Starting phenix.real_space_refine on Tue Aug 26 16:26:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7i_41983/08_2025/8u7i_41983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7i_41983/08_2025/8u7i_41983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u7i_41983/08_2025/8u7i_41983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7i_41983/08_2025/8u7i_41983.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u7i_41983/08_2025/8u7i_41983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7i_41983/08_2025/8u7i_41983.map" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 136 5.16 5 C 24956 2.51 5 N 6452 2.21 5 O 7320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38864 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5111 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 12, 'TRANS': 613} Chain breaks: 3 Chain: "B" Number of atoms: 5111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5111 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 12, 'TRANS': 613} Chain breaks: 3 Chain: "C" Number of atoms: 5111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5111 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 12, 'TRANS': 613} Chain breaks: 3 Chain: "D" Number of atoms: 5111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5111 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 12, 'TRANS': 613} Chain breaks: 3 Chain: "E" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2326 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 6, 'TRANS': 281} Chain breaks: 5 Chain: "F" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2326 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 6, 'TRANS': 281} Chain breaks: 5 Chain: "G" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2326 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 6, 'TRANS': 281} Chain breaks: 5 Chain: "H" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2326 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 6, 'TRANS': 281} Chain breaks: 5 Chain: "I" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1346 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 9, 'TRANS': 152} Chain: "J" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1346 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 9, 'TRANS': 152} Chain: "K" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1346 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 9, 'TRANS': 152} Chain: "L" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1346 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 9, 'TRANS': 152} Chain: "M" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 933 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "N" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 933 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "O" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 933 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "P" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 933 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Time building chain proxies: 9.33, per 1000 atoms: 0.24 Number of scatterers: 38864 At special positions: 0 Unit cell: (189.57, 167.32, 153.97, 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 136 16.00 O 7320 8.00 N 6452 7.00 C 24956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS I 282 " - pdb=" SG CYS M 285 " distance=2.03 Simple disulfide: pdb=" SG CYS I 284 " - pdb=" SG CYS M 284 " distance=2.03 Simple disulfide: pdb=" SG CYS I 285 " - pdb=" SG CYS M 282 " distance=2.03 Simple disulfide: pdb=" SG CYS J 282 " - pdb=" SG CYS N 285 " distance=2.03 Simple disulfide: pdb=" SG CYS J 284 " - pdb=" SG CYS N 284 " distance=2.04 Simple disulfide: pdb=" SG CYS J 285 " - pdb=" SG CYS N 282 " distance=2.03 Simple disulfide: pdb=" SG CYS K 282 " - pdb=" SG CYS O 285 " distance=2.02 Simple disulfide: pdb=" SG CYS K 284 " - pdb=" SG CYS O 284 " distance=2.03 Simple disulfide: pdb=" SG CYS K 285 " - pdb=" SG CYS O 282 " distance=2.03 Simple disulfide: pdb=" SG CYS L 282 " - pdb=" SG CYS P 285 " distance=2.03 Simple disulfide: pdb=" SG CYS L 284 " - pdb=" SG CYS P 284 " distance=2.03 Simple disulfide: pdb=" SG CYS L 285 " - pdb=" SG CYS P 282 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9048 Finding SS restraints... Secondary structure from input PDB file: 212 helices and 53 sheets defined 51.3% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid -53 through -42 Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 83 through 94 removed outlier: 3.702A pdb=" N LYS A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.622A pdb=" N ALA A 102 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.960A pdb=" N VAL A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 148' Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.613A pdb=" N GLN A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 201 Processing helix chain 'A' and resid 202 through 220 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 259 through 277 removed outlier: 3.890A pdb=" N TYR A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 353 through 357 removed outlier: 4.352A pdb=" N SER A 357 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 4.099A pdb=" N SER A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 395 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 447 through 458 removed outlier: 3.645A pdb=" N CYS A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 493 Processing helix chain 'A' and resid 493 through 503 Processing helix chain 'A' and resid 511 through 520 Processing helix chain 'A' and resid 520 through 529 removed outlier: 3.677A pdb=" N MET A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 540 removed outlier: 4.110A pdb=" N SER A 540 " --> pdb=" O TYR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 552 Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 566 through 574 removed outlier: 4.170A pdb=" N LYS A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing helix chain 'B' and resid -53 through -42 Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.707A pdb=" N LYS B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.937A pdb=" N VAL B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 148' Processing helix chain 'B' and resid 159 through 174 removed outlier: 3.935A pdb=" N GLN B 166 " --> pdb=" O LYS B 162 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR B 170 " --> pdb=" O GLN B 166 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 201 Processing helix chain 'B' and resid 202 through 220 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 259 through 277 removed outlier: 3.574A pdb=" N TYR B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 308 Processing helix chain 'B' and resid 321 through 326 Processing helix chain 'B' and resid 353 through 357 removed outlier: 4.361A pdb=" N SER B 357 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 370 removed outlier: 4.100A pdb=" N SER B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 395 Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 447 through 458 removed outlier: 3.634A pdb=" N CYS B 453 " --> pdb=" O GLY B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 493 Processing helix chain 'B' and resid 493 through 503 Processing helix chain 'B' and resid 511 through 520 Processing helix chain 'B' and resid 521 through 529 Processing helix chain 'B' and resid 532 through 540 removed outlier: 4.095A pdb=" N SER B 540 " --> pdb=" O TYR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 552 Processing helix chain 'B' and resid 553 through 563 Processing helix chain 'B' and resid 566 through 574 removed outlier: 4.156A pdb=" N LYS B 570 " --> pdb=" O PHE B 566 " (cutoff:3.500A) Processing helix chain 'C' and resid -53 through -42 Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 83 through 94 removed outlier: 3.624A pdb=" N LYS C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 144 through 148 removed outlier: 3.922A pdb=" N VAL C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 144 through 148' Processing helix chain 'C' and resid 159 through 175 removed outlier: 3.628A pdb=" N GLN C 166 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C 167 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS C 169 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR C 170 " --> pdb=" O GLN C 166 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 172 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER C 175 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 201 Processing helix chain 'C' and resid 202 through 220 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 259 through 277 removed outlier: 3.618A pdb=" N LYS C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 308 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 353 through 357 removed outlier: 4.353A pdb=" N SER C 357 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 removed outlier: 4.100A pdb=" N SER C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 369 " --> pdb=" O ALA C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 447 through 458 removed outlier: 3.682A pdb=" N CYS C 453 " --> pdb=" O GLY C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 493 Processing helix chain 'C' and resid 493 through 503 Processing helix chain 'C' and resid 511 through 529 removed outlier: 7.418A pdb=" N GLU C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 540 removed outlier: 4.154A pdb=" N SER C 540 " --> pdb=" O TYR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 552 Processing helix chain 'C' and resid 553 through 563 Processing helix chain 'C' and resid 566 through 574 removed outlier: 4.221A pdb=" N LYS C 570 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing helix chain 'D' and resid -53 through -42 Processing helix chain 'D' and resid 31 through 47 Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 83 through 94 removed outlier: 3.656A pdb=" N LYS D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.618A pdb=" N ALA D 102 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 removed outlier: 3.951A pdb=" N VAL D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 148' Processing helix chain 'D' and resid 159 through 175 removed outlier: 3.869A pdb=" N GLN D 166 " --> pdb=" O LYS D 162 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TYR D 170 " --> pdb=" O GLN D 166 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE D 172 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER D 175 " --> pdb=" O ILE D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 201 Processing helix chain 'D' and resid 202 through 220 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 259 through 277 removed outlier: 3.731A pdb=" N LYS D 276 " --> pdb=" O TYR D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 308 Processing helix chain 'D' and resid 321 through 326 Processing helix chain 'D' and resid 353 through 357 removed outlier: 4.352A pdb=" N SER D 357 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 370 removed outlier: 4.092A pdb=" N SER D 368 " --> pdb=" O LYS D 364 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 369 " --> pdb=" O ALA D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 395 Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 413 through 423 Processing helix chain 'D' and resid 447 through 458 removed outlier: 3.663A pdb=" N CYS D 453 " --> pdb=" O GLY D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 493 Processing helix chain 'D' and resid 493 through 503 Processing helix chain 'D' and resid 511 through 520 Processing helix chain 'D' and resid 520 through 529 removed outlier: 3.771A pdb=" N MET D 524 " --> pdb=" O ILE D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 540 removed outlier: 4.110A pdb=" N SER D 540 " --> pdb=" O TYR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 552 Processing helix chain 'D' and resid 553 through 563 Processing helix chain 'D' and resid 566 through 574 removed outlier: 4.233A pdb=" N LYS D 570 " --> pdb=" O PHE D 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 9 Processing helix chain 'E' and resid 22 through 38 Processing helix chain 'E' and resid 50 through 62 removed outlier: 3.693A pdb=" N ARG E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 81 removed outlier: 3.575A pdb=" N VAL E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 91 removed outlier: 5.370A pdb=" N LYS E 87 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASP E 88 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 121 removed outlier: 4.958A pdb=" N GLN E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR E 119 " --> pdb=" O GLN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 145 Processing helix chain 'E' and resid 145 through 155 Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'E' and resid 168 through 181 removed outlier: 3.688A pdb=" N GLN E 181 " --> pdb=" O TYR E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 214 removed outlier: 4.356A pdb=" N PHE E 207 " --> pdb=" O GLU E 203 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU E 212 " --> pdb=" O ASN E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 326 removed outlier: 3.885A pdb=" N THR E 325 " --> pdb=" O PRO E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 342 through 348 Processing helix chain 'E' and resid 353 through 368 removed outlier: 3.626A pdb=" N GLU E 359 " --> pdb=" O ARG E 355 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS E 362 " --> pdb=" O LYS E 358 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE E 363 " --> pdb=" O GLU E 359 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 367 " --> pdb=" O ILE E 363 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU E 368 " --> pdb=" O ILE E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 388 removed outlier: 3.572A pdb=" N VAL E 380 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E 381 " --> pdb=" O ILE E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 403 removed outlier: 3.651A pdb=" N THR E 398 " --> pdb=" O THR E 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 9 removed outlier: 3.580A pdb=" N LYS F 8 " --> pdb=" O GLU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 38 Processing helix chain 'F' and resid 50 through 62 Processing helix chain 'F' and resid 73 through 81 Processing helix chain 'F' and resid 81 through 91 removed outlier: 5.387A pdb=" N LYS F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASP F 88 " --> pdb=" O PRO F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 121 removed outlier: 3.812A pdb=" N LYS F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR F 119 " --> pdb=" O GLN F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 145 removed outlier: 3.549A pdb=" N GLN F 136 " --> pdb=" O ASN F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 164 through 167 Processing helix chain 'F' and resid 168 through 181 Processing helix chain 'F' and resid 203 through 214 removed outlier: 4.335A pdb=" N PHE F 207 " --> pdb=" O GLU F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 335 removed outlier: 4.276A pdb=" N LEU F 327 " --> pdb=" O ASN F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 348 Processing helix chain 'F' and resid 353 through 368 removed outlier: 3.878A pdb=" N LYS F 362 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 368 " --> pdb=" O ILE F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 388 removed outlier: 4.418A pdb=" N ASN F 383 " --> pdb=" O GLN F 379 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 403 Processing helix chain 'G' and resid 3 through 9 Processing helix chain 'G' and resid 22 through 38 Processing helix chain 'G' and resid 50 through 62 Processing helix chain 'G' and resid 73 through 81 removed outlier: 3.620A pdb=" N VAL G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU G 78 " --> pdb=" O ASP G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 91 removed outlier: 5.449A pdb=" N LYS G 87 " --> pdb=" O ARG G 83 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP G 88 " --> pdb=" O PRO G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 121 removed outlier: 3.807A pdb=" N LYS G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR G 119 " --> pdb=" O GLN G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 145 Processing helix chain 'G' and resid 145 through 155 Processing helix chain 'G' and resid 163 through 167 Processing helix chain 'G' and resid 168 through 181 removed outlier: 3.666A pdb=" N GLN G 181 " --> pdb=" O TYR G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 214 removed outlier: 4.229A pdb=" N PHE G 207 " --> pdb=" O GLU G 203 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE G 211 " --> pdb=" O PHE G 207 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU G 212 " --> pdb=" O ASN G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 335 removed outlier: 3.963A pdb=" N LEU G 327 " --> pdb=" O ASN G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 348 removed outlier: 3.549A pdb=" N GLU G 347 " --> pdb=" O ASP G 343 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE G 348 " --> pdb=" O LEU G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 368 Processing helix chain 'G' and resid 374 through 388 Processing helix chain 'G' and resid 394 through 403 removed outlier: 3.691A pdb=" N THR G 398 " --> pdb=" O THR G 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 9 removed outlier: 3.621A pdb=" N ASP H 9 " --> pdb=" O GLN H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 38 removed outlier: 3.737A pdb=" N THR H 24 " --> pdb=" O GLY H 20 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR H 25 " --> pdb=" O SER H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 59 Processing helix chain 'H' and resid 73 through 81 Processing helix chain 'H' and resid 81 through 91 removed outlier: 5.500A pdb=" N LYS H 87 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ASP H 88 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 121 removed outlier: 3.614A pdb=" N TYR H 119 " --> pdb=" O GLN H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 145 removed outlier: 3.758A pdb=" N GLN H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 155 Processing helix chain 'H' and resid 163 through 167 Processing helix chain 'H' and resid 168 through 181 Processing helix chain 'H' and resid 204 through 214 removed outlier: 4.054A pdb=" N GLU H 212 " --> pdb=" O ASN H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 335 removed outlier: 4.073A pdb=" N LEU H 327 " --> pdb=" O ASN H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 348 removed outlier: 3.751A pdb=" N ILE H 348 " --> pdb=" O LEU H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 365 Processing helix chain 'H' and resid 374 through 388 Processing helix chain 'H' and resid 394 through 403 removed outlier: 3.522A pdb=" N THR H 398 " --> pdb=" O THR H 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 156 removed outlier: 4.030A pdb=" N GLU I 156 " --> pdb=" O MET I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 179 Processing helix chain 'I' and resid 256 through 277 removed outlier: 3.556A pdb=" N ILE I 275 " --> pdb=" O LEU I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 286 Processing helix chain 'J' and resid 143 through 150 removed outlier: 3.864A pdb=" N ILE J 148 " --> pdb=" O LEU J 144 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN J 149 " --> pdb=" O LEU J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 158 removed outlier: 4.097A pdb=" N GLU J 156 " --> pdb=" O MET J 153 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR J 157 " --> pdb=" O LEU J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 179 Processing helix chain 'J' and resid 256 through 276 removed outlier: 3.662A pdb=" N ILE J 275 " --> pdb=" O LEU J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 286 Processing helix chain 'K' and resid 143 through 148 removed outlier: 4.365A pdb=" N ILE K 148 " --> pdb=" O LEU K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 155 Processing helix chain 'K' and resid 163 through 179 Processing helix chain 'K' and resid 256 through 276 Processing helix chain 'L' and resid 151 through 156 Processing helix chain 'L' and resid 163 through 179 Processing helix chain 'L' and resid 256 through 277 Processing helix chain 'L' and resid 283 through 286 removed outlier: 3.515A pdb=" N LYS L 286 " --> pdb=" O LYS L 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 283 through 286' Processing helix chain 'M' and resid 163 through 179 removed outlier: 3.601A pdb=" N ILE M 171 " --> pdb=" O SER M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 215 removed outlier: 3.649A pdb=" N MET M 215 " --> pdb=" O ASP M 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 277 Processing helix chain 'N' and resid 163 through 179 removed outlier: 3.671A pdb=" N ILE N 171 " --> pdb=" O SER N 167 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE N 179 " --> pdb=" O ILE N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 208 through 215 removed outlier: 3.815A pdb=" N MET N 215 " --> pdb=" O ASP N 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 256 through 277 removed outlier: 3.566A pdb=" N ASP N 270 " --> pdb=" O LYS N 266 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU N 271 " --> pdb=" O PHE N 267 " (cutoff:3.500A) Processing helix chain 'O' and resid 163 through 179 Processing helix chain 'O' and resid 206 through 215 removed outlier: 3.563A pdb=" N VAL O 210 " --> pdb=" O HIS O 206 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP O 211 " --> pdb=" O GLU O 207 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU O 212 " --> pdb=" O TYR O 208 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN O 213 " --> pdb=" O ILE O 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 256 through 276 removed outlier: 3.517A pdb=" N LYS O 274 " --> pdb=" O ASP O 270 " (cutoff:3.500A) Processing helix chain 'O' and resid 282 through 286 removed outlier: 3.996A pdb=" N CYS O 285 " --> pdb=" O CYS O 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 179 removed outlier: 3.594A pdb=" N ILE P 171 " --> pdb=" O SER P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 215 Processing helix chain 'P' and resid 256 through 276 Processing sheet with id=AA1, first strand: chain 'A' and resid -28 through -27 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 20 removed outlier: 6.547A pdb=" N GLU A 15 " --> pdb=" O ASN A 10 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N PHE A 3 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASP A 76 " --> pdb=" O PHE A 3 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 5 " --> pdb=" O THR A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 154 removed outlier: 6.507A pdb=" N VAL A 283 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N PHE A 316 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR A 285 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N SER A 318 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A 287 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS A 24 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE A 334 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE A 28 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.506A pdb=" N ILE A 142 " --> pdb=" O ARG A 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 230 Processing sheet with id=AA7, first strand: chain 'A' and resid 241 through 247 Processing sheet with id=AA8, first strand: chain 'A' and resid 403 through 407 removed outlier: 8.185A pdb=" N TYR A 506 " --> pdb=" O HIS A 427 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 429 " --> pdb=" O TYR A 506 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N SER A 508 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR A 431 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 436 through 437 Processing sheet with id=AB1, first strand: chain 'B' and resid -28 through -27 Processing sheet with id=AB2, first strand: chain 'B' and resid 14 through 20 removed outlier: 6.619A pdb=" N GLU B 15 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE B 3 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASP B 76 " --> pdb=" O PHE B 3 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 5 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS B 112 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN B 121 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 149 through 154 removed outlier: 6.497A pdb=" N VAL B 283 " --> pdb=" O TYR B 314 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N PHE B 316 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR B 285 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N SER B 318 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B 287 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS B 24 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE B 334 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL B 26 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL B 336 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE B 28 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.517A pdb=" N ILE B 142 " --> pdb=" O ARG B 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 224 through 230 Processing sheet with id=AB6, first strand: chain 'B' and resid 241 through 247 Processing sheet with id=AB7, first strand: chain 'B' and resid 403 through 407 removed outlier: 8.205A pdb=" N TYR B 506 " --> pdb=" O HIS B 427 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE B 429 " --> pdb=" O TYR B 506 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER B 508 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N THR B 431 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 436 through 437 Processing sheet with id=AB9, first strand: chain 'C' and resid -28 through -27 Processing sheet with id=AC1, first strand: chain 'C' and resid 14 through 20 removed outlier: 6.556A pdb=" N GLU C 15 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N PHE C 3 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASP C 76 " --> pdb=" O PHE C 3 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN C 5 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS C 112 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN C 121 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 149 through 154 removed outlier: 3.531A pdb=" N GLU C 288 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL C 283 " --> pdb=" O TYR C 314 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE C 316 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR C 285 " --> pdb=" O PHE C 316 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N SER C 318 " --> pdb=" O TYR C 285 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE C 287 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASN C 25 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS C 24 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE C 334 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL C 26 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL C 336 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE C 28 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.520A pdb=" N ILE C 142 " --> pdb=" O ARG C 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 403 through 407 removed outlier: 8.156A pdb=" N TYR C 506 " --> pdb=" O HIS C 427 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE C 429 " --> pdb=" O TYR C 506 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER C 508 " --> pdb=" O ILE C 429 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR C 431 " --> pdb=" O SER C 508 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 436 through 437 Processing sheet with id=AC6, first strand: chain 'D' and resid -28 through -27 Processing sheet with id=AC7, first strand: chain 'D' and resid 14 through 20 removed outlier: 6.554A pdb=" N GLU D 15 " --> pdb=" O ASN D 10 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N PHE D 3 " --> pdb=" O ASP D 76 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASP D 76 " --> pdb=" O PHE D 3 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN D 5 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 149 through 154 removed outlier: 6.475A pdb=" N VAL D 283 " --> pdb=" O TYR D 314 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N PHE D 316 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR D 285 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N SER D 318 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE D 287 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS D 24 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE D 334 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL D 26 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL D 336 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE D 28 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 113 through 114 Processing sheet with id=AD1, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.528A pdb=" N ILE D 142 " --> pdb=" O ARG D 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 403 through 407 removed outlier: 8.154A pdb=" N TYR D 506 " --> pdb=" O HIS D 427 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE D 429 " --> pdb=" O TYR D 506 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER D 508 " --> pdb=" O ILE D 429 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR D 431 " --> pdb=" O SER D 508 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 436 through 437 Processing sheet with id=AD4, first strand: chain 'E' and resid 69 through 72 removed outlier: 6.911A pdb=" N SER E 43 " --> pdb=" O LYS E 158 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N PHE E 160 " --> pdb=" O SER E 43 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA E 45 " --> pdb=" O PHE E 160 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 69 through 72 removed outlier: 6.907A pdb=" N SER F 43 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N PHE F 160 " --> pdb=" O SER F 43 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA F 45 " --> pdb=" O PHE F 160 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASP F 162 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL F 47 " --> pdb=" O ASP F 162 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 69 through 72 removed outlier: 6.885A pdb=" N SER G 43 " --> pdb=" O LYS G 158 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N PHE G 160 " --> pdb=" O SER G 43 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA G 45 " --> pdb=" O PHE G 160 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 106 through 107 Processing sheet with id=AD8, first strand: chain 'H' and resid 69 through 72 removed outlier: 6.874A pdb=" N SER H 43 " --> pdb=" O LYS H 158 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N PHE H 160 " --> pdb=" O SER H 43 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA H 45 " --> pdb=" O PHE H 160 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE H 157 " --> pdb=" O LYS H 185 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N PHE H 187 " --> pdb=" O PHE H 157 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE H 159 " --> pdb=" O PHE H 187 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL H 189 " --> pdb=" O ILE H 159 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE H 161 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE H 13 " --> pdb=" O ILE H 188 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 100 through 101 Processing sheet with id=AE1, first strand: chain 'I' and resid 160 through 161 Processing sheet with id=AE2, first strand: chain 'I' and resid 184 through 189 removed outlier: 4.763A pdb=" N ALA I 184 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL I 199 " --> pdb=" O ALA I 184 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE I 186 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL I 197 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER I 188 " --> pdb=" O THR I 195 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LYS I 198 " --> pdb=" O GLU I 234 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLU I 234 " --> pdb=" O LYS I 198 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU I 200 " --> pdb=" O GLU I 232 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLU I 232 " --> pdb=" O LEU I 200 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU I 202 " --> pdb=" O LYS I 230 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LYS I 230 " --> pdb=" O LEU I 202 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LYS I 204 " --> pdb=" O GLN I 228 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLN I 228 " --> pdb=" O LYS I 204 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N HIS I 206 " --> pdb=" O ARG I 226 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG I 226 " --> pdb=" O HIS I 206 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR I 208 " --> pdb=" O GLU I 224 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU I 224 " --> pdb=" O TYR I 208 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 280 through 281 Processing sheet with id=AE4, first strand: chain 'J' and resid 160 through 161 Processing sheet with id=AE5, first strand: chain 'J' and resid 184 through 189 removed outlier: 6.794A pdb=" N THR J 195 " --> pdb=" O THR J 187 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU J 194 " --> pdb=" O LYS J 237 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS J 237 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL J 196 " --> pdb=" O ILE J 235 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR J 229 " --> pdb=" O LEU J 202 " (cutoff:3.500A) removed outlier: 11.904A pdb=" N LYS J 204 " --> pdb=" O PHE J 227 " (cutoff:3.500A) removed outlier: 10.330A pdb=" N PHE J 227 " --> pdb=" O LYS J 204 " (cutoff:3.500A) removed outlier: 11.199A pdb=" N HIS J 206 " --> pdb=" O LYS J 225 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N LYS J 225 " --> pdb=" O HIS J 206 " (cutoff:3.500A) removed outlier: 11.157A pdb=" N TYR J 208 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N LEU J 223 " --> pdb=" O TYR J 208 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 280 through 281 Processing sheet with id=AE7, first strand: chain 'K' and resid 160 through 161 Processing sheet with id=AE8, first strand: chain 'K' and resid 184 through 189 removed outlier: 6.857A pdb=" N THR K 195 " --> pdb=" O THR K 187 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU K 194 " --> pdb=" O LYS K 237 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS K 237 " --> pdb=" O LEU K 194 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL K 196 " --> pdb=" O ILE K 235 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR K 229 " --> pdb=" O LEU K 202 " (cutoff:3.500A) removed outlier: 11.652A pdb=" N LYS K 204 " --> pdb=" O PHE K 227 " (cutoff:3.500A) removed outlier: 9.933A pdb=" N PHE K 227 " --> pdb=" O LYS K 204 " (cutoff:3.500A) removed outlier: 11.422A pdb=" N HIS K 206 " --> pdb=" O LYS K 225 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N LYS K 225 " --> pdb=" O HIS K 206 " (cutoff:3.500A) removed outlier: 11.363A pdb=" N TYR K 208 " --> pdb=" O LEU K 223 " (cutoff:3.500A) removed outlier: 9.873A pdb=" N LEU K 223 " --> pdb=" O TYR K 208 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 280 through 281 removed outlier: 3.783A pdb=" N VAL K 280 " --> pdb=" O ILE K 291 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 160 through 161 Processing sheet with id=AF2, first strand: chain 'L' and resid 184 through 189 removed outlier: 6.781A pdb=" N THR L 195 " --> pdb=" O THR L 187 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS L 198 " --> pdb=" O GLU L 234 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLU L 234 " --> pdb=" O LYS L 198 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU L 200 " --> pdb=" O GLU L 232 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU L 232 " --> pdb=" O LEU L 200 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU L 202 " --> pdb=" O LYS L 230 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LYS L 230 " --> pdb=" O LEU L 202 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LYS L 204 " --> pdb=" O GLN L 228 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN L 228 " --> pdb=" O LYS L 204 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 210 through 211 removed outlier: 3.566A pdb=" N VAL L 210 " --> pdb=" O GLU L 224 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 279 through 281 Processing sheet with id=AF5, first strand: chain 'M' and resid 184 through 189 removed outlier: 6.493A pdb=" N THR M 195 " --> pdb=" O THR M 187 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS M 198 " --> pdb=" O GLU M 234 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU M 234 " --> pdb=" O LYS M 198 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 184 through 189 removed outlier: 6.646A pdb=" N THR N 195 " --> pdb=" O THR N 187 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS N 198 " --> pdb=" O GLU N 234 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLU N 234 " --> pdb=" O LYS N 198 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 184 through 190 removed outlier: 6.595A pdb=" N THR O 195 " --> pdb=" O THR O 187 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP O 189 " --> pdb=" O CYS O 193 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N CYS O 193 " --> pdb=" O ASP O 189 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU O 194 " --> pdb=" O LYS O 237 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS O 237 " --> pdb=" O LEU O 194 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL O 196 " --> pdb=" O ILE O 235 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 184 through 190 removed outlier: 6.528A pdb=" N THR P 195 " --> pdb=" O THR P 187 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP P 189 " --> pdb=" O CYS P 193 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N CYS P 193 " --> pdb=" O ASP P 189 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS P 198 " --> pdb=" O GLU P 234 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLU P 234 " --> pdb=" O LYS P 198 " (cutoff:3.500A) 1861 hydrogen bonds defined for protein. 5295 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: 9.89 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12468 1.34 - 1.46: 8857 1.46 - 1.59: 18010 1.59 - 1.71: 1 1.71 - 1.83: 208 Bond restraints: 39544 Sorted by residual: bond pdb=" C LYS N 204 " pdb=" N PRO N 205 " ideal model delta sigma weight residual 1.335 1.358 -0.023 8.70e-03 1.32e+04 6.70e+00 bond pdb=" CB PRO F 129 " pdb=" CG PRO F 129 " ideal model delta sigma weight residual 1.492 1.612 -0.120 5.00e-02 4.00e+02 5.71e+00 bond pdb=" CB GLU N 165 " pdb=" CG GLU N 165 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.21e+00 bond pdb=" CA ASP E 111 " pdb=" C ASP E 111 " ideal model delta sigma weight residual 1.522 1.502 0.020 1.38e-02 5.25e+03 2.10e+00 bond pdb=" CB GLU F 58 " pdb=" CG GLU F 58 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.06e+00 ... (remaining 39539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 52406 2.22 - 4.45: 524 4.45 - 6.67: 123 6.67 - 8.90: 36 8.90 - 11.12: 15 Bond angle restraints: 53104 Sorted by residual: angle pdb=" CA PRO F 129 " pdb=" N PRO F 129 " pdb=" CD PRO F 129 " ideal model delta sigma weight residual 112.00 102.93 9.07 1.40e+00 5.10e-01 4.20e+01 angle pdb=" CA LYS D 162 " pdb=" CB LYS D 162 " pdb=" CG LYS D 162 " ideal model delta sigma weight residual 114.10 123.07 -8.97 2.00e+00 2.50e-01 2.01e+01 angle pdb=" N LYS O 204 " pdb=" CA LYS O 204 " pdb=" C LYS O 204 " ideal model delta sigma weight residual 109.81 118.95 -9.14 2.21e+00 2.05e-01 1.71e+01 angle pdb=" N LYS M 204 " pdb=" CA LYS M 204 " pdb=" C LYS M 204 " ideal model delta sigma weight residual 109.81 118.68 -8.87 2.21e+00 2.05e-01 1.61e+01 angle pdb=" CA GLN H 115 " pdb=" CB GLN H 115 " pdb=" CG GLN H 115 " ideal model delta sigma weight residual 114.10 122.11 -8.01 2.00e+00 2.50e-01 1.60e+01 ... (remaining 53099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 20534 17.95 - 35.91: 2782 35.91 - 53.86: 758 53.86 - 71.82: 129 71.82 - 89.77: 49 Dihedral angle restraints: 24252 sinusoidal: 10244 harmonic: 14008 Sorted by residual: dihedral pdb=" CB CYS I 282 " pdb=" SG CYS I 282 " pdb=" SG CYS M 285 " pdb=" CB CYS M 285 " ideal model delta sinusoidal sigma weight residual -86.00 -0.39 -85.61 1 1.00e+01 1.00e-02 8.86e+01 dihedral pdb=" CB CYS L 285 " pdb=" SG CYS L 285 " pdb=" SG CYS P 282 " pdb=" CB CYS P 282 " ideal model delta sinusoidal sigma weight residual 93.00 164.40 -71.40 1 1.00e+01 1.00e-02 6.54e+01 dihedral pdb=" CB CYS J 285 " pdb=" SG CYS J 285 " pdb=" SG CYS N 282 " pdb=" CB CYS N 282 " ideal model delta sinusoidal sigma weight residual 93.00 142.71 -49.71 1 1.00e+01 1.00e-02 3.39e+01 ... (remaining 24249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4677 0.048 - 0.096: 908 0.096 - 0.144: 253 0.144 - 0.193: 7 0.193 - 0.241: 3 Chirality restraints: 5848 Sorted by residual: chirality pdb=" CG LEU F 222 " pdb=" CB LEU F 222 " pdb=" CD1 LEU F 222 " pdb=" CD2 LEU F 222 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE N 179 " pdb=" CA ILE N 179 " pdb=" CG1 ILE N 179 " pdb=" CG2 ILE N 179 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA PRO O 205 " pdb=" N PRO O 205 " pdb=" C PRO O 205 " pdb=" CB PRO O 205 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 5845 not shown) Planarity restraints: 6764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 128 " -0.085 5.00e-02 4.00e+02 1.23e-01 2.41e+01 pdb=" N PRO F 129 " 0.212 5.00e-02 4.00e+02 pdb=" CA PRO F 129 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO F 129 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 204 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO L 205 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO L 205 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO L 205 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 58 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" CD GLU F 58 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU F 58 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU F 58 " 0.014 2.00e-02 2.50e+03 ... (remaining 6761 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 768 2.66 - 3.22: 37559 3.22 - 3.78: 61823 3.78 - 4.34: 85836 4.34 - 4.90: 138219 Nonbonded interactions: 324205 Sorted by model distance: nonbonded pdb=" OH TYR C 170 " pdb=" O LYS C 276 " model vdw 2.101 3.040 nonbonded pdb=" OH TYR I 203 " pdb=" O GLU I 281 " model vdw 2.147 3.040 nonbonded pdb=" OD2 ASP C 250 " pdb=" OH TYR C 254 " model vdw 2.156 3.040 nonbonded pdb=" O GLY H 75 " pdb=" OG SER H 79 " model vdw 2.178 3.040 nonbonded pdb=" O LYS B 162 " pdb=" NZ LYS B 162 " model vdw 2.184 3.120 ... (remaining 324200 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 38.440 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.130 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:7.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 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 : 0.004 0.120 39556 Z= 0.171 Angle : 0.622 11.122 53128 Z= 0.315 Chirality : 0.041 0.241 5848 Planarity : 0.004 0.123 6764 Dihedral : 17.450 89.772 15168 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.86 % Favored : 97.06 % Rotamer: Outliers : 3.23 % Allowed : 28.69 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.12), residues: 4656 helix: 1.14 (0.12), residues: 2048 sheet: 0.60 (0.20), residues: 716 loop : -0.30 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 226 TYR 0.034 0.001 TYR M 203 PHE 0.012 0.001 PHE F 226 TRP 0.010 0.001 TRP F 199 HIS 0.008 0.001 HIS P 174 Details of bonding type rmsd covalent geometry : bond 0.00406 (39544) covalent geometry : angle 0.62214 (53104) SS BOND : bond 0.00357 ( 12) SS BOND : angle 1.12848 ( 24) hydrogen bonds : bond 0.22141 ( 1861) hydrogen bonds : angle 7.04362 ( 5295) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 386 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 102 TYR cc_start: 0.6906 (p90) cc_final: 0.6665 (p90) REVERT: G 176 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8658 (mpp) REVERT: I 144 LEU cc_start: 0.8819 (pp) cc_final: 0.8418 (mm) REVERT: I 270 ASP cc_start: 0.9404 (p0) cc_final: 0.9198 (p0) REVERT: O 166 GLU cc_start: 0.8776 (pm20) cc_final: 0.8575 (pm20) REVERT: P 166 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9206 (tp30) outliers start: 140 outliers final: 119 residues processed: 510 average time/residue: 0.6944 time to fit residues: 433.6764 Evaluate side-chains 496 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 376 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -71 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue -30 ASP Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue -2 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue -71 VAL Chi-restraints excluded: chain D residue -67 ASP Chi-restraints excluded: chain D residue -10 THR Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 313 LYS Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 176 MET Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 323 ASN Chi-restraints excluded: chain H residue 352 LEU Chi-restraints excluded: chain H residue 354 SER Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 215 MET Chi-restraints excluded: chain K residue 141 ASN Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 228 GLN Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 253 SER Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 141 ASN Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 194 LEU Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 203 TYR Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 231 ARG Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 250 GLU Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 253 SER Chi-restraints excluded: chain O residue 282 CYS Chi-restraints excluded: chain P residue 167 SER Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 269 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.9980 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C -3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 ASN D 13 ASN G 121 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 GLN J 244 GLN K 164 GLN ** K 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN M 164 GLN ** N 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 164 GLN O 213 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.118750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.070097 restraints weight = 84712.432| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.30 r_work: 0.2826 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 39556 Z= 0.257 Angle : 0.614 9.112 53128 Z= 0.324 Chirality : 0.044 0.230 5848 Planarity : 0.004 0.065 6764 Dihedral : 7.028 164.503 5334 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.32 % Rotamer: Outliers : 4.76 % Allowed : 25.16 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.13), residues: 4656 helix: 1.63 (0.11), residues: 2076 sheet: 0.61 (0.20), residues: 692 loop : -0.27 (0.15), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 226 TYR 0.021 0.001 TYR M 203 PHE 0.013 0.001 PHE N 252 TRP 0.008 0.001 TRP F 199 HIS 0.005 0.001 HIS P 174 Details of bonding type rmsd covalent geometry : bond 0.00594 (39544) covalent geometry : angle 0.61361 (53104) SS BOND : bond 0.00365 ( 12) SS BOND : angle 1.16646 ( 24) hydrogen bonds : bond 0.05416 ( 1861) hydrogen bonds : angle 5.28560 ( 5295) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 395 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.9214 (tppt) cc_final: 0.8935 (mppt) REVERT: A 261 ARG cc_start: 0.8637 (ttm110) cc_final: 0.8422 (tpp-160) REVERT: A 288 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8633 (tt0) REVERT: A 455 ASN cc_start: 0.9207 (OUTLIER) cc_final: 0.8462 (t0) REVERT: B 288 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8591 (tt0) REVERT: C 202 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8187 (mtp) REVERT: C 221 LYS cc_start: 0.9200 (tppt) cc_final: 0.8889 (mppt) REVERT: C 281 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8953 (ptpt) REVERT: C 288 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8636 (tt0) REVERT: C 452 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7297 (mtp180) REVERT: C 455 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8398 (t0) REVERT: D 281 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8991 (ptpt) REVERT: D 288 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8666 (tt0) REVERT: D 452 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7340 (mtp180) REVERT: D 455 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8808 (t0) REVERT: E 102 TYR cc_start: 0.7262 (p90) cc_final: 0.7045 (p90) REVERT: G 60 ARG cc_start: 0.8775 (mtp180) cc_final: 0.8520 (mtm-85) REVERT: G 176 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8617 (mpp) REVERT: H 83 ARG cc_start: 0.9052 (ttm170) cc_final: 0.8701 (ttm170) REVERT: H 217 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.7022 (t80) REVERT: H 222 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7784 (tm) REVERT: I 218 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8170 (mtp85) REVERT: J 142 TYR cc_start: 0.8441 (m-80) cc_final: 0.8018 (m-80) REVERT: J 163 SER cc_start: 0.9596 (t) cc_final: 0.9314 (p) REVERT: J 226 ARG cc_start: 0.9089 (ttm170) cc_final: 0.8747 (ttm170) REVERT: K 164 GLN cc_start: 0.9073 (tp-100) cc_final: 0.8864 (tp40) REVERT: M 165 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8419 (tm-30) REVERT: M 169 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.9009 (ttmm) REVERT: N 166 GLU cc_start: 0.9454 (mm-30) cc_final: 0.9107 (tp30) REVERT: N 189 ASP cc_start: 0.8918 (t0) cc_final: 0.8675 (t0) REVERT: P 166 GLU cc_start: 0.9468 (mm-30) cc_final: 0.8962 (tp30) REVERT: P 169 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.8908 (tmmm) outliers start: 206 outliers final: 79 residues processed: 563 average time/residue: 0.6805 time to fit residues: 469.5884 Evaluate side-chains 456 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 359 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue -30 ASP Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue -71 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain G residue 176 MET Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 262 SER Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 200 LEU Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 208 TYR Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 212 LEU Chi-restraints excluded: chain P residue 233 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 349 optimal weight: 5.9990 chunk 451 optimal weight: 20.0000 chunk 228 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 381 optimal weight: 10.0000 chunk 216 optimal weight: 8.9990 chunk 206 optimal weight: 0.6980 chunk 215 optimal weight: 5.9990 chunk 253 optimal weight: 8.9990 chunk 382 optimal weight: 1.9990 chunk 384 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 GLN ** C -3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN F 181 GLN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 GLN J 174 HIS J 244 GLN ** K 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN M 164 GLN O 164 GLN ** P 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 276 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.118921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.070552 restraints weight = 84386.294| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.22 r_work: 0.2842 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 39556 Z= 0.236 Angle : 0.597 9.234 53128 Z= 0.310 Chirality : 0.044 0.210 5848 Planarity : 0.003 0.060 6764 Dihedral : 5.389 53.561 5201 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.73 % Favored : 97.19 % Rotamer: Outliers : 4.73 % Allowed : 25.42 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.13), residues: 4656 helix: 1.71 (0.11), residues: 2100 sheet: 0.57 (0.20), residues: 664 loop : -0.28 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 226 TYR 0.024 0.001 TYR I 161 PHE 0.013 0.001 PHE C 315 TRP 0.007 0.001 TRP F 199 HIS 0.005 0.001 HIS P 174 Details of bonding type rmsd covalent geometry : bond 0.00549 (39544) covalent geometry : angle 0.59713 (53104) SS BOND : bond 0.00392 ( 12) SS BOND : angle 1.12117 ( 24) hydrogen bonds : bond 0.04516 ( 1861) hydrogen bonds : angle 5.03514 ( 5295) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 410 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.9198 (tppt) cc_final: 0.8971 (mppt) REVERT: A 261 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8271 (tpp80) REVERT: A 288 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8634 (tt0) REVERT: A 397 GLU cc_start: 0.8659 (pm20) cc_final: 0.8354 (pm20) REVERT: A 455 ASN cc_start: 0.9196 (OUTLIER) cc_final: 0.8440 (t0) REVERT: B 157 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9249 (pp) REVERT: B 162 LYS cc_start: 0.9499 (tptp) cc_final: 0.9279 (tptp) REVERT: B 166 GLN cc_start: 0.8934 (mm110) cc_final: 0.8717 (mm110) REVERT: B 288 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8559 (tt0) REVERT: C 162 LYS cc_start: 0.9587 (tptp) cc_final: 0.9353 (tppt) REVERT: C 202 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8087 (mtp) REVERT: C 221 LYS cc_start: 0.9182 (tppt) cc_final: 0.8904 (mppt) REVERT: C 281 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8963 (ptpt) REVERT: C 288 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8623 (tt0) REVERT: C 397 GLU cc_start: 0.8695 (pm20) cc_final: 0.8479 (pm20) REVERT: C 452 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7432 (mtp180) REVERT: C 455 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8384 (t0) REVERT: C 463 ASP cc_start: 0.8999 (p0) cc_final: 0.8781 (p0) REVERT: D 281 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8996 (ptpt) REVERT: D 288 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8644 (tt0) REVERT: D 452 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7471 (mtp180) REVERT: D 455 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.8849 (t0) REVERT: E 102 TYR cc_start: 0.7262 (p90) cc_final: 0.7020 (p90) REVERT: F 115 GLN cc_start: 0.9026 (pp30) cc_final: 0.8745 (pp30) REVERT: G 60 ARG cc_start: 0.8746 (mtp180) cc_final: 0.8536 (mtm-85) REVERT: G 176 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8598 (mpp) REVERT: G 332 LYS cc_start: 0.5334 (mptt) cc_final: 0.5094 (pptt) REVERT: H 83 ARG cc_start: 0.9116 (ttm170) cc_final: 0.8717 (ttm170) REVERT: H 172 HIS cc_start: 0.8711 (OUTLIER) cc_final: 0.8342 (t70) REVERT: H 217 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.7046 (t80) REVERT: H 222 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7672 (tm) REVERT: I 218 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8124 (mtp85) REVERT: J 142 TYR cc_start: 0.8500 (m-80) cc_final: 0.8138 (m-80) REVERT: J 163 SER cc_start: 0.9559 (t) cc_final: 0.9287 (p) REVERT: J 226 ARG cc_start: 0.9052 (ttm170) cc_final: 0.8169 (ttm170) REVERT: J 272 MET cc_start: 0.8888 (mmm) cc_final: 0.8438 (tpp) REVERT: L 157 THR cc_start: 0.9627 (t) cc_final: 0.9412 (p) REVERT: L 270 ASP cc_start: 0.9368 (p0) cc_final: 0.9118 (p0) REVERT: M 165 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8352 (tm-30) REVERT: M 169 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8996 (ttmm) REVERT: N 166 GLU cc_start: 0.9409 (mm-30) cc_final: 0.9105 (tp30) REVERT: O 270 ASP cc_start: 0.9416 (OUTLIER) cc_final: 0.9066 (p0) REVERT: P 166 GLU cc_start: 0.9469 (mm-30) cc_final: 0.8870 (tp30) REVERT: P 169 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.8878 (tmmm) outliers start: 205 outliers final: 86 residues processed: 570 average time/residue: 0.7321 time to fit residues: 510.0942 Evaluate side-chains 486 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 378 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue -30 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue -71 VAL Chi-restraints excluded: chain D residue -10 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 176 MET Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 172 HIS Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 203 TYR Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 215 MET Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 262 SER Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 194 LEU Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 270 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 208 TYR Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 212 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 21 optimal weight: 2.9990 chunk 379 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 343 optimal weight: 7.9990 chunk 192 optimal weight: 0.7980 chunk 341 optimal weight: 0.9990 chunk 413 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 296 optimal weight: 7.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C -3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN D 305 GLN E 181 GLN F 181 GLN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 HIS ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 244 GLN L 164 GLN M 164 GLN ** P 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.120827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.072790 restraints weight = 83654.798| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.23 r_work: 0.2890 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39556 Z= 0.119 Angle : 0.569 8.721 53128 Z= 0.291 Chirality : 0.042 0.220 5848 Planarity : 0.003 0.056 6764 Dihedral : 5.073 56.038 5186 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.45 % Favored : 97.47 % Rotamer: Outliers : 4.27 % Allowed : 25.72 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.13), residues: 4656 helix: 1.80 (0.11), residues: 2092 sheet: 0.58 (0.20), residues: 664 loop : -0.27 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 226 TYR 0.024 0.001 TYR M 203 PHE 0.010 0.001 PHE N 252 TRP 0.008 0.001 TRP F 199 HIS 0.004 0.001 HIS K 174 Details of bonding type rmsd covalent geometry : bond 0.00267 (39544) covalent geometry : angle 0.56893 (53104) SS BOND : bond 0.00683 ( 12) SS BOND : angle 1.21696 ( 24) hydrogen bonds : bond 0.03763 ( 1861) hydrogen bonds : angle 4.85217 ( 5295) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 414 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: A 397 GLU cc_start: 0.8624 (pm20) cc_final: 0.8212 (pm20) REVERT: A 455 ASN cc_start: 0.9181 (OUTLIER) cc_final: 0.8402 (t0) REVERT: B 30 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.9011 (tpp) REVERT: B 157 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9261 (pp) REVERT: B 288 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: C 162 LYS cc_start: 0.9616 (tptp) cc_final: 0.9375 (tppt) REVERT: C 170 TYR cc_start: 0.7823 (t80) cc_final: 0.7386 (t80) REVERT: C 173 GLU cc_start: 0.8757 (pp20) cc_final: 0.8546 (pp20) REVERT: C 221 LYS cc_start: 0.9185 (tppt) cc_final: 0.8906 (mppt) REVERT: C 288 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8527 (tt0) REVERT: C 397 GLU cc_start: 0.8650 (pm20) cc_final: 0.8405 (pm20) REVERT: C 452 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7431 (mtp180) REVERT: C 455 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8422 (t0) REVERT: D 170 TYR cc_start: 0.7876 (t80) cc_final: 0.7409 (t80) REVERT: D 206 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8589 (mtmm) REVERT: D 288 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: D 452 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7807 (mtp180) REVERT: D 455 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8489 (t0) REVERT: E 102 TYR cc_start: 0.7298 (p90) cc_final: 0.7054 (p90) REVERT: F 60 ARG cc_start: 0.8763 (mtp180) cc_final: 0.8444 (mtp180) REVERT: F 115 GLN cc_start: 0.9020 (pp30) cc_final: 0.8802 (pp30) REVERT: F 136 GLN cc_start: 0.8793 (pt0) cc_final: 0.8274 (pm20) REVERT: G 115 GLN cc_start: 0.8870 (pp30) cc_final: 0.8639 (pp30) REVERT: H 83 ARG cc_start: 0.9182 (ttm170) cc_final: 0.8747 (ttm170) REVERT: H 172 HIS cc_start: 0.8679 (OUTLIER) cc_final: 0.8266 (t70) REVERT: H 217 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.7097 (t80) REVERT: H 222 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7818 (tm) REVERT: I 218 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8081 (mtp85) REVERT: I 222 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8385 (ptmm) REVERT: J 142 TYR cc_start: 0.8685 (m-80) cc_final: 0.8292 (m-80) REVERT: J 163 SER cc_start: 0.9550 (t) cc_final: 0.9292 (p) REVERT: J 226 ARG cc_start: 0.9019 (ttm170) cc_final: 0.8156 (ttm170) REVERT: J 241 LYS cc_start: 0.9521 (OUTLIER) cc_final: 0.9282 (ttpp) REVERT: K 163 SER cc_start: 0.9486 (t) cc_final: 0.9147 (p) REVERT: K 164 GLN cc_start: 0.9290 (OUTLIER) cc_final: 0.9054 (tp-100) REVERT: K 218 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8205 (mtp85) REVERT: K 226 ARG cc_start: 0.8102 (mtm110) cc_final: 0.7431 (ttp-170) REVERT: L 270 ASP cc_start: 0.9332 (p0) cc_final: 0.9099 (p0) REVERT: M 165 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8397 (tm-30) REVERT: M 166 GLU cc_start: 0.8924 (pm20) cc_final: 0.8719 (pm20) REVERT: M 169 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9064 (ttmm) REVERT: M 172 ARG cc_start: 0.9234 (ttt180) cc_final: 0.8976 (ttt180) REVERT: N 166 GLU cc_start: 0.9432 (mm-30) cc_final: 0.9079 (tp30) REVERT: O 166 GLU cc_start: 0.8893 (pm20) cc_final: 0.7246 (pm20) REVERT: O 270 ASP cc_start: 0.9397 (OUTLIER) cc_final: 0.9020 (p0) REVERT: P 166 GLU cc_start: 0.9427 (mm-30) cc_final: 0.8733 (tp30) REVERT: P 169 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.8931 (tmmm) outliers start: 185 outliers final: 73 residues processed: 557 average time/residue: 0.7370 time to fit residues: 500.6888 Evaluate side-chains 484 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 388 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue -55 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue -10 THR Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 172 HIS Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 203 TYR Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 241 LYS Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 218 ARG Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 279 LEU Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 270 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 208 TYR Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 212 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 375 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 350 optimal weight: 8.9990 chunk 464 optimal weight: 8.9990 chunk 240 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 360 optimal weight: 9.9990 chunk 410 optimal weight: 7.9990 chunk 189 optimal weight: 20.0000 chunk 435 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C -3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 HIS ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 244 GLN ** K 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN ** P 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.118601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.070309 restraints weight = 84553.427| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.21 r_work: 0.2838 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 39556 Z= 0.284 Angle : 0.626 9.750 53128 Z= 0.322 Chirality : 0.045 0.272 5848 Planarity : 0.003 0.054 6764 Dihedral : 4.979 58.990 5174 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.16 % Rotamer: Outliers : 4.50 % Allowed : 25.81 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.13), residues: 4656 helix: 1.78 (0.12), residues: 2092 sheet: 0.52 (0.20), residues: 664 loop : -0.29 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 261 TYR 0.023 0.001 TYR I 161 PHE 0.015 0.001 PHE C 315 TRP 0.008 0.001 TRP F 199 HIS 0.008 0.001 HIS L 151 Details of bonding type rmsd covalent geometry : bond 0.00663 (39544) covalent geometry : angle 0.62563 (53104) SS BOND : bond 0.00675 ( 12) SS BOND : angle 1.25408 ( 24) hydrogen bonds : bond 0.04189 ( 1861) hydrogen bonds : angle 4.87050 ( 5295) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 391 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8701 (tt0) REVERT: A 288 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8647 (tt0) REVERT: A 397 GLU cc_start: 0.8640 (pm20) cc_final: 0.8367 (pm20) REVERT: A 439 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8751 (ptmm) REVERT: A 455 ASN cc_start: 0.9190 (OUTLIER) cc_final: 0.8432 (t0) REVERT: B 157 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9264 (pp) REVERT: B 288 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8587 (tt0) REVERT: B 395 GLU cc_start: 0.8860 (tp30) cc_final: 0.8600 (tp30) REVERT: C 221 LYS cc_start: 0.9185 (tppt) cc_final: 0.8888 (mppt) REVERT: C 281 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8978 (ptpt) REVERT: C 288 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8631 (tt0) REVERT: C 397 GLU cc_start: 0.8671 (pm20) cc_final: 0.8409 (pm20) REVERT: C 452 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7509 (mtp180) REVERT: C 455 ASN cc_start: 0.9219 (OUTLIER) cc_final: 0.8408 (t0) REVERT: D 15 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8700 (tt0) REVERT: D 206 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8738 (mtmm) REVERT: D 281 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.9007 (ptpt) REVERT: D 288 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8666 (tt0) REVERT: D 395 GLU cc_start: 0.8926 (tp30) cc_final: 0.8484 (tp30) REVERT: D 452 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7532 (mtp180) REVERT: D 455 ASN cc_start: 0.9223 (OUTLIER) cc_final: 0.8456 (t0) REVERT: E 111 ASP cc_start: 0.8686 (t0) cc_final: 0.8015 (p0) REVERT: F 60 ARG cc_start: 0.8699 (mtp180) cc_final: 0.8436 (mtp180) REVERT: F 115 GLN cc_start: 0.9047 (pp30) cc_final: 0.8841 (pp30) REVERT: F 136 GLN cc_start: 0.8796 (pt0) cc_final: 0.8240 (pm20) REVERT: G 8 LYS cc_start: 0.8897 (mtmm) cc_final: 0.8629 (mttt) REVERT: G 115 GLN cc_start: 0.8927 (pp30) cc_final: 0.8717 (pp30) REVERT: H 83 ARG cc_start: 0.9132 (ttm170) cc_final: 0.8644 (ttm170) REVERT: H 172 HIS cc_start: 0.8719 (OUTLIER) cc_final: 0.8319 (t70) REVERT: H 217 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.7088 (t80) REVERT: H 222 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7909 (tm) REVERT: I 222 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8644 (ptmm) REVERT: J 142 TYR cc_start: 0.8687 (m-80) cc_final: 0.8279 (m-80) REVERT: J 163 SER cc_start: 0.9564 (t) cc_final: 0.9292 (p) REVERT: J 226 ARG cc_start: 0.9028 (ttm170) cc_final: 0.8108 (ttm170) REVERT: J 241 LYS cc_start: 0.9525 (OUTLIER) cc_final: 0.9294 (ttpp) REVERT: J 270 ASP cc_start: 0.9463 (OUTLIER) cc_final: 0.9187 (p0) REVERT: K 163 SER cc_start: 0.9509 (t) cc_final: 0.9170 (p) REVERT: K 164 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8980 (tp-100) REVERT: L 180 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7911 (p0) REVERT: L 225 LYS cc_start: 0.8852 (tppt) cc_final: 0.8597 (tppp) REVERT: L 270 ASP cc_start: 0.9375 (p0) cc_final: 0.9169 (p0) REVERT: M 165 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8485 (tm-30) REVERT: M 169 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9039 (ttmm) REVERT: M 172 ARG cc_start: 0.9172 (ttt180) cc_final: 0.8894 (ttt180) REVERT: N 166 GLU cc_start: 0.9452 (mm-30) cc_final: 0.9155 (tp30) REVERT: O 270 ASP cc_start: 0.9409 (OUTLIER) cc_final: 0.8957 (p0) REVERT: P 166 GLU cc_start: 0.9429 (mm-30) cc_final: 0.8739 (tp30) REVERT: P 169 LYS cc_start: 0.9379 (OUTLIER) cc_final: 0.8915 (tmmm) outliers start: 195 outliers final: 96 residues processed: 542 average time/residue: 0.7539 time to fit residues: 498.3089 Evaluate side-chains 497 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 374 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue -55 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue -10 THR Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 221 HIS Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 172 HIS Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 203 TYR Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 241 LYS Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 146 ASP Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 180 ASN Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 270 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 208 TYR Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 212 LEU Chi-restraints excluded: chain P residue 231 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 356 optimal weight: 40.0000 chunk 143 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 348 optimal weight: 10.0000 chunk 385 optimal weight: 8.9990 chunk 399 optimal weight: 5.9990 chunk 367 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 296 optimal weight: 30.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C -3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 244 GLN L 164 GLN L 293 ASN O 164 GLN ** P 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.119789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.071486 restraints weight = 84385.311| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.28 r_work: 0.2852 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 39556 Z= 0.172 Angle : 0.603 9.725 53128 Z= 0.306 Chirality : 0.043 0.247 5848 Planarity : 0.003 0.052 6764 Dihedral : 4.868 59.973 5170 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.58 % Favored : 97.34 % Rotamer: Outliers : 4.04 % Allowed : 26.41 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.13), residues: 4656 helix: 1.81 (0.11), residues: 2092 sheet: 0.51 (0.20), residues: 664 loop : -0.29 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 261 TYR 0.026 0.001 TYR M 203 PHE 0.012 0.001 PHE C 315 TRP 0.008 0.001 TRP F 199 HIS 0.004 0.001 HIS K 174 Details of bonding type rmsd covalent geometry : bond 0.00403 (39544) covalent geometry : angle 0.60218 (53104) SS BOND : bond 0.00316 ( 12) SS BOND : angle 1.20003 ( 24) hydrogen bonds : bond 0.03780 ( 1861) hydrogen bonds : angle 4.76535 ( 5295) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 401 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.8746 (pp20) cc_final: 0.8503 (pp20) REVERT: A 288 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8569 (tt0) REVERT: A 397 GLU cc_start: 0.8565 (pm20) cc_final: 0.8290 (pm20) REVERT: A 455 ASN cc_start: 0.9185 (OUTLIER) cc_final: 0.8476 (t0) REVERT: B 157 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9252 (pp) REVERT: B 288 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8507 (tt0) REVERT: B 395 GLU cc_start: 0.8834 (tp30) cc_final: 0.8561 (tp30) REVERT: B 455 ASN cc_start: 0.9215 (OUTLIER) cc_final: 0.8453 (t0) REVERT: C 162 LYS cc_start: 0.9597 (tptp) cc_final: 0.9386 (tppt) REVERT: C 173 GLU cc_start: 0.8768 (pp20) cc_final: 0.8541 (pp20) REVERT: C 202 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7661 (mtp) REVERT: C 206 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8596 (mtmm) REVERT: C 221 LYS cc_start: 0.9183 (tppt) cc_final: 0.8888 (mppt) REVERT: C 266 SER cc_start: 0.9247 (OUTLIER) cc_final: 0.9019 (p) REVERT: C 288 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8577 (tt0) REVERT: C 397 GLU cc_start: 0.8659 (pm20) cc_final: 0.8395 (pm20) REVERT: C 452 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7467 (mtp180) REVERT: C 455 ASN cc_start: 0.9227 (OUTLIER) cc_final: 0.8424 (t0) REVERT: D 206 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8612 (mtmm) REVERT: D 288 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8615 (tt0) REVERT: D 395 GLU cc_start: 0.8954 (tp30) cc_final: 0.8504 (tp30) REVERT: D 452 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7516 (mtp180) REVERT: D 455 ASN cc_start: 0.9237 (OUTLIER) cc_final: 0.8509 (t0) REVERT: E 102 TYR cc_start: 0.7368 (p90) cc_final: 0.7039 (p90) REVERT: F 60 ARG cc_start: 0.8647 (mtp180) cc_final: 0.8342 (mtp180) REVERT: F 115 GLN cc_start: 0.9061 (pp30) cc_final: 0.8858 (pp30) REVERT: F 136 GLN cc_start: 0.8793 (pt0) cc_final: 0.8248 (pm20) REVERT: G 8 LYS cc_start: 0.8896 (mtmm) cc_final: 0.8616 (mttt) REVERT: H 83 ARG cc_start: 0.9127 (ttm170) cc_final: 0.8685 (ttm170) REVERT: H 172 HIS cc_start: 0.8638 (OUTLIER) cc_final: 0.8245 (t70) REVERT: H 217 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.7164 (t80) REVERT: H 222 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7852 (tm) REVERT: I 222 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8659 (ptmm) REVERT: I 241 LYS cc_start: 0.9535 (OUTLIER) cc_final: 0.9251 (ttpp) REVERT: I 270 ASP cc_start: 0.9370 (p0) cc_final: 0.9086 (p0) REVERT: J 142 TYR cc_start: 0.8635 (m-80) cc_final: 0.8192 (m-80) REVERT: J 163 SER cc_start: 0.9554 (t) cc_final: 0.9284 (p) REVERT: J 226 ARG cc_start: 0.9027 (ttm170) cc_final: 0.8112 (ttm170) REVERT: J 241 LYS cc_start: 0.9521 (OUTLIER) cc_final: 0.9269 (ttpp) REVERT: J 270 ASP cc_start: 0.9467 (OUTLIER) cc_final: 0.9198 (p0) REVERT: K 163 SER cc_start: 0.9493 (t) cc_final: 0.9154 (p) REVERT: K 164 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.9025 (tp-100) REVERT: K 218 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8267 (mtp85) REVERT: L 180 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7789 (p0) REVERT: M 165 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8455 (tm-30) REVERT: M 166 GLU cc_start: 0.8874 (pm20) cc_final: 0.8667 (pm20) REVERT: M 169 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.9034 (ttmm) REVERT: M 172 ARG cc_start: 0.9135 (ttt180) cc_final: 0.8880 (ttt180) REVERT: M 236 TYR cc_start: 0.8991 (t80) cc_final: 0.8656 (t80) REVERT: N 166 GLU cc_start: 0.9441 (mm-30) cc_final: 0.9146 (tp30) REVERT: N 201 GLU cc_start: 0.8820 (tp30) cc_final: 0.8578 (mm-30) REVERT: O 270 ASP cc_start: 0.9420 (OUTLIER) cc_final: 0.8987 (p0) REVERT: P 165 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8514 (tm-30) REVERT: P 166 GLU cc_start: 0.9406 (mm-30) cc_final: 0.8968 (tp30) REVERT: P 169 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9006 (ttmm) outliers start: 175 outliers final: 93 residues processed: 537 average time/residue: 0.6937 time to fit residues: 453.9010 Evaluate side-chains 503 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 382 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue -55 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain D residue -10 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 171 MET Chi-restraints excluded: chain G residue 221 HIS Chi-restraints excluded: chain G residue 332 LYS Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 172 HIS Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 203 TYR Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain I residue 241 LYS Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 241 LYS Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 218 ARG Chi-restraints excluded: chain K residue 228 GLN Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 180 ASN Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 207 GLU Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 279 LEU Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain O residue 270 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 208 TYR Chi-restraints excluded: chain P residue 212 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 74 optimal weight: 3.9990 chunk 190 optimal weight: 20.0000 chunk 208 optimal weight: 9.9990 chunk 423 optimal weight: 6.9990 chunk 399 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 283 optimal weight: 1.9990 chunk 410 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 460 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 GLN ** C -3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 GLN ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN ** P 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.119011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.070773 restraints weight = 84476.390| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.19 r_work: 0.2841 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 39556 Z= 0.240 Angle : 0.631 10.495 53128 Z= 0.321 Chirality : 0.044 0.263 5848 Planarity : 0.003 0.059 6764 Dihedral : 4.864 59.286 5168 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.95 % Rotamer: Outliers : 3.95 % Allowed : 27.05 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.13), residues: 4656 helix: 1.83 (0.12), residues: 2084 sheet: 0.47 (0.20), residues: 664 loop : -0.26 (0.15), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 261 TYR 0.023 0.001 TYR I 161 PHE 0.014 0.001 PHE C 315 TRP 0.008 0.001 TRP F 199 HIS 0.004 0.001 HIS K 174 Details of bonding type rmsd covalent geometry : bond 0.00564 (39544) covalent geometry : angle 0.63085 (53104) SS BOND : bond 0.00468 ( 12) SS BOND : angle 1.44205 ( 24) hydrogen bonds : bond 0.03951 ( 1861) hydrogen bonds : angle 4.77500 ( 5295) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 389 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -68 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7140 (mt0) REVERT: A 288 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8616 (tt0) REVERT: A 397 GLU cc_start: 0.8609 (pm20) cc_final: 0.8334 (pm20) REVERT: B 157 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9260 (pp) REVERT: B 288 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8528 (tt0) REVERT: B 395 GLU cc_start: 0.8864 (tp30) cc_final: 0.8596 (tp30) REVERT: B 455 ASN cc_start: 0.9224 (OUTLIER) cc_final: 0.8460 (t0) REVERT: C 15 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8687 (tt0) REVERT: C 173 GLU cc_start: 0.8784 (pp20) cc_final: 0.8558 (pp20) REVERT: C 206 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8610 (mtmm) REVERT: C 221 LYS cc_start: 0.9184 (tppt) cc_final: 0.8885 (mppt) REVERT: C 281 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8922 (ptpt) REVERT: C 288 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8615 (tt0) REVERT: C 397 GLU cc_start: 0.8638 (pm20) cc_final: 0.8323 (pm20) REVERT: C 452 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7526 (mtp180) REVERT: C 455 ASN cc_start: 0.9214 (OUTLIER) cc_final: 0.8414 (t0) REVERT: D 206 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8735 (mtmm) REVERT: D 281 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8956 (ptpt) REVERT: D 288 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8648 (tt0) REVERT: D 395 GLU cc_start: 0.8966 (tp30) cc_final: 0.8548 (tp30) REVERT: D 452 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7548 (mtp180) REVERT: D 455 ASN cc_start: 0.9228 (OUTLIER) cc_final: 0.8493 (t0) REVERT: E 102 TYR cc_start: 0.7334 (p90) cc_final: 0.7093 (p90) REVERT: F 60 ARG cc_start: 0.8634 (mtp180) cc_final: 0.8338 (mtp180) REVERT: F 136 GLN cc_start: 0.8779 (pt0) cc_final: 0.8237 (pm20) REVERT: G 115 GLN cc_start: 0.8893 (pp30) cc_final: 0.8663 (pp30) REVERT: H 83 ARG cc_start: 0.9117 (ttm170) cc_final: 0.8616 (ttm170) REVERT: H 172 HIS cc_start: 0.8671 (OUTLIER) cc_final: 0.8331 (t70) REVERT: H 181 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8485 (tm-30) REVERT: H 217 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7080 (t80) REVERT: H 222 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7934 (tm) REVERT: I 222 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8834 (ptmm) REVERT: I 241 LYS cc_start: 0.9554 (OUTLIER) cc_final: 0.9278 (ttpp) REVERT: I 270 ASP cc_start: 0.9358 (p0) cc_final: 0.9117 (p0) REVERT: J 142 TYR cc_start: 0.8641 (m-80) cc_final: 0.8186 (m-80) REVERT: J 163 SER cc_start: 0.9555 (t) cc_final: 0.9282 (p) REVERT: J 241 LYS cc_start: 0.9514 (OUTLIER) cc_final: 0.9278 (ttpp) REVERT: J 270 ASP cc_start: 0.9469 (OUTLIER) cc_final: 0.9204 (p0) REVERT: J 272 MET cc_start: 0.8832 (mmm) cc_final: 0.8383 (tpt) REVERT: K 163 SER cc_start: 0.9492 (t) cc_final: 0.9155 (p) REVERT: K 218 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8273 (mtp85) REVERT: L 164 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8361 (mm-40) REVERT: L 180 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7741 (p0) REVERT: L 227 PHE cc_start: 0.9108 (m-80) cc_final: 0.8779 (m-10) REVERT: M 165 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8470 (tm-30) REVERT: M 169 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9020 (ttmm) REVERT: M 209 ILE cc_start: 0.4739 (mt) cc_final: 0.4454 (mt) REVERT: N 166 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9080 (tp30) REVERT: N 201 GLU cc_start: 0.8854 (tp30) cc_final: 0.8594 (mm-30) REVERT: O 270 ASP cc_start: 0.9435 (OUTLIER) cc_final: 0.9012 (p0) REVERT: P 165 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8446 (tm-30) REVERT: P 166 GLU cc_start: 0.9394 (mm-30) cc_final: 0.8931 (tp30) REVERT: P 169 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8994 (ttmm) outliers start: 171 outliers final: 98 residues processed: 527 average time/residue: 0.6483 time to fit residues: 416.1302 Evaluate side-chains 502 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 375 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -68 GLN Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain B residue -55 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain D residue -10 THR Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 171 MET Chi-restraints excluded: chain G residue 221 HIS Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 172 HIS Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 203 TYR Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain I residue 241 LYS Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 241 LYS Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 218 ARG Chi-restraints excluded: chain K residue 228 GLN Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 164 GLN Chi-restraints excluded: chain L residue 180 ASN Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 207 GLU Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain O residue 270 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 208 TYR Chi-restraints excluded: chain P residue 212 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 330 optimal weight: 40.0000 chunk 245 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 448 optimal weight: 0.0980 chunk 418 optimal weight: 7.9990 chunk 124 optimal weight: 60.0000 chunk 282 optimal weight: 6.9990 chunk 416 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 141 ASN ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 HIS ** P 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.119850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.071896 restraints weight = 84100.629| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.25 r_work: 0.2862 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 39556 Z= 0.168 Angle : 0.623 10.749 53128 Z= 0.316 Chirality : 0.043 0.246 5848 Planarity : 0.003 0.063 6764 Dihedral : 4.824 56.902 5168 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.81 % Favored : 97.10 % Rotamer: Outliers : 3.81 % Allowed : 27.31 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.13), residues: 4656 helix: 1.84 (0.11), residues: 2096 sheet: 0.49 (0.20), residues: 664 loop : -0.29 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 261 TYR 0.028 0.001 TYR M 203 PHE 0.011 0.001 PHE C 315 TRP 0.009 0.001 TRP F 199 HIS 0.004 0.001 HIS K 174 Details of bonding type rmsd covalent geometry : bond 0.00397 (39544) covalent geometry : angle 0.62280 (53104) SS BOND : bond 0.00314 ( 12) SS BOND : angle 1.38623 ( 24) hydrogen bonds : bond 0.03720 ( 1861) hydrogen bonds : angle 4.73321 ( 5295) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 399 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.9546 (tptp) cc_final: 0.9328 (tppt) REVERT: A 173 GLU cc_start: 0.8774 (pp20) cc_final: 0.8553 (pp20) REVERT: A 288 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8559 (tt0) REVERT: A 397 GLU cc_start: 0.8557 (pm20) cc_final: 0.8288 (pm20) REVERT: A 455 ASN cc_start: 0.9192 (OUTLIER) cc_final: 0.8518 (t0) REVERT: B 157 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9265 (pp) REVERT: B 281 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8776 (ptpp) REVERT: B 288 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: B 395 GLU cc_start: 0.8865 (tp30) cc_final: 0.8586 (tp30) REVERT: B 455 ASN cc_start: 0.9212 (OUTLIER) cc_final: 0.8492 (t0) REVERT: C 162 LYS cc_start: 0.9600 (tptp) cc_final: 0.9385 (tppt) REVERT: C 173 GLU cc_start: 0.8791 (pp20) cc_final: 0.8584 (pp20) REVERT: C 206 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8606 (mtmm) REVERT: C 221 LYS cc_start: 0.9172 (tppt) cc_final: 0.8869 (mppt) REVERT: C 266 SER cc_start: 0.9230 (OUTLIER) cc_final: 0.8979 (p) REVERT: C 281 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8913 (ptpp) REVERT: C 288 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8561 (tt0) REVERT: C 397 GLU cc_start: 0.8640 (pm20) cc_final: 0.8310 (pm20) REVERT: C 452 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7518 (mtp180) REVERT: C 455 ASN cc_start: 0.9226 (OUTLIER) cc_final: 0.8419 (t0) REVERT: D 206 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8618 (mtmm) REVERT: D 281 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8890 (ptpt) REVERT: D 288 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8591 (tt0) REVERT: D 395 GLU cc_start: 0.8947 (tp30) cc_final: 0.8533 (tp30) REVERT: D 452 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7558 (mtp180) REVERT: D 455 ASN cc_start: 0.9245 (OUTLIER) cc_final: 0.8495 (t0) REVERT: E 55 LYS cc_start: 0.9092 (mppt) cc_final: 0.8756 (pttm) REVERT: E 102 TYR cc_start: 0.7413 (p90) cc_final: 0.7167 (p90) REVERT: F 58 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8957 (tm-30) REVERT: F 60 ARG cc_start: 0.8650 (mtp180) cc_final: 0.8349 (mtp180) REVERT: F 136 GLN cc_start: 0.8789 (pt0) cc_final: 0.8239 (pm20) REVERT: G 115 GLN cc_start: 0.8914 (pp30) cc_final: 0.8691 (pp30) REVERT: H 83 ARG cc_start: 0.9139 (ttm170) cc_final: 0.8681 (ttm170) REVERT: H 172 HIS cc_start: 0.8645 (OUTLIER) cc_final: 0.8284 (t70) REVERT: H 181 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8475 (tm-30) REVERT: H 217 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7113 (t80) REVERT: H 222 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7910 (tm) REVERT: I 222 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8801 (ptmm) REVERT: I 241 LYS cc_start: 0.9538 (OUTLIER) cc_final: 0.9286 (ttpp) REVERT: J 142 TYR cc_start: 0.8668 (m-80) cc_final: 0.8175 (m-80) REVERT: J 163 SER cc_start: 0.9555 (t) cc_final: 0.9287 (p) REVERT: J 228 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7530 (pp30) REVERT: J 241 LYS cc_start: 0.9515 (OUTLIER) cc_final: 0.9261 (ttpp) REVERT: J 270 ASP cc_start: 0.9463 (OUTLIER) cc_final: 0.9194 (p0) REVERT: K 163 SER cc_start: 0.9488 (t) cc_final: 0.9166 (p) REVERT: K 164 GLN cc_start: 0.9182 (tp-100) cc_final: 0.8674 (tp-100) REVERT: K 218 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8255 (mtp85) REVERT: L 164 GLN cc_start: 0.9463 (OUTLIER) cc_final: 0.8751 (mm-40) REVERT: L 180 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.7835 (p0) REVERT: L 270 ASP cc_start: 0.9409 (p0) cc_final: 0.9171 (p0) REVERT: M 165 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8471 (tm-30) REVERT: M 166 GLU cc_start: 0.8901 (pm20) cc_final: 0.8664 (pm20) REVERT: M 169 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.9019 (ttmm) REVERT: N 166 GLU cc_start: 0.9430 (mm-30) cc_final: 0.9063 (tp30) REVERT: N 201 GLU cc_start: 0.8840 (tp30) cc_final: 0.8374 (mm-30) REVERT: N 202 LEU cc_start: 0.8840 (mm) cc_final: 0.8435 (tp) REVERT: N 207 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7880 (tp30) REVERT: O 270 ASP cc_start: 0.9425 (OUTLIER) cc_final: 0.9001 (p0) REVERT: P 165 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8469 (tm-30) REVERT: P 166 GLU cc_start: 0.9385 (mm-30) cc_final: 0.8963 (tp30) REVERT: P 169 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9018 (ttmm) outliers start: 165 outliers final: 98 residues processed: 530 average time/residue: 0.6601 time to fit residues: 427.4201 Evaluate side-chains 509 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 379 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue -55 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue -10 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 171 MET Chi-restraints excluded: chain G residue 221 HIS Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 172 HIS Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 162 LEU Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 203 TYR Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain I residue 241 LYS Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 228 GLN Chi-restraints excluded: chain J residue 241 LYS Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 139 ASN Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 218 ARG Chi-restraints excluded: chain K residue 228 GLN Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 164 GLN Chi-restraints excluded: chain L residue 180 ASN Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 207 GLU Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 270 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 208 TYR Chi-restraints excluded: chain P residue 212 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 182 optimal weight: 4.9990 chunk 332 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 454 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 362 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 445 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 254 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 120 GLN F 121 ASN F 181 GLN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 GLN ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN ** P 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.119136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.070948 restraints weight = 84732.501| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.17 r_work: 0.2850 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 39556 Z= 0.230 Angle : 0.652 10.509 53128 Z= 0.331 Chirality : 0.044 0.269 5848 Planarity : 0.003 0.049 6764 Dihedral : 4.860 57.344 5168 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.84 % Favored : 97.08 % Rotamer: Outliers : 3.83 % Allowed : 27.40 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.13), residues: 4656 helix: 1.81 (0.11), residues: 2096 sheet: 0.45 (0.20), residues: 664 loop : -0.30 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 226 TYR 0.024 0.001 TYR L 203 PHE 0.014 0.001 PHE C 315 TRP 0.009 0.001 TRP F 199 HIS 0.004 0.001 HIS K 174 Details of bonding type rmsd covalent geometry : bond 0.00544 (39544) covalent geometry : angle 0.65110 (53104) SS BOND : bond 0.00374 ( 12) SS BOND : angle 1.31681 ( 24) hydrogen bonds : bond 0.03879 ( 1861) hydrogen bonds : angle 4.75974 ( 5295) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 387 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.8798 (pp20) cc_final: 0.8579 (pp20) REVERT: A 288 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8605 (tt0) REVERT: A 397 GLU cc_start: 0.8602 (pm20) cc_final: 0.8323 (pm20) REVERT: A 455 ASN cc_start: 0.9214 (OUTLIER) cc_final: 0.8549 (t0) REVERT: B 157 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9287 (pp) REVERT: B 281 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8503 (ptpt) REVERT: B 288 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8518 (tt0) REVERT: B 395 GLU cc_start: 0.8872 (tp30) cc_final: 0.8591 (tp30) REVERT: B 455 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8435 (t0) REVERT: C 162 LYS cc_start: 0.9594 (tptp) cc_final: 0.9359 (tppt) REVERT: C 173 GLU cc_start: 0.8824 (pp20) cc_final: 0.8622 (pp20) REVERT: C 206 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8595 (mtmm) REVERT: C 221 LYS cc_start: 0.9184 (tppt) cc_final: 0.8870 (mppt) REVERT: C 266 SER cc_start: 0.9268 (OUTLIER) cc_final: 0.8996 (p) REVERT: C 281 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8913 (ptpt) REVERT: C 288 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8570 (tt0) REVERT: C 397 GLU cc_start: 0.8654 (pm20) cc_final: 0.8322 (pm20) REVERT: C 452 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7556 (mtp180) REVERT: C 455 ASN cc_start: 0.9223 (OUTLIER) cc_final: 0.8410 (t0) REVERT: D 206 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8735 (mtmm) REVERT: D 281 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8907 (ptpt) REVERT: D 288 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8637 (tt0) REVERT: D 395 GLU cc_start: 0.8953 (tp30) cc_final: 0.8544 (tp30) REVERT: D 452 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7573 (mtp180) REVERT: D 455 ASN cc_start: 0.9229 (OUTLIER) cc_final: 0.8520 (t0) REVERT: E 102 TYR cc_start: 0.7388 (p90) cc_final: 0.7116 (p90) REVERT: F 58 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8965 (tm-30) REVERT: F 115 GLN cc_start: 0.9003 (pp30) cc_final: 0.8704 (pp30) REVERT: F 136 GLN cc_start: 0.8767 (pt0) cc_final: 0.8219 (pm20) REVERT: G 115 GLN cc_start: 0.8933 (pp30) cc_final: 0.8720 (pp30) REVERT: H 83 ARG cc_start: 0.9129 (ttm170) cc_final: 0.8628 (ttm170) REVERT: H 172 HIS cc_start: 0.8660 (OUTLIER) cc_final: 0.8377 (t70) REVERT: H 181 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8482 (tm-30) REVERT: H 217 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.7098 (t80) REVERT: H 222 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7802 (tm) REVERT: I 222 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8843 (ptmm) REVERT: I 241 LYS cc_start: 0.9555 (OUTLIER) cc_final: 0.9271 (ttpp) REVERT: I 270 ASP cc_start: 0.9390 (p0) cc_final: 0.9096 (p0) REVERT: J 142 TYR cc_start: 0.8686 (m-80) cc_final: 0.8480 (m-80) REVERT: J 163 SER cc_start: 0.9557 (t) cc_final: 0.9286 (p) REVERT: J 228 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7580 (pp30) REVERT: J 241 LYS cc_start: 0.9508 (OUTLIER) cc_final: 0.9270 (ttpp) REVERT: J 270 ASP cc_start: 0.9456 (OUTLIER) cc_final: 0.9184 (p0) REVERT: K 163 SER cc_start: 0.9486 (t) cc_final: 0.9149 (p) REVERT: K 164 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8588 (tp-100) REVERT: K 218 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8267 (mtp85) REVERT: L 164 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.8612 (mm-40) REVERT: L 180 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.7908 (p0) REVERT: L 228 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: L 270 ASP cc_start: 0.9404 (p0) cc_final: 0.9169 (p0) REVERT: M 165 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8468 (tm-30) REVERT: M 169 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9015 (ttmm) REVERT: N 166 GLU cc_start: 0.9435 (mm-30) cc_final: 0.9077 (tp30) REVERT: N 201 GLU cc_start: 0.8859 (tp30) cc_final: 0.8400 (mm-30) REVERT: O 270 ASP cc_start: 0.9420 (OUTLIER) cc_final: 0.8995 (p0) REVERT: P 165 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8494 (tm-30) REVERT: P 166 GLU cc_start: 0.9391 (mm-30) cc_final: 0.8929 (tp30) REVERT: P 169 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9005 (ttmm) outliers start: 166 outliers final: 106 residues processed: 520 average time/residue: 0.6738 time to fit residues: 427.7707 Evaluate side-chains 512 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 373 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue -55 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue -10 THR Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 171 MET Chi-restraints excluded: chain G residue 221 HIS Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 172 HIS Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 162 LEU Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 203 TYR Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain I residue 241 LYS Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 228 GLN Chi-restraints excluded: chain J residue 241 LYS Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 139 ASN Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 218 ARG Chi-restraints excluded: chain K residue 228 GLN Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 164 GLN Chi-restraints excluded: chain L residue 180 ASN Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 228 GLN Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 248 ILE Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 279 LEU Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 270 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 208 TYR Chi-restraints excluded: chain P residue 212 LEU Chi-restraints excluded: chain P residue 231 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 354 optimal weight: 0.5980 chunk 457 optimal weight: 9.9990 chunk 247 optimal weight: 0.9990 chunk 425 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 176 optimal weight: 8.9990 chunk 361 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 315 optimal weight: 6.9990 chunk 441 optimal weight: 2.9990 chunk 276 optimal weight: 0.0670 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN G 136 GLN I 141 ASN ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN ** L 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.120493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.072599 restraints weight = 83559.797| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.24 r_work: 0.2884 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 39556 Z= 0.138 Angle : 0.643 10.783 53128 Z= 0.324 Chirality : 0.043 0.304 5848 Planarity : 0.003 0.049 6764 Dihedral : 4.796 55.964 5168 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.64 % Favored : 97.27 % Rotamer: Outliers : 3.42 % Allowed : 28.00 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.13), residues: 4656 helix: 1.83 (0.11), residues: 2100 sheet: 0.48 (0.20), residues: 664 loop : -0.31 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG K 226 TYR 0.035 0.001 TYR N 203 PHE 0.012 0.001 PHE G 103 TRP 0.010 0.001 TRP F 199 HIS 0.005 0.001 HIS K 174 Details of bonding type rmsd covalent geometry : bond 0.00322 (39544) covalent geometry : angle 0.64224 (53104) SS BOND : bond 0.00278 ( 12) SS BOND : angle 1.26901 ( 24) hydrogen bonds : bond 0.03559 ( 1861) hydrogen bonds : angle 4.70552 ( 5295) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 392 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.9551 (tptp) cc_final: 0.9344 (tppt) REVERT: A 288 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8507 (tt0) REVERT: A 397 GLU cc_start: 0.8545 (pm20) cc_final: 0.8273 (pm20) REVERT: A 455 ASN cc_start: 0.9201 (OUTLIER) cc_final: 0.8521 (t0) REVERT: B 157 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9276 (pp) REVERT: B 281 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8795 (ptpp) REVERT: B 288 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: B 395 GLU cc_start: 0.8859 (tp30) cc_final: 0.8258 (tp30) REVERT: B 455 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8437 (t0) REVERT: C 162 LYS cc_start: 0.9610 (tptp) cc_final: 0.9376 (tppt) REVERT: C 206 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8594 (mtmm) REVERT: C 221 LYS cc_start: 0.9186 (tppt) cc_final: 0.8872 (mppt) REVERT: C 266 SER cc_start: 0.9200 (OUTLIER) cc_final: 0.8936 (p) REVERT: C 281 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8915 (ptpp) REVERT: C 288 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: C 397 GLU cc_start: 0.8631 (pm20) cc_final: 0.8298 (pm20) REVERT: C 452 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7582 (mtp180) REVERT: C 455 ASN cc_start: 0.9213 (OUTLIER) cc_final: 0.8434 (t0) REVERT: D 206 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8591 (mtmm) REVERT: D 232 MET cc_start: 0.9290 (tmt) cc_final: 0.9051 (tmm) REVERT: D 281 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8910 (ptpp) REVERT: D 288 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: D 395 GLU cc_start: 0.8928 (tp30) cc_final: 0.8427 (tp30) REVERT: D 397 GLU cc_start: 0.8658 (pm20) cc_final: 0.8411 (pm20) REVERT: D 452 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7607 (mtp180) REVERT: D 455 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8506 (t0) REVERT: E 102 TYR cc_start: 0.7392 (p90) cc_final: 0.7132 (p90) REVERT: F 58 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8935 (tm-30) REVERT: F 115 GLN cc_start: 0.8971 (pp30) cc_final: 0.8669 (pp30) REVERT: F 136 GLN cc_start: 0.8797 (pt0) cc_final: 0.8234 (pm20) REVERT: G 115 GLN cc_start: 0.8913 (pp30) cc_final: 0.8704 (pp30) REVERT: H 83 ARG cc_start: 0.9195 (ttm170) cc_final: 0.8727 (ttm170) REVERT: H 172 HIS cc_start: 0.8668 (OUTLIER) cc_final: 0.8350 (t70) REVERT: H 181 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8853 (tm-30) REVERT: H 217 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.7035 (t80) REVERT: H 222 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7910 (tm) REVERT: I 163 SER cc_start: 0.9410 (t) cc_final: 0.9135 (p) REVERT: I 222 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8709 (ptmm) REVERT: I 241 LYS cc_start: 0.9547 (OUTLIER) cc_final: 0.9278 (ttpp) REVERT: I 270 ASP cc_start: 0.9347 (p0) cc_final: 0.9056 (p0) REVERT: J 163 SER cc_start: 0.9565 (t) cc_final: 0.9305 (p) REVERT: J 228 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7740 (pp30) REVERT: J 241 LYS cc_start: 0.9520 (OUTLIER) cc_final: 0.9295 (ttpp) REVERT: J 270 ASP cc_start: 0.9435 (OUTLIER) cc_final: 0.9166 (p0) REVERT: J 272 MET cc_start: 0.8799 (mmm) cc_final: 0.8547 (tpp) REVERT: K 163 SER cc_start: 0.9482 (t) cc_final: 0.9146 (p) REVERT: K 164 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8619 (tp-100) REVERT: K 218 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8219 (mtp85) REVERT: K 226 ARG cc_start: 0.7865 (mtm110) cc_final: 0.7256 (ttp-170) REVERT: L 164 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.8559 (mm-40) REVERT: L 180 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.8006 (p0) REVERT: L 220 LYS cc_start: 0.9504 (tppp) cc_final: 0.9068 (pttm) REVERT: L 241 LYS cc_start: 0.9539 (ttmm) cc_final: 0.9257 (ttpp) REVERT: L 270 ASP cc_start: 0.9368 (p0) cc_final: 0.9137 (p0) REVERT: M 165 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8441 (tm-30) REVERT: M 166 GLU cc_start: 0.8852 (pm20) cc_final: 0.8652 (pm20) REVERT: M 169 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.9040 (ttmm) REVERT: N 201 GLU cc_start: 0.8800 (tp30) cc_final: 0.8539 (tm-30) REVERT: N 202 LEU cc_start: 0.9001 (tp) cc_final: 0.8793 (tt) REVERT: O 164 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8248 (mm110) REVERT: O 270 ASP cc_start: 0.9385 (OUTLIER) cc_final: 0.8978 (p0) REVERT: P 165 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8449 (tm-30) REVERT: P 166 GLU cc_start: 0.9363 (mm-30) cc_final: 0.8886 (tp30) REVERT: P 169 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9049 (ttmm) outliers start: 148 outliers final: 91 residues processed: 507 average time/residue: 0.6714 time to fit residues: 415.1758 Evaluate side-chains 509 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 385 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue -55 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue -10 THR Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue -10 THR Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 221 HIS Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 172 HIS Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 PHE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 162 LEU Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 203 TYR Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain I residue 241 LYS Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 228 GLN Chi-restraints excluded: chain J residue 241 LYS Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 216 TYR Chi-restraints excluded: chain K residue 218 ARG Chi-restraints excluded: chain K residue 228 GLN Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain L residue 164 GLN Chi-restraints excluded: chain L residue 180 ASN Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 216 TYR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 279 LEU Chi-restraints excluded: chain O residue 164 GLN Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 270 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 208 TYR Chi-restraints excluded: chain P residue 212 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 294 optimal weight: 6.9990 chunk 466 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 269 optimal weight: 9.9990 chunk 360 optimal weight: 20.0000 chunk 335 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 353 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 293 optimal weight: 0.9990 chunk 354 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN I 141 ASN ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 244 GLN ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 ASN ** L 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.120279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.072452 restraints weight = 84322.538| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.27 r_work: 0.2878 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.174 39556 Z= 0.237 Angle : 0.742 59.200 53128 Z= 0.400 Chirality : 0.046 1.007 5848 Planarity : 0.004 0.166 6764 Dihedral : 4.682 48.504 5164 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.66 % Favored : 97.25 % Rotamer: Outliers : 3.23 % Allowed : 28.28 % Favored : 68.49 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.13), residues: 4656 helix: 1.82 (0.11), residues: 2100 sheet: 0.49 (0.20), residues: 664 loop : -0.32 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 226 TYR 0.033 0.001 TYR N 203 PHE 0.010 0.001 PHE F 187 TRP 0.010 0.001 TRP F 199 HIS 0.005 0.001 HIS K 174 Details of bonding type rmsd covalent geometry : bond 0.00483 (39544) covalent geometry : angle 0.74131 (53104) SS BOND : bond 0.00307 ( 12) SS BOND : angle 1.23827 ( 24) hydrogen bonds : bond 0.03625 ( 1861) hydrogen bonds : angle 4.70070 ( 5295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18105.59 seconds wall clock time: 308 minutes 48.03 seconds (18528.03 seconds total)