4.989 66.899 7023 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.41 % Favored : 91.42 % Rotamer: Outliers : 2.45 % Allowed : 19.73 % Favored : 77.82 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.11), residues: 6432 helix: 1.00 (0.10), residues: 2628 sheet: -0.34 (0.18), residues: 912 loop : -1.70 (0.11), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 116 HIS 0.177 0.003 HIS G 26 PHE 0.031 0.002 PHE C 317 TYR 0.054 0.002 TYR W 88 ARG 0.005 0.000 ARG I 359 =============================================================================== Job complete usr+sys time: 14793.58 seconds wall clock time: 258 minutes 26.75 seconds (15506.75 seconds total)