Starting phenix.real_space_refine on Mon Aug 25 23:23:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jqb_36563/08_2025/8jqb_36563.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jqb_36563/08_2025/8jqb_36563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jqb_36563/08_2025/8jqb_36563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jqb_36563/08_2025/8jqb_36563.map" model { file = "/net/cci-nas-00/data/ceres_data/8jqb_36563/08_2025/8jqb_36563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jqb_36563/08_2025/8jqb_36563.cif" } resolution = 3.2 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= 0.001 sd= 0.021 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 96 5.16 5 C 20268 2.51 5 N 5204 2.21 5 O 6040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 residue(s): 0.03s 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: 31608 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3835 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 8, 'TRANS': 459} Chain breaks: 1 Chain: "A" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3835 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 8, 'TRANS': 459} Chain breaks: 1 Chain: "B" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3835 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 8, 'TRANS': 459} Chain breaks: 1 Chain: "D" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3835 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 8, 'TRANS': 459} Chain breaks: 1 Chain: "E" Number of atoms: 4067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 4067 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 10, 'TRANS': 488} Chain: "F" Number of atoms: 4067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 4067 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 10, 'TRANS': 488} Chain: "G" Number of atoms: 4067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 4067 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 10, 'TRANS': 488} Chain: "H" Number of atoms: 4067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 4067 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 10, 'TRANS': 488} Time building chain proxies: 6.02, per 1000 atoms: 0.19 Number of scatterers: 31608 At special positions: 0 Unit cell: (187.32, 162.12, 162.96, 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 96 16.00 O 6040 8.00 N 5204 7.00 C 20268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7384 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 33 sheets defined 48.6% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'C' and resid 31 through 47 removed outlier: 3.946A pdb=" N LYS C 35 " --> pdb=" O ASN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 56 through 64 removed outlier: 3.606A pdb=" N ASP C 59 " --> pdb=" O ASN C 56 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 60 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N HIS C 61 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYS C 62 " --> pdb=" O ASP C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 removed outlier: 4.370A pdb=" N VAL C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 148 removed outlier: 3.713A pdb=" N ASN C 147 " --> pdb=" O ASN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 277 removed outlier: 3.807A pdb=" N TYR C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 308 Processing helix chain 'C' and resid 321 through 325 removed outlier: 3.643A pdb=" N LEU C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.523A pdb=" N GLY C 356 " --> pdb=" O GLU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 removed outlier: 3.607A pdb=" N ALA C 365 " --> pdb=" O LYS C 361 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 394 removed outlier: 3.701A pdb=" N GLU C 393 " --> pdb=" O LYS C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 423 removed outlier: 3.864A pdb=" N ASP C 422 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 423 " --> pdb=" O THR C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 4.152A pdb=" N LEU C 456 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU C 457 " --> pdb=" O CYS C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 493 removed outlier: 3.848A pdb=" N GLU C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C 493 " --> pdb=" O ILE C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 503 Processing helix chain 'C' and resid 511 through 518 Processing helix chain 'C' and resid 521 through 529 Processing helix chain 'C' and resid 532 through 538 removed outlier: 3.569A pdb=" N TYR C 536 " --> pdb=" O ASP C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 552 removed outlier: 3.776A pdb=" N MET C 545 " --> pdb=" O LYS C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 562 removed outlier: 3.664A pdb=" N ASP C 559 " --> pdb=" O LYS C 555 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 565 No H-bonds generated for 'chain 'C' and resid 563 through 565' Processing helix chain 'C' and resid 566 through 574 removed outlier: 4.015A pdb=" N LYS C 570 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.919A pdb=" N LYS A 35 " --> pdb=" O ASN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 56 through 64 removed outlier: 3.573A pdb=" N ASP A 59 " --> pdb=" O ASN A 56 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR A 60 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N HIS A 61 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LYS A 62 " --> pdb=" O ASP A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 removed outlier: 4.368A pdb=" N VAL A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 148 removed outlier: 3.718A pdb=" N ASN A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 277 removed outlier: 3.789A pdb=" N TYR A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.640A pdb=" N LEU A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 3.591A pdb=" N ALA A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 394 removed outlier: 3.704A pdb=" N GLU A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 removed outlier: 3.856A pdb=" N ASP A 422 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 423 " --> pdb=" O THR A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 4.192A pdb=" N LEU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 457 " --> pdb=" O CYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 493 removed outlier: 3.997A pdb=" N GLU A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG A 485 " --> pdb=" O ARG A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 503 Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 521 through 529 Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.560A pdb=" N TYR A 536 " --> pdb=" O ASP A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 552 removed outlier: 3.771A pdb=" N MET A 545 " --> pdb=" O LYS A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 562 Processing helix chain 'A' and resid 563 through 565 No H-bonds generated for 'chain 'A' and resid 563 through 565' Processing helix chain 'A' and resid 566 through 574 removed outlier: 4.015A pdb=" N LYS A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.923A pdb=" N LYS B 35 " --> pdb=" O ASN B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 56 through 64 removed outlier: 3.563A pdb=" N ASP B 59 " --> pdb=" O ASN B 56 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR B 60 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N HIS B 61 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LYS B 62 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 removed outlier: 4.359A pdb=" N VAL B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 148 removed outlier: 3.712A pdb=" N ASN B 147 " --> pdb=" O ASN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.812A pdb=" N TYR B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 308 Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.640A pdb=" N LEU B 324 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 371 removed outlier: 3.607A pdb=" N ALA B 365 " --> pdb=" O LYS B 361 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 394 removed outlier: 3.707A pdb=" N GLU B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 423 removed outlier: 3.853A pdb=" N ASP B 422 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 423 " --> pdb=" O THR B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 4.191A pdb=" N LEU B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU B 457 " --> pdb=" O CYS B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 493 removed outlier: 3.839A pdb=" N GLU B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG B 485 " --> pdb=" O ARG B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 503 Processing helix chain 'B' and resid 511 through 518 Processing helix chain 'B' and resid 521 through 529 Processing helix chain 'B' and resid 532 through 538 removed outlier: 3.593A pdb=" N TYR B 536 " --> pdb=" O ASP B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 552 removed outlier: 3.762A pdb=" N MET B 545 " --> pdb=" O LYS B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 562 Processing helix chain 'B' and resid 563 through 565 No H-bonds generated for 'chain 'B' and resid 563 through 565' Processing helix chain 'B' and resid 566 through 574 removed outlier: 4.023A pdb=" N LYS B 570 " --> pdb=" O PHE B 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.917A pdb=" N LYS D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 56 through 64 removed outlier: 3.572A pdb=" N ASP D 59 " --> pdb=" O ASN D 56 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR D 60 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N HIS D 61 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LYS D 62 " --> pdb=" O ASP D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 94 removed outlier: 4.363A pdb=" N LYS D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 148 removed outlier: 3.711A pdb=" N ASN D 147 " --> pdb=" O ASN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 277 removed outlier: 3.799A pdb=" N TYR D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 308 Processing helix chain 'D' and resid 321 through 325 removed outlier: 3.644A pdb=" N LEU D 324 " --> pdb=" O SER D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 370 removed outlier: 3.619A pdb=" N ALA D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER D 368 " --> pdb=" O LYS D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 394 removed outlier: 3.727A pdb=" N GLU D 393 " --> pdb=" O LYS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 423 removed outlier: 3.877A pdb=" N ASP D 422 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 423 " --> pdb=" O THR D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 4.155A pdb=" N LEU D 456 " --> pdb=" O ARG D 452 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU D 457 " --> pdb=" O CYS D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 493 removed outlier: 3.849A pdb=" N GLU D 480 " --> pdb=" O LYS D 476 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG D 485 " --> pdb=" O ARG D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 503 Processing helix chain 'D' and resid 511 through 518 Processing helix chain 'D' and resid 521 through 529 Processing helix chain 'D' and resid 532 through 538 removed outlier: 3.613A pdb=" N TYR D 536 " --> pdb=" O ASP D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 552 removed outlier: 3.787A pdb=" N MET D 545 " --> pdb=" O LYS D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 562 Processing helix chain 'D' and resid 563 through 565 No H-bonds generated for 'chain 'D' and resid 563 through 565' Processing helix chain 'D' and resid 566 through 574 removed outlier: 4.031A pdb=" N LYS D 570 " --> pdb=" O PHE D 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 removed outlier: 3.632A pdb=" N LYS E 13 " --> pdb=" O GLU E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 43 removed outlier: 3.598A pdb=" N ILE E 31 " --> pdb=" O GLY E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 67 removed outlier: 3.627A pdb=" N ALA E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 86 Processing helix chain 'E' and resid 86 through 95 removed outlier: 3.783A pdb=" N PHE E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LYS E 92 " --> pdb=" O ARG E 88 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP E 93 " --> pdb=" O PRO E 89 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE E 95 " --> pdb=" O ILE E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 137 through 150 Processing helix chain 'E' and resid 150 through 160 removed outlier: 3.838A pdb=" N ARG E 154 " --> pdb=" O SER E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 186 removed outlier: 3.522A pdb=" N GLN E 186 " --> pdb=" O TYR E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 215 Processing helix chain 'E' and resid 236 through 243 removed outlier: 3.512A pdb=" N ASN E 239 " --> pdb=" O ASP E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 279 removed outlier: 4.114A pdb=" N LEU E 275 " --> pdb=" O SER E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 311 Processing helix chain 'E' and resid 320 through 324 removed outlier: 3.825A pdb=" N ARG E 324 " --> pdb=" O PRO E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 342 removed outlier: 3.806A pdb=" N LEU E 332 " --> pdb=" O ASN E 328 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU E 334 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP E 342 " --> pdb=" O TYR E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 351 removed outlier: 3.530A pdb=" N LEU E 349 " --> pdb=" O SER E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 373 removed outlier: 4.056A pdb=" N ILE E 365 " --> pdb=" O GLU E 361 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE E 368 " --> pdb=" O GLU E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 393 removed outlier: 4.334A pdb=" N ASN E 383 " --> pdb=" O GLN E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 410 removed outlier: 3.569A pdb=" N THR E 403 " --> pdb=" O THR E 399 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL E 408 " --> pdb=" O ALA E 404 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET E 409 " --> pdb=" O PHE E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 413 No H-bonds generated for 'chain 'E' and resid 411 through 413' Processing helix chain 'E' and resid 449 through 453 Processing helix chain 'E' and resid 455 through 464 removed outlier: 3.854A pdb=" N HIS E 459 " --> pdb=" O ASP E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 490 Processing helix chain 'F' and resid 2 through 13 removed outlier: 3.643A pdb=" N LYS F 13 " --> pdb=" O GLU F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 43 removed outlier: 3.597A pdb=" N ILE F 31 " --> pdb=" O GLY F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 67 removed outlier: 3.744A pdb=" N ALA F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 86 Processing helix chain 'F' and resid 86 through 95 removed outlier: 3.777A pdb=" N PHE F 90 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS F 92 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASP F 93 " --> pdb=" O PRO F 89 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE F 95 " --> pdb=" O ILE F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 137 through 150 Processing helix chain 'F' and resid 150 through 160 removed outlier: 3.708A pdb=" N ARG F 154 " --> pdb=" O SER F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 186 removed outlier: 3.513A pdb=" N GLN F 186 " --> pdb=" O TYR F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 215 Processing helix chain 'F' and resid 236 through 243 removed outlier: 3.526A pdb=" N ASN F 239 " --> pdb=" O ASP F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 279 removed outlier: 4.082A pdb=" N LEU F 275 " --> pdb=" O SER F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 311 Processing helix chain 'F' and resid 320 through 324 removed outlier: 3.842A pdb=" N ARG F 324 " --> pdb=" O PRO F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 342 removed outlier: 3.803A pdb=" N LEU F 332 " --> pdb=" O ASN F 328 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU F 334 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN F 341 " --> pdb=" O LYS F 337 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP F 342 " --> pdb=" O TYR F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 351 removed outlier: 3.516A pdb=" N LEU F 349 " --> pdb=" O SER F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 372 removed outlier: 4.033A pdb=" N ILE F 365 " --> pdb=" O GLU F 361 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 393 removed outlier: 4.179A pdb=" N ASN F 383 " --> pdb=" O GLN F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 410 removed outlier: 3.583A pdb=" N THR F 403 " --> pdb=" O THR F 399 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL F 408 " --> pdb=" O ALA F 404 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET F 409 " --> pdb=" O PHE F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 413 No H-bonds generated for 'chain 'F' and resid 411 through 413' Processing helix chain 'F' and resid 444 through 447 removed outlier: 4.250A pdb=" N ASP F 447 " --> pdb=" O THR F 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 444 through 447' Processing helix chain 'F' and resid 455 through 464 removed outlier: 3.776A pdb=" N HIS F 459 " --> pdb=" O ASP F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 490 Processing helix chain 'G' and resid 2 through 13 removed outlier: 3.642A pdb=" N LYS G 13 " --> pdb=" O GLU G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 43 removed outlier: 3.679A pdb=" N ILE G 31 " --> pdb=" O GLY G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 67 removed outlier: 3.657A pdb=" N ALA G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 86 Processing helix chain 'G' and resid 86 through 95 removed outlier: 3.785A pdb=" N PHE G 90 " --> pdb=" O ILE G 86 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LYS G 92 " --> pdb=" O ARG G 88 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ASP G 93 " --> pdb=" O PRO G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 125 Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'G' and resid 150 through 160 removed outlier: 3.832A pdb=" N ARG G 154 " --> pdb=" O SER G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 186 Processing helix chain 'G' and resid 211 through 216 removed outlier: 3.796A pdb=" N ILE G 216 " --> pdb=" O ASN G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 242 removed outlier: 3.801A pdb=" N ASN G 239 " --> pdb=" O ASP G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 252 removed outlier: 3.778A pdb=" N ILE G 252 " --> pdb=" O ARG G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 279 removed outlier: 4.087A pdb=" N LEU G 275 " --> pdb=" O SER G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 311 removed outlier: 3.591A pdb=" N ALA G 300 " --> pdb=" O ARG G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 324 removed outlier: 3.832A pdb=" N ARG G 324 " --> pdb=" O PRO G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 342 removed outlier: 3.600A pdb=" N LEU G 332 " --> pdb=" O ASN G 328 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU G 334 " --> pdb=" O THR G 330 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN G 341 " --> pdb=" O LYS G 337 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP G 342 " --> pdb=" O TYR G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 351 removed outlier: 3.586A pdb=" N LEU G 349 " --> pdb=" O SER G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 372 removed outlier: 3.967A pdb=" N ILE G 365 " --> pdb=" O GLU G 361 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE G 368 " --> pdb=" O GLU G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 393 removed outlier: 4.400A pdb=" N ASN G 383 " --> pdb=" O GLN G 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 399 through 410 removed outlier: 3.817A pdb=" N THR G 403 " --> pdb=" O THR G 399 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL G 408 " --> pdb=" O ALA G 404 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET G 409 " --> pdb=" O PHE G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 413 No H-bonds generated for 'chain 'G' and resid 411 through 413' Processing helix chain 'G' and resid 444 through 447 removed outlier: 4.206A pdb=" N ASP G 447 " --> pdb=" O THR G 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 444 through 447' Processing helix chain 'G' and resid 449 through 453 Processing helix chain 'G' and resid 455 through 464 removed outlier: 3.890A pdb=" N HIS G 459 " --> pdb=" O ASP G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 490 Processing helix chain 'H' and resid 2 through 13 removed outlier: 3.653A pdb=" N LYS H 13 " --> pdb=" O GLU H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 43 removed outlier: 3.600A pdb=" N ILE H 31 " --> pdb=" O GLY H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 67 removed outlier: 3.733A pdb=" N ALA H 59 " --> pdb=" O THR H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 86 through 95 removed outlier: 3.804A pdb=" N PHE H 90 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LYS H 92 " --> pdb=" O ARG H 88 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ASP H 93 " --> pdb=" O PRO H 89 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE H 95 " --> pdb=" O ILE H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 125 Processing helix chain 'H' and resid 137 through 150 Processing helix chain 'H' and resid 150 through 160 removed outlier: 3.838A pdb=" N ARG H 154 " --> pdb=" O SER H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 186 removed outlier: 3.518A pdb=" N GLN H 186 " --> pdb=" O TYR H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'H' and resid 236 through 242 removed outlier: 3.615A pdb=" N ASN H 239 " --> pdb=" O ASP H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 279 removed outlier: 4.171A pdb=" N LEU H 275 " --> pdb=" O SER H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 311 Processing helix chain 'H' and resid 320 through 324 removed outlier: 3.829A pdb=" N ARG H 324 " --> pdb=" O PRO H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 342 removed outlier: 3.747A pdb=" N LEU H 332 " --> pdb=" O ASN H 328 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU H 334 " --> pdb=" O THR H 330 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN H 341 " --> pdb=" O LYS H 337 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP H 342 " --> pdb=" O TYR H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 351 removed outlier: 3.507A pdb=" N LEU H 349 " --> pdb=" O SER H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 361 through 372 removed outlier: 3.967A pdb=" N ILE H 365 " --> pdb=" O GLU H 361 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE H 368 " --> pdb=" O GLU H 364 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 393 removed outlier: 4.438A pdb=" N ASN H 383 " --> pdb=" O GLN H 379 " (cutoff:3.500A) Processing helix chain 'H' and resid 399 through 410 removed outlier: 3.849A pdb=" N THR H 403 " --> pdb=" O THR H 399 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL H 408 " --> pdb=" O ALA H 404 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET H 409 " --> pdb=" O PHE H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 413 No H-bonds generated for 'chain 'H' and resid 411 through 413' Processing helix chain 'H' and resid 443 through 447 removed outlier: 3.862A pdb=" N SER H 446 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP H 447 " --> pdb=" O THR H 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 443 through 447' Processing helix chain 'H' and resid 449 through 453 Processing helix chain 'H' and resid 455 through 464 removed outlier: 3.847A pdb=" N HIS H 459 " --> pdb=" O ASP H 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 490 Processing sheet with id=AA1, first strand: chain 'C' and resid 17 through 20 removed outlier: 6.718A pdb=" N THR C 74 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE C 6 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE C 72 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE C 8 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLU C 70 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS C 112 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN C 121 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 149 through 154 removed outlier: 4.605A pdb=" N TYR C 314 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL C 26 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL C 336 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE C 28 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 403 through 407 removed outlier: 6.414A pdb=" N ARG C 374 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU C 406 " --> pdb=" O ARG C 374 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 376 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 435 through 437 Processing sheet with id=AA5, first strand: chain 'A' and resid 17 through 20 removed outlier: 6.720A pdb=" N THR A 74 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE A 6 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 72 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE A 8 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLU A 70 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A 112 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN A 121 " --> pdb=" O LYS A 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 149 through 154 removed outlier: 4.605A pdb=" N TYR A 314 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE A 28 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 403 through 407 removed outlier: 6.416A pdb=" N ARG A 374 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU A 406 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 376 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 435 through 437 Processing sheet with id=AA9, first strand: chain 'B' and resid 17 through 20 removed outlier: 6.721A pdb=" N THR B 74 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE B 6 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 72 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE B 8 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLU B 70 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS B 112 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN B 121 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 149 through 154 removed outlier: 4.605A pdb=" N TYR B 314 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL B 26 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL B 336 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE B 28 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 403 through 407 removed outlier: 6.412A pdb=" N ARG B 374 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU B 406 " --> pdb=" O ARG B 374 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU B 376 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 435 through 437 Processing sheet with id=AB4, first strand: chain 'D' and resid 17 through 20 removed outlier: 6.723A pdb=" N THR D 74 " --> pdb=" O SER D 4 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE D 6 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE D 72 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE D 8 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU D 70 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS D 112 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN D 121 " --> pdb=" O LYS D 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 149 through 154 removed outlier: 4.605A pdb=" N TYR D 314 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL D 26 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL D 336 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE D 28 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 403 through 407 removed outlier: 6.413A pdb=" N ARG D 374 " --> pdb=" O PHE D 404 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU D 406 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU D 376 " --> pdb=" O LEU D 406 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 435 through 437 Processing sheet with id=AB8, first strand: chain 'E' and resid 74 through 77 removed outlier: 7.622A pdb=" N SER E 48 " --> pdb=" O PHE E 162 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE E 164 " --> pdb=" O SER E 48 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA E 50 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ILE E 166 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E 52 " --> pdb=" O ILE E 166 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE E 162 " --> pdb=" O LYS E 190 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N PHE E 192 " --> pdb=" O PHE E 162 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE E 164 " --> pdb=" O PHE E 192 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL E 194 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE E 166 " --> pdb=" O VAL E 194 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE E 18 " --> pdb=" O ILE E 193 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N GLY E 195 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL E 20 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 104 through 105 removed outlier: 6.374A pdb=" N THR E 104 " --> pdb=" O LEU E 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 261 through 262 removed outlier: 3.727A pdb=" N ILE E 262 " --> pdb=" O LEU E 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 290 through 291 Processing sheet with id=AC3, first strand: chain 'E' and resid 315 through 316 removed outlier: 6.699A pdb=" N ILE E 315 " --> pdb=" O ILE E 427 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 74 through 77 removed outlier: 7.622A pdb=" N SER F 48 " --> pdb=" O PHE F 162 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE F 164 " --> pdb=" O SER F 48 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA F 50 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE F 166 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL F 52 " --> pdb=" O ILE F 166 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE F 162 " --> pdb=" O LYS F 190 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N PHE F 192 " --> pdb=" O PHE F 162 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE F 164 " --> pdb=" O PHE F 192 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL F 194 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE F 166 " --> pdb=" O VAL F 194 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE F 18 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLY F 195 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL F 20 " --> pdb=" O GLY F 195 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 104 through 105 removed outlier: 6.293A pdb=" N THR F 104 " --> pdb=" O LEU F 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 315 through 316 removed outlier: 6.770A pdb=" N ILE F 315 " --> pdb=" O ILE F 427 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU F 290 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N PHE F 428 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE F 292 " --> pdb=" O PHE F 428 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE F 442 " --> pdb=" O VAL F 291 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU F 293 " --> pdb=" O ILE F 442 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL F 441 " --> pdb=" O ILE F 471 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 74 through 77 removed outlier: 7.672A pdb=" N SER G 48 " --> pdb=" O PHE G 162 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE G 164 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA G 50 " --> pdb=" O ILE G 164 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE G 166 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL G 52 " --> pdb=" O ILE G 166 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE G 162 " --> pdb=" O LYS G 190 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N PHE G 192 " --> pdb=" O PHE G 162 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE G 164 " --> pdb=" O PHE G 192 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL G 194 " --> pdb=" O ILE G 164 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE G 166 " --> pdb=" O VAL G 194 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE G 18 " --> pdb=" O ILE G 193 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLY G 195 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL G 20 " --> pdb=" O GLY G 195 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 104 through 105 removed outlier: 3.671A pdb=" N LEU G 128 " --> pdb=" O THR G 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 261 through 262 removed outlier: 3.584A pdb=" N ILE G 262 " --> pdb=" O LEU G 470 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N ASN G 439 " --> pdb=" O ASP G 468 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU G 470 " --> pdb=" O ASN G 439 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL G 441 " --> pdb=" O LEU G 470 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL G 291 " --> pdb=" O ILE G 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 315 through 316 removed outlier: 6.495A pdb=" N ILE G 315 " --> pdb=" O ILE G 427 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'H' and resid 74 through 77 removed outlier: 7.629A pdb=" N SER H 48 " --> pdb=" O PHE H 162 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE H 164 " --> pdb=" O SER H 48 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA H 50 " --> pdb=" O ILE H 164 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE H 166 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL H 52 " --> pdb=" O ILE H 166 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE H 162 " --> pdb=" O LYS H 190 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N PHE H 192 " --> pdb=" O PHE H 162 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE H 164 " --> pdb=" O PHE H 192 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL H 194 " --> pdb=" O ILE H 164 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE H 166 " --> pdb=" O VAL H 194 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE H 18 " --> pdb=" O ILE H 193 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLY H 195 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL H 20 " --> pdb=" O GLY H 195 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 104 through 105 removed outlier: 5.992A pdb=" N THR H 104 " --> pdb=" O LEU H 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'H' and resid 261 through 262 removed outlier: 3.705A pdb=" N ILE H 262 " --> pdb=" O LEU H 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'H' and resid 290 through 291 Processing sheet with id=AD6, first strand: chain 'H' and resid 315 through 316 removed outlier: 6.567A pdb=" N ILE H 315 " --> pdb=" O ILE H 427 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 1238 hydrogen bonds defined for protein. 3477 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: 4.97 Time building geometry restraints manager: 3.15 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: 9206 1.34 - 1.46: 5040 1.46 - 1.57: 17737 1.57 - 1.69: 5 1.69 - 1.81: 164 Bond restraints: 32152 Sorted by residual: bond pdb=" N ILE G 270 " pdb=" CA ILE G 270 " ideal model delta sigma weight residual 1.461 1.497 -0.037 1.19e-02 7.06e+03 9.46e+00 bond pdb=" N MET G 268 " pdb=" CA MET G 268 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.25e-02 6.40e+03 9.36e+00 bond pdb=" N ILE E 270 " pdb=" CA ILE E 270 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.33e+00 bond pdb=" N MET E 268 " pdb=" CA MET E 268 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.32e-02 5.74e+03 8.57e+00 bond pdb=" N ILE F 273 " pdb=" CA ILE F 273 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.14e-02 7.69e+03 7.37e+00 ... (remaining 32147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 42250 3.22 - 6.43: 794 6.43 - 9.65: 164 9.65 - 12.87: 49 12.87 - 16.09: 19 Bond angle restraints: 43276 Sorted by residual: angle pdb=" C ASN G 341 " pdb=" N ASP G 342 " pdb=" CA ASP G 342 " ideal model delta sigma weight residual 121.54 134.48 -12.94 1.91e+00 2.74e-01 4.59e+01 angle pdb=" C ASN H 341 " pdb=" N ASP H 342 " pdb=" CA ASP H 342 " ideal model delta sigma weight residual 121.54 134.41 -12.87 1.91e+00 2.74e-01 4.54e+01 angle pdb=" C ASN F 341 " pdb=" N ASP F 342 " pdb=" CA ASP F 342 " ideal model delta sigma weight residual 121.54 134.38 -12.84 1.91e+00 2.74e-01 4.52e+01 angle pdb=" C ASN E 341 " pdb=" N ASP E 342 " pdb=" CA ASP E 342 " ideal model delta sigma weight residual 121.54 134.37 -12.83 1.91e+00 2.74e-01 4.52e+01 angle pdb=" N ILE F 273 " pdb=" CA ILE F 273 " pdb=" C ILE F 273 " ideal model delta sigma weight residual 110.36 103.44 6.92 1.05e+00 9.07e-01 4.34e+01 ... (remaining 43271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 16192 17.62 - 35.23: 2462 35.23 - 52.85: 792 52.85 - 70.47: 127 70.47 - 88.08: 47 Dihedral angle restraints: 19620 sinusoidal: 8188 harmonic: 11432 Sorted by residual: dihedral pdb=" CA ASP E 272 " pdb=" C ASP E 272 " pdb=" N ILE E 273 " pdb=" CA ILE E 273 " ideal model delta harmonic sigma weight residual 180.00 150.69 29.31 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA MET F 268 " pdb=" C MET F 268 " pdb=" N PRO F 269 " pdb=" CA PRO F 269 " ideal model delta harmonic sigma weight residual -180.00 -151.01 -28.99 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA MET H 268 " pdb=" C MET H 268 " pdb=" N PRO H 269 " pdb=" CA PRO H 269 " ideal model delta harmonic sigma weight residual -180.00 -152.02 -27.98 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 19617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4045 0.079 - 0.159: 719 0.159 - 0.238: 56 0.238 - 0.317: 17 0.317 - 0.396: 3 Chirality restraints: 4840 Sorted by residual: chirality pdb=" CB ILE F 292 " pdb=" CA ILE F 292 " pdb=" CG1 ILE F 292 " pdb=" CG2 ILE F 292 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CB ILE H 292 " pdb=" CA ILE H 292 " pdb=" CG1 ILE H 292 " pdb=" CG2 ILE H 292 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CG LEU F 332 " pdb=" CB LEU F 332 " pdb=" CD1 LEU F 332 " pdb=" CD2 LEU F 332 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 4837 not shown) Planarity restraints: 5532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 65 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.33e+00 pdb=" C THR B 65 " -0.053 2.00e-02 2.50e+03 pdb=" O THR B 65 " 0.020 2.00e-02 2.50e+03 pdb=" N SER B 66 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 65 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C THR A 65 " 0.053 2.00e-02 2.50e+03 pdb=" O THR A 65 " -0.020 2.00e-02 2.50e+03 pdb=" N SER A 66 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 65 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C THR C 65 " -0.052 2.00e-02 2.50e+03 pdb=" O THR C 65 " 0.019 2.00e-02 2.50e+03 pdb=" N SER C 66 " 0.017 2.00e-02 2.50e+03 ... (remaining 5529 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 8417 2.81 - 3.33: 28078 3.33 - 3.85: 51809 3.85 - 4.38: 59827 4.38 - 4.90: 101373 Nonbonded interactions: 249504 Sorted by model distance: nonbonded pdb=" O ILE E 402 " pdb=" OG1 THR E 406 " model vdw 2.285 3.040 nonbonded pdb=" O GLY E 80 " pdb=" OG SER E 84 " model vdw 2.287 3.040 nonbonded pdb=" O ILE G 402 " pdb=" OG1 THR G 406 " model vdw 2.291 3.040 nonbonded pdb=" O GLY F 80 " pdb=" OG SER F 84 " model vdw 2.291 3.040 nonbonded pdb=" O GLY H 80 " pdb=" OG SER H 84 " model vdw 2.295 3.040 ... (remaining 249499 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' } 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: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 23.860 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 32152 Z= 0.257 Angle : 1.156 16.086 43276 Z= 0.620 Chirality : 0.060 0.396 4840 Planarity : 0.006 0.107 5532 Dihedral : 18.554 88.084 12236 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.44 % Favored : 91.73 % Rotamer: Outliers : 0.51 % Allowed : 33.93 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.29 (0.11), residues: 3844 helix: -2.28 (0.11), residues: 1504 sheet: -0.41 (0.22), residues: 508 loop : -2.61 (0.12), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 232 TYR 0.018 0.001 TYR G 202 PHE 0.042 0.002 PHE H 112 TRP 0.021 0.003 TRP F 204 HIS 0.016 0.001 HIS F 459 Details of bonding type rmsd covalent geometry : bond 0.00494 (32152) covalent geometry : angle 1.15602 (43276) hydrogen bonds : bond 0.17055 ( 1238) hydrogen bonds : angle 7.23261 ( 3477) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 295 time to evaluate : 0.955 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: C 309 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: B 536 TYR cc_start: 0.8604 (t80) cc_final: 0.8381 (t80) REVERT: D 536 TYR cc_start: 0.8570 (t80) cc_final: 0.8352 (t80) REVERT: E 439 ASN cc_start: 0.9175 (m-40) cc_final: 0.8478 (t0) REVERT: F 439 ASN cc_start: 0.9376 (m-40) cc_final: 0.8800 (t0) REVERT: H 293 LEU cc_start: 0.8243 (tp) cc_final: 0.7857 (mt) outliers start: 18 outliers final: 4 residues processed: 302 average time/residue: 0.1697 time to fit residues: 84.5653 Evaluate side-chains 269 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 264 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain G residue 474 MET Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 474 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 40.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 363 ASN ** A 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN B 363 ASN ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS F 226 HIS ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 GLN G 226 HIS G 459 HIS H 226 HIS ** H 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 425 HIS ** H 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.226282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128067 restraints weight = 41649.858| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.26 r_work: 0.3160 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 32152 Z= 0.306 Angle : 0.785 9.130 43276 Z= 0.412 Chirality : 0.050 0.186 4840 Planarity : 0.005 0.044 5532 Dihedral : 5.607 42.199 4194 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.09 % Favored : 91.18 % Rotamer: Outliers : 4.51 % Allowed : 29.62 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.61 (0.12), residues: 3844 helix: -1.36 (0.12), residues: 1532 sheet: -0.71 (0.20), residues: 572 loop : -2.40 (0.13), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 374 TYR 0.025 0.002 TYR E 202 PHE 0.024 0.002 PHE B 413 TRP 0.006 0.001 TRP G 204 HIS 0.011 0.002 HIS F 177 Details of bonding type rmsd covalent geometry : bond 0.00745 (32152) covalent geometry : angle 0.78452 (43276) hydrogen bonds : bond 0.05684 ( 1238) hydrogen bonds : angle 5.39017 ( 3477) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 303 time to evaluate : 0.785 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: C 42 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8523 (mm) REVERT: C 67 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8364 (ptpt) REVERT: C 309 GLN cc_start: 0.7924 (tt0) cc_final: 0.7630 (tt0) REVERT: C 452 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8055 (ttp-170) REVERT: C 509 GLU cc_start: 0.8556 (tt0) cc_final: 0.8331 (tt0) REVERT: C 511 ASP cc_start: 0.8300 (t0) cc_final: 0.7860 (t0) REVERT: A 42 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8531 (mm) REVERT: A 309 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.6935 (tt0) REVERT: A 452 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8052 (ttp-170) REVERT: A 509 GLU cc_start: 0.8506 (tt0) cc_final: 0.8288 (tt0) REVERT: B 42 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8511 (mm) REVERT: B 67 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8320 (ptpt) REVERT: B 452 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8056 (ttp-170) REVERT: B 509 GLU cc_start: 0.8468 (tt0) cc_final: 0.8259 (tt0) REVERT: B 551 ASN cc_start: 0.8582 (m-40) cc_final: 0.8328 (m-40) REVERT: D 42 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8532 (mm) REVERT: D 67 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8351 (ptpt) REVERT: D 129 GLU cc_start: 0.8168 (mp0) cc_final: 0.7872 (mp0) REVERT: D 379 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8235 (mm-30) REVERT: D 509 GLU cc_start: 0.8484 (tt0) cc_final: 0.8276 (tt0) REVERT: D 511 ASP cc_start: 0.8298 (t0) cc_final: 0.7850 (t0) REVERT: E 204 TRP cc_start: 0.7530 (OUTLIER) cc_final: 0.7219 (t-100) REVERT: E 439 ASN cc_start: 0.9270 (m110) cc_final: 0.8737 (t0) REVERT: F 204 TRP cc_start: 0.7629 (OUTLIER) cc_final: 0.7334 (t-100) REVERT: F 268 MET cc_start: 0.5678 (pp-130) cc_final: 0.5371 (pp-130) REVERT: F 292 ILE cc_start: 0.8898 (mp) cc_final: 0.8629 (mm) REVERT: F 307 LEU cc_start: 0.7315 (mm) cc_final: 0.6659 (pt) REVERT: F 439 ASN cc_start: 0.9369 (m110) cc_final: 0.8895 (t0) REVERT: F 440 GLN cc_start: 0.8608 (mt0) cc_final: 0.8154 (mt0) REVERT: F 443 ILE cc_start: 0.4136 (OUTLIER) cc_final: 0.3826 (tp) REVERT: G 204 TRP cc_start: 0.7516 (OUTLIER) cc_final: 0.7304 (t60) REVERT: G 474 MET cc_start: 0.5571 (pmm) cc_final: 0.5254 (pmm) REVERT: H 108 PHE cc_start: 0.8649 (m-10) cc_final: 0.8420 (m-10) REVERT: H 204 TRP cc_start: 0.7535 (OUTLIER) cc_final: 0.7188 (t-100) REVERT: H 268 MET cc_start: 0.5839 (pp-130) cc_final: 0.5631 (pp-130) REVERT: H 293 LEU cc_start: 0.8520 (tp) cc_final: 0.8315 (mt) REVERT: H 439 ASN cc_start: 0.9374 (m110) cc_final: 0.8849 (t0) REVERT: H 443 ILE cc_start: 0.3543 (OUTLIER) cc_final: 0.3301 (tp) REVERT: H 471 ILE cc_start: 0.8938 (mp) cc_final: 0.8397 (tp) REVERT: H 474 MET cc_start: 0.5953 (pmm) cc_final: 0.5704 (pmm) outliers start: 159 outliers final: 67 residues processed: 444 average time/residue: 0.1810 time to fit residues: 127.9649 Evaluate side-chains 357 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 272 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 67 LYS Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 204 TRP Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 204 TRP Chi-restraints excluded: chain F residue 431 HIS Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 204 TRP Chi-restraints excluded: chain G residue 268 MET Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 431 HIS Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 204 TRP Chi-restraints excluded: chain H residue 431 HIS Chi-restraints excluded: chain H residue 443 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 366 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 156 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 217 optimal weight: 20.0000 chunk 202 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 360 optimal weight: 50.0000 chunk 326 optimal weight: 7.9990 chunk 342 optimal weight: 6.9990 chunk 317 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 ASN ** A 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN B 563 HIS D 10 ASN ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN E 97 ASN E 213 ASN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 ASN ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 GLN ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 ASN ** H 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.228305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.130822 restraints weight = 41564.310| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.32 r_work: 0.3203 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.004 0.038 32152 Z= 0.166 Angle : 0.669 8.946 43276 Z= 0.352 Chirality : 0.046 0.185 4840 Planarity : 0.003 0.036 5532 Dihedral : 5.161 23.259 4180 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.65 % Favored : 91.65 % Rotamer: Outliers : 3.68 % Allowed : 30.13 % Favored : 66.18 % 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: -2.18 (0.12), residues: 3844 helix: -0.80 (0.13), residues: 1528 sheet: -0.88 (0.20), residues: 556 loop : -2.20 (0.13), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 485 TYR 0.021 0.001 TYR F 202 PHE 0.013 0.001 PHE B 413 TRP 0.005 0.001 TRP G 204 HIS 0.007 0.001 HIS H 459 Details of bonding type rmsd covalent geometry : bond 0.00381 (32152) covalent geometry : angle 0.66859 (43276) hydrogen bonds : bond 0.04284 ( 1238) hydrogen bonds : angle 5.03163 ( 3477) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 310 time to evaluate : 0.893 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: C 379 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8373 (mm-30) REVERT: C 452 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7893 (ttp-170) REVERT: C 485 ARG cc_start: 0.8807 (tpt90) cc_final: 0.8472 (tpp80) REVERT: C 509 GLU cc_start: 0.8594 (tt0) cc_final: 0.8391 (tt0) REVERT: C 520 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8263 (pp) REVERT: A 42 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8397 (mm) REVERT: A 360 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7322 (mppt) REVERT: A 379 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8375 (mm-30) REVERT: A 452 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7910 (ttp-170) REVERT: A 483 ASN cc_start: 0.8438 (m-40) cc_final: 0.8233 (m-40) REVERT: A 520 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8211 (pp) REVERT: B 379 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8404 (mm-30) REVERT: B 452 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7921 (ttp-170) REVERT: B 520 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8233 (pp) REVERT: D 10 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.7208 (t0) REVERT: D 129 GLU cc_start: 0.8177 (mp0) cc_final: 0.7698 (tp30) REVERT: D 379 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8338 (mm-30) REVERT: D 520 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8181 (pp) REVERT: E 174 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7976 (pmtt) REVERT: E 202 TYR cc_start: 0.8728 (m-80) cc_final: 0.8484 (m-80) REVERT: E 204 TRP cc_start: 0.7504 (OUTLIER) cc_final: 0.7205 (t-100) REVERT: E 439 ASN cc_start: 0.9260 (m110) cc_final: 0.8735 (t0) REVERT: F 174 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7969 (pmtt) REVERT: F 204 TRP cc_start: 0.7598 (OUTLIER) cc_final: 0.7264 (t-100) REVERT: F 268 MET cc_start: 0.5484 (pp-130) cc_final: 0.5218 (pp-130) REVERT: F 307 LEU cc_start: 0.7348 (mm) cc_final: 0.6757 (pt) REVERT: F 439 ASN cc_start: 0.9371 (m110) cc_final: 0.8914 (t0) REVERT: F 440 GLN cc_start: 0.8618 (mt0) cc_final: 0.8172 (mt0) REVERT: G 204 TRP cc_start: 0.7577 (OUTLIER) cc_final: 0.7341 (t60) REVERT: G 471 ILE cc_start: 0.8834 (mm) cc_final: 0.8548 (tp) REVERT: G 474 MET cc_start: 0.5855 (pmm) cc_final: 0.5557 (pmm) REVERT: H 167 ASP cc_start: 0.7993 (t0) cc_final: 0.7549 (m-30) REVERT: H 174 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7970 (pmtt) REVERT: H 202 TYR cc_start: 0.8699 (m-80) cc_final: 0.8470 (m-80) REVERT: H 204 TRP cc_start: 0.7539 (OUTLIER) cc_final: 0.7203 (t-100) REVERT: H 405 PHE cc_start: 0.6678 (OUTLIER) cc_final: 0.6445 (t80) REVERT: H 439 ASN cc_start: 0.9369 (m110) cc_final: 0.8864 (t0) REVERT: H 443 ILE cc_start: 0.3930 (OUTLIER) cc_final: 0.3498 (tp) REVERT: H 471 ILE cc_start: 0.8827 (mp) cc_final: 0.8609 (mp) REVERT: H 474 MET cc_start: 0.5883 (pmm) cc_final: 0.5594 (pmm) outliers start: 130 outliers final: 50 residues processed: 424 average time/residue: 0.1832 time to fit residues: 123.4303 Evaluate side-chains 351 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 278 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 204 TRP Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 174 LYS Chi-restraints excluded: chain F residue 204 TRP Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 431 HIS Chi-restraints excluded: chain G residue 204 TRP Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain H residue 204 TRP Chi-restraints excluded: chain H residue 405 PHE Chi-restraints excluded: chain H residue 443 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 120 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 128 optimal weight: 0.0050 chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN A 155 ASN A 563 HIS ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.230459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.176159 restraints weight = 41848.322| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 2.45 r_work: 0.3409 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32152 Z= 0.125 Angle : 0.636 9.594 43276 Z= 0.333 Chirality : 0.045 0.180 4840 Planarity : 0.003 0.044 5532 Dihedral : 4.923 23.756 4180 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.91 % Favored : 91.47 % Rotamer: Outliers : 3.63 % Allowed : 29.51 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.90 (0.13), residues: 3844 helix: -0.49 (0.13), residues: 1560 sheet: -0.84 (0.21), residues: 556 loop : -2.10 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 485 TYR 0.011 0.001 TYR A 113 PHE 0.013 0.001 PHE H 112 TRP 0.004 0.001 TRP F 204 HIS 0.007 0.001 HIS F 459 Details of bonding type rmsd covalent geometry : bond 0.00270 (32152) covalent geometry : angle 0.63640 (43276) hydrogen bonds : bond 0.03747 ( 1238) hydrogen bonds : angle 4.82621 ( 3477) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 306 time to evaluate : 1.231 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: C 42 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8600 (mm) REVERT: C 379 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8170 (mm-30) REVERT: C 452 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8434 (ttp-170) REVERT: C 511 ASP cc_start: 0.8032 (t0) cc_final: 0.7511 (t0) REVERT: A 42 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8605 (mm) REVERT: A 360 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7545 (mppt) REVERT: A 379 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8136 (mm-30) REVERT: A 452 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8434 (ttp-170) REVERT: A 483 ASN cc_start: 0.8613 (m-40) cc_final: 0.8369 (m-40) REVERT: B 42 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8586 (mm) REVERT: B 379 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8159 (mm-30) REVERT: B 452 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8435 (ttp-170) REVERT: B 511 ASP cc_start: 0.8008 (t0) cc_final: 0.7541 (t0) REVERT: D 42 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8591 (mm) REVERT: D 483 ASN cc_start: 0.8534 (m-40) cc_final: 0.8321 (m-40) REVERT: D 511 ASP cc_start: 0.8030 (t0) cc_final: 0.7531 (t0) REVERT: E 167 ASP cc_start: 0.7971 (t0) cc_final: 0.7546 (m-30) REVERT: E 174 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7809 (pmtt) REVERT: E 439 ASN cc_start: 0.8773 (m110) cc_final: 0.8569 (t0) REVERT: F 204 TRP cc_start: 0.6773 (OUTLIER) cc_final: 0.6535 (t-100) REVERT: F 292 ILE cc_start: 0.8221 (mp) cc_final: 0.7961 (mm) REVERT: F 307 LEU cc_start: 0.7494 (mm) cc_final: 0.6913 (pt) REVERT: G 474 MET cc_start: 0.6225 (OUTLIER) cc_final: 0.5941 (pmm) REVERT: G 487 MET cc_start: -0.0117 (pp-130) cc_final: -0.0424 (pp-130) REVERT: H 106 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6246 (tm-30) REVERT: H 268 MET cc_start: 0.2626 (pp-130) cc_final: 0.2247 (pp-130) REVERT: H 443 ILE cc_start: 0.3017 (OUTLIER) cc_final: 0.2794 (tp) REVERT: H 474 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.6188 (pmm) outliers start: 128 outliers final: 57 residues processed: 416 average time/residue: 0.1823 time to fit residues: 121.0977 Evaluate side-chains 350 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 276 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 555 LYS Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain F residue 204 TRP Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 431 HIS Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 268 MET Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain G residue 474 MET Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 405 PHE Chi-restraints excluded: chain H residue 443 ILE Chi-restraints excluded: chain H residue 474 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 293 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 356 optimal weight: 50.0000 chunk 208 optimal weight: 0.3980 chunk 193 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 373 optimal weight: 50.0000 chunk 53 optimal weight: 0.8980 chunk 229 optimal weight: 50.0000 chunk 236 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 308 ASN ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 GLN ** H 260 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 = 0.4598 r_free = 0.4598 target = 0.229354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.165215 restraints weight = 41947.068| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.21 r_work: 0.3377 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32152 Z= 0.163 Angle : 0.654 9.396 43276 Z= 0.342 Chirality : 0.046 0.177 4840 Planarity : 0.003 0.061 5532 Dihedral : 4.927 24.978 4180 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.83 % Favored : 91.55 % Rotamer: Outliers : 4.17 % Allowed : 29.82 % Favored : 66.01 % 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: -1.80 (0.13), residues: 3844 helix: -0.38 (0.13), residues: 1560 sheet: -0.81 (0.21), residues: 556 loop : -2.07 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 485 TYR 0.023 0.001 TYR H 202 PHE 0.013 0.001 PHE A 315 TRP 0.004 0.001 TRP E 204 HIS 0.007 0.001 HIS F 459 Details of bonding type rmsd covalent geometry : bond 0.00380 (32152) covalent geometry : angle 0.65441 (43276) hydrogen bonds : bond 0.04038 ( 1238) hydrogen bonds : angle 4.77210 ( 3477) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 298 time to evaluate : 1.287 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: C 42 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8619 (mm) REVERT: C 67 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8200 (ptpt) REVERT: A 42 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8628 (mm) REVERT: A 48 LYS cc_start: 0.8622 (ttpt) cc_final: 0.8418 (ttpp) REVERT: A 67 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8185 (ptpt) REVERT: A 360 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7528 (mppt) REVERT: A 483 ASN cc_start: 0.8607 (m-40) cc_final: 0.8389 (m-40) REVERT: A 511 ASP cc_start: 0.8033 (t0) cc_final: 0.7604 (t0) REVERT: B 42 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8605 (mm) REVERT: B 48 LYS cc_start: 0.8628 (ttpt) cc_final: 0.8421 (ttpp) REVERT: B 511 ASP cc_start: 0.8006 (t0) cc_final: 0.7594 (t0) REVERT: D 42 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8635 (mm) REVERT: E 108 PHE cc_start: 0.8411 (m-10) cc_final: 0.8206 (m-10) REVERT: E 167 ASP cc_start: 0.8008 (t0) cc_final: 0.7574 (m-30) REVERT: E 174 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7751 (pmtt) REVERT: E 439 ASN cc_start: 0.8768 (m110) cc_final: 0.8556 (t0) REVERT: F 204 TRP cc_start: 0.6838 (OUTLIER) cc_final: 0.6610 (t-100) REVERT: F 268 MET cc_start: 0.2760 (pp-130) cc_final: 0.2310 (pp-130) REVERT: F 292 ILE cc_start: 0.8316 (mp) cc_final: 0.8077 (mm) REVERT: F 307 LEU cc_start: 0.7398 (mm) cc_final: 0.6826 (pt) REVERT: G 474 MET cc_start: 0.6251 (OUTLIER) cc_final: 0.5917 (pmm) REVERT: H 106 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6421 (tm-30) REVERT: H 167 ASP cc_start: 0.7890 (t0) cc_final: 0.7580 (m-30) REVERT: H 268 MET cc_start: 0.2930 (pp-130) cc_final: 0.2462 (pp-130) REVERT: H 443 ILE cc_start: 0.3124 (OUTLIER) cc_final: 0.2856 (tp) REVERT: H 474 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.6190 (pmm) outliers start: 147 outliers final: 86 residues processed: 429 average time/residue: 0.1945 time to fit residues: 133.0854 Evaluate side-chains 374 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 275 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 555 LYS Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 204 TRP Chi-restraints excluded: chain F residue 431 HIS Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain G residue 474 MET Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 315 ILE Chi-restraints excluded: chain H residue 431 HIS Chi-restraints excluded: chain H residue 443 ILE Chi-restraints excluded: chain H residue 474 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 105 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 350 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 152 optimal weight: 0.4980 chunk 303 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 ASN ** A 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 ASN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 308 ASN ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.230157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.167826 restraints weight = 41929.609| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.26 r_work: 0.3401 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32152 Z= 0.143 Angle : 0.655 10.286 43276 Z= 0.341 Chirality : 0.046 0.176 4840 Planarity : 0.004 0.071 5532 Dihedral : 4.917 26.612 4180 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.88 % Favored : 91.49 % Rotamer: Outliers : 3.80 % Allowed : 29.93 % Favored : 66.27 % 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: -1.68 (0.13), residues: 3844 helix: -0.25 (0.13), residues: 1556 sheet: -0.81 (0.20), residues: 588 loop : -2.02 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 232 TYR 0.009 0.001 TYR G 161 PHE 0.014 0.001 PHE H 108 TRP 0.004 0.001 TRP E 204 HIS 0.007 0.001 HIS F 459 Details of bonding type rmsd covalent geometry : bond 0.00323 (32152) covalent geometry : angle 0.65544 (43276) hydrogen bonds : bond 0.03783 ( 1238) hydrogen bonds : angle 4.70020 ( 3477) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 296 time to evaluate : 1.391 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: C 42 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8622 (mm) REVERT: A 42 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8614 (mm) REVERT: A 48 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8389 (ttpp) REVERT: A 360 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7492 (mppt) REVERT: A 483 ASN cc_start: 0.8588 (m-40) cc_final: 0.8377 (m-40) REVERT: A 511 ASP cc_start: 0.8005 (t0) cc_final: 0.7585 (t0) REVERT: B 42 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8605 (mm) REVERT: B 48 LYS cc_start: 0.8609 (ttpt) cc_final: 0.8395 (ttpp) REVERT: B 483 ASN cc_start: 0.8407 (m-40) cc_final: 0.8196 (m-40) REVERT: B 524 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8493 (ttp) REVERT: D 42 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8616 (mm) REVERT: D 388 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7899 (mt-10) REVERT: E 108 PHE cc_start: 0.8427 (m-10) cc_final: 0.8205 (m-10) REVERT: E 167 ASP cc_start: 0.8012 (t0) cc_final: 0.7507 (m-30) REVERT: F 268 MET cc_start: 0.2638 (pp-130) cc_final: 0.2053 (pp-130) REVERT: F 292 ILE cc_start: 0.8307 (mp) cc_final: 0.8084 (mm) REVERT: F 307 LEU cc_start: 0.7401 (mm) cc_final: 0.6943 (pt) REVERT: G 474 MET cc_start: 0.6319 (OUTLIER) cc_final: 0.5999 (pmm) REVERT: H 106 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6446 (tm-30) REVERT: H 167 ASP cc_start: 0.7951 (t0) cc_final: 0.7476 (m-30) REVERT: H 268 MET cc_start: 0.2850 (pp-130) cc_final: 0.2425 (pp-130) REVERT: H 443 ILE cc_start: 0.3248 (OUTLIER) cc_final: 0.2869 (tp) REVERT: H 474 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.6211 (pmm) outliers start: 134 outliers final: 85 residues processed: 419 average time/residue: 0.2071 time to fit residues: 139.3300 Evaluate side-chains 370 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 275 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 555 LYS Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 431 HIS Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain G residue 474 MET Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 315 ILE Chi-restraints excluded: chain H residue 431 HIS Chi-restraints excluded: chain H residue 443 ILE Chi-restraints excluded: chain H residue 474 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 325 optimal weight: 50.0000 chunk 25 optimal weight: 0.7980 chunk 355 optimal weight: 50.0000 chunk 147 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 357 optimal weight: 50.0000 chunk 71 optimal weight: 0.7980 chunk 285 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.230089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.167671 restraints weight = 42325.968| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.32 r_work: 0.3374 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 32152 Z= 0.170 Angle : 0.668 9.341 43276 Z= 0.347 Chirality : 0.046 0.173 4840 Planarity : 0.004 0.066 5532 Dihedral : 4.900 27.354 4180 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.35 % Favored : 91.02 % Rotamer: Outliers : 3.91 % Allowed : 29.85 % Favored : 66.24 % 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: -1.63 (0.13), residues: 3844 helix: -0.24 (0.13), residues: 1564 sheet: -0.80 (0.20), residues: 596 loop : -1.98 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 485 TYR 0.022 0.001 TYR H 202 PHE 0.015 0.001 PHE H 108 TRP 0.004 0.001 TRP H 204 HIS 0.007 0.001 HIS F 459 Details of bonding type rmsd covalent geometry : bond 0.00399 (32152) covalent geometry : angle 0.66758 (43276) hydrogen bonds : bond 0.04033 ( 1238) hydrogen bonds : angle 4.71093 ( 3477) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 287 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8574 (mm) REVERT: C 67 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8213 (ptpt) REVERT: A 42 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8609 (mm) REVERT: A 48 LYS cc_start: 0.8650 (ttpt) cc_final: 0.8440 (ttpp) REVERT: A 67 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8134 (ptpt) REVERT: A 360 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7549 (mppt) REVERT: A 483 ASN cc_start: 0.8621 (m-40) cc_final: 0.8411 (m-40) REVERT: A 511 ASP cc_start: 0.8104 (t0) cc_final: 0.7721 (t0) REVERT: B 42 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8604 (mm) REVERT: B 48 LYS cc_start: 0.8650 (ttpt) cc_final: 0.8435 (ttpp) REVERT: B 483 ASN cc_start: 0.8497 (m-40) cc_final: 0.8277 (m-40) REVERT: B 511 ASP cc_start: 0.8057 (t0) cc_final: 0.7677 (t0) REVERT: D 42 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8621 (mm) REVERT: E 108 PHE cc_start: 0.8456 (m-10) cc_final: 0.8221 (m-10) REVERT: E 167 ASP cc_start: 0.8226 (t0) cc_final: 0.7935 (m-30) REVERT: F 268 MET cc_start: 0.2702 (pp-130) cc_final: 0.2015 (pp-130) REVERT: F 292 ILE cc_start: 0.8334 (mp) cc_final: 0.8110 (mm) REVERT: F 307 LEU cc_start: 0.7399 (mm) cc_final: 0.6949 (pt) REVERT: G 474 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.5976 (pmm) REVERT: H 106 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6490 (tm-30) REVERT: H 268 MET cc_start: 0.2963 (pp-130) cc_final: 0.2725 (pp-130) REVERT: H 443 ILE cc_start: 0.3143 (OUTLIER) cc_final: 0.2752 (tp) REVERT: H 474 MET cc_start: 0.6449 (OUTLIER) cc_final: 0.6186 (pmm) outliers start: 138 outliers final: 104 residues processed: 412 average time/residue: 0.2127 time to fit residues: 140.4290 Evaluate side-chains 388 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 273 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 67 LYS Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 555 LYS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 431 HIS Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 204 TRP Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain G residue 431 HIS Chi-restraints excluded: chain G residue 474 MET Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 315 ILE Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 366 GLN Chi-restraints excluded: chain H residue 431 HIS Chi-restraints excluded: chain H residue 443 ILE Chi-restraints excluded: chain H residue 474 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 141 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 225 optimal weight: 40.0000 chunk 361 optimal weight: 50.0000 chunk 338 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 144 optimal weight: 0.4980 chunk 162 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 ASN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.231488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.177284 restraints weight = 41997.703| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.53 r_work: 0.3422 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32152 Z= 0.124 Angle : 0.650 10.308 43276 Z= 0.336 Chirality : 0.045 0.173 4840 Planarity : 0.003 0.061 5532 Dihedral : 4.798 29.830 4180 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.06 % Favored : 91.31 % Rotamer: Outliers : 3.37 % Allowed : 30.13 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.50 (0.13), residues: 3844 helix: -0.09 (0.13), residues: 1548 sheet: -0.79 (0.20), residues: 600 loop : -1.91 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 485 TYR 0.010 0.001 TYR F 240 PHE 0.017 0.001 PHE H 108 TRP 0.004 0.001 TRP H 204 HIS 0.008 0.001 HIS F 459 Details of bonding type rmsd covalent geometry : bond 0.00267 (32152) covalent geometry : angle 0.65050 (43276) hydrogen bonds : bond 0.03467 ( 1238) hydrogen bonds : angle 4.63518 ( 3477) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 289 time to evaluate : 1.270 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: C 42 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8589 (mm) REVERT: C 67 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8107 (ptpt) REVERT: C 388 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7915 (mt-10) REVERT: A 42 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8573 (mm) REVERT: A 48 LYS cc_start: 0.8607 (ttpt) cc_final: 0.8389 (ttpp) REVERT: A 67 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8105 (ptpt) REVERT: A 360 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7569 (mppt) REVERT: A 388 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7961 (mt-10) REVERT: A 483 ASN cc_start: 0.8580 (m-40) cc_final: 0.8377 (m-40) REVERT: B 42 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8577 (mm) REVERT: B 48 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8366 (ttpp) REVERT: B 388 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7937 (mt-10) REVERT: B 483 ASN cc_start: 0.8496 (m-40) cc_final: 0.8290 (m-40) REVERT: B 511 ASP cc_start: 0.8017 (t0) cc_final: 0.7581 (t0) REVERT: B 524 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8512 (ttp) REVERT: D 42 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8587 (mm) REVERT: E 108 PHE cc_start: 0.8383 (m-10) cc_final: 0.8150 (m-10) REVERT: F 268 MET cc_start: 0.2444 (pp-130) cc_final: 0.1768 (pp-130) REVERT: F 292 ILE cc_start: 0.8233 (mp) cc_final: 0.8015 (mm) REVERT: F 307 LEU cc_start: 0.7328 (mm) cc_final: 0.6961 (pt) REVERT: G 307 LEU cc_start: 0.7067 (mm) cc_final: 0.6438 (pt) REVERT: G 474 MET cc_start: 0.6124 (OUTLIER) cc_final: 0.5877 (pmm) REVERT: H 106 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6417 (tm-30) REVERT: H 443 ILE cc_start: 0.3347 (OUTLIER) cc_final: 0.2976 (tp) outliers start: 119 outliers final: 82 residues processed: 397 average time/residue: 0.2169 time to fit residues: 136.6510 Evaluate side-chains 376 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 283 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 155 GLN Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 431 HIS Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 204 TRP Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain G residue 431 HIS Chi-restraints excluded: chain G residue 474 MET Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 315 ILE Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 366 GLN Chi-restraints excluded: chain H residue 431 HIS Chi-restraints excluded: chain H residue 443 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 217 optimal weight: 30.0000 chunk 364 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 346 optimal weight: 1.9990 chunk 245 optimal weight: 9.9990 chunk 285 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 259 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 340 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 483 ASN E 141 GLN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 GLN ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.227863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159562 restraints weight = 41999.087| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.34 r_work: 0.3317 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 32152 Z= 0.218 Angle : 0.713 10.004 43276 Z= 0.368 Chirality : 0.047 0.175 4840 Planarity : 0.004 0.052 5532 Dihedral : 5.022 33.312 4180 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.66 % Favored : 90.71 % Rotamer: Outliers : 3.29 % Allowed : 30.36 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.58 (0.13), residues: 3844 helix: -0.22 (0.13), residues: 1544 sheet: -0.80 (0.20), residues: 600 loop : -1.90 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 485 TYR 0.022 0.001 TYR E 202 PHE 0.017 0.002 PHE H 108 TRP 0.004 0.001 TRP H 204 HIS 0.008 0.001 HIS F 459 Details of bonding type rmsd covalent geometry : bond 0.00526 (32152) covalent geometry : angle 0.71270 (43276) hydrogen bonds : bond 0.04446 ( 1238) hydrogen bonds : angle 4.78122 ( 3477) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 294 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8629 (mm) REVERT: C 67 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8324 (ptpt) REVERT: C 483 ASN cc_start: 0.8338 (m110) cc_final: 0.8137 (m-40) REVERT: A 42 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8663 (mm) REVERT: A 48 LYS cc_start: 0.8797 (ttpt) cc_final: 0.8535 (ttpp) REVERT: A 67 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8303 (ptpt) REVERT: A 360 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7718 (mppt) REVERT: B 42 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8664 (mm) REVERT: B 48 LYS cc_start: 0.8804 (ttpt) cc_final: 0.8544 (ttpp) REVERT: B 483 ASN cc_start: 0.8693 (m-40) cc_final: 0.8463 (m-40) REVERT: D 42 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8671 (mm) REVERT: E 108 PHE cc_start: 0.8642 (m-10) cc_final: 0.8367 (m-10) REVERT: F 232 ARG cc_start: 0.6570 (mtt180) cc_final: 0.6097 (mmt90) REVERT: F 268 MET cc_start: 0.3891 (pp-130) cc_final: 0.3174 (pp-130) REVERT: F 292 ILE cc_start: 0.8809 (mp) cc_final: 0.8567 (mm) REVERT: F 307 LEU cc_start: 0.7530 (mm) cc_final: 0.6997 (pt) REVERT: G 167 ASP cc_start: 0.8088 (t0) cc_final: 0.7716 (t70) REVERT: G 474 MET cc_start: 0.6275 (OUTLIER) cc_final: 0.5926 (pmm) REVERT: H 106 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6436 (tm-30) REVERT: H 443 ILE cc_start: 0.3913 (OUTLIER) cc_final: 0.3361 (tp) outliers start: 116 outliers final: 90 residues processed: 405 average time/residue: 0.2152 time to fit residues: 138.8458 Evaluate side-chains 373 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 273 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 366 GLN Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 155 GLN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 431 HIS Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 204 TRP Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain G residue 431 HIS Chi-restraints excluded: chain G residue 474 MET Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 315 ILE Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 366 GLN Chi-restraints excluded: chain H residue 431 HIS Chi-restraints excluded: chain H residue 443 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 326 optimal weight: 4.9990 chunk 370 optimal weight: 30.0000 chunk 222 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 264 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 chunk 367 optimal weight: 10.0000 chunk 371 optimal weight: 7.9990 chunk 190 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 ASN ** H 260 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 = 0.4577 r_free = 0.4577 target = 0.226627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.156640 restraints weight = 41614.797| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.12 r_work: 0.3335 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 32152 Z= 0.248 Angle : 0.748 11.918 43276 Z= 0.385 Chirality : 0.048 0.208 4840 Planarity : 0.004 0.057 5532 Dihedral : 5.152 36.828 4180 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.53 % Favored : 90.84 % Rotamer: Outliers : 3.26 % Allowed : 30.56 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.70 (0.13), residues: 3844 helix: -0.35 (0.13), residues: 1544 sheet: -0.86 (0.20), residues: 596 loop : -1.91 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 485 TYR 0.013 0.001 TYR G 161 PHE 0.018 0.002 PHE A 413 TRP 0.003 0.001 TRP G 204 HIS 0.008 0.001 HIS F 459 Details of bonding type rmsd covalent geometry : bond 0.00602 (32152) covalent geometry : angle 0.74800 (43276) hydrogen bonds : bond 0.04632 ( 1238) hydrogen bonds : angle 4.85022 ( 3477) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 282 time to evaluate : 1.341 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: C 42 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8655 (mm) REVERT: C 67 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8346 (ptpt) REVERT: A 42 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8697 (mm) REVERT: A 67 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8305 (ptpt) REVERT: A 360 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7641 (mppt) REVERT: A 483 ASN cc_start: 0.8727 (m-40) cc_final: 0.8501 (m-40) REVERT: B 42 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8674 (mm) REVERT: B 483 ASN cc_start: 0.8691 (m-40) cc_final: 0.8479 (m-40) REVERT: D 42 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8648 (mm) REVERT: E 108 PHE cc_start: 0.8680 (m-10) cc_final: 0.8408 (m-10) REVERT: F 232 ARG cc_start: 0.6675 (mtt180) cc_final: 0.6160 (mmt90) REVERT: F 268 MET cc_start: 0.4449 (pp-130) cc_final: 0.3675 (pp-130) REVERT: F 292 ILE cc_start: 0.8893 (mp) cc_final: 0.8659 (mm) REVERT: F 307 LEU cc_start: 0.7556 (mm) cc_final: 0.7003 (pt) REVERT: G 167 ASP cc_start: 0.8089 (t0) cc_final: 0.7740 (t70) REVERT: G 307 LEU cc_start: 0.7297 (mm) cc_final: 0.6577 (pt) REVERT: G 474 MET cc_start: 0.6273 (OUTLIER) cc_final: 0.5941 (pmm) REVERT: H 106 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6374 (tm-30) REVERT: H 443 ILE cc_start: 0.4098 (OUTLIER) cc_final: 0.3528 (tp) outliers start: 115 outliers final: 96 residues processed: 388 average time/residue: 0.2164 time to fit residues: 133.5240 Evaluate side-chains 383 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 277 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 67 LYS Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 366 GLN Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 439 ASN Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 155 GLN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 431 HIS Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 204 TRP Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain G residue 431 HIS Chi-restraints excluded: chain G residue 474 MET Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 315 ILE Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 366 GLN Chi-restraints excluded: chain H residue 431 HIS Chi-restraints excluded: chain H residue 443 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 276 optimal weight: 30.0000 chunk 328 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 271 optimal weight: 40.0000 chunk 64 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 220 optimal weight: 7.9990 chunk 348 optimal weight: 0.9990 chunk 264 optimal weight: 50.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 483 ASN D 79 ASN D 483 ASN ** E 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 ASN ** H 260 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 = 0.4591 r_free = 0.4591 target = 0.228598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.166318 restraints weight = 41862.025| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.41 r_work: 0.3336 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 32152 Z= 0.239 Angle : 0.826 59.200 43276 Z= 0.445 Chirality : 0.054 1.809 4840 Planarity : 0.004 0.056 5532 Dihedral : 5.134 35.444 4180 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.61 % Favored : 90.76 % Rotamer: Outliers : 3.17 % Allowed : 30.44 % Favored : 66.38 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.70 (0.13), residues: 3844 helix: -0.35 (0.13), residues: 1544 sheet: -0.88 (0.20), residues: 596 loop : -1.92 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 485 TYR 0.013 0.001 TYR G 161 PHE 0.017 0.002 PHE A 413 TRP 0.003 0.001 TRP G 204 HIS 0.008 0.001 HIS F 459 Details of bonding type rmsd covalent geometry : bond 0.00574 (32152) covalent geometry : angle 0.82562 (43276) hydrogen bonds : bond 0.04585 ( 1238) hydrogen bonds : angle 4.85268 ( 3477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9906.26 seconds wall clock time: 170 minutes 22.64 seconds (10222.64 seconds total)