Starting phenix.real_space_refine on Fri Jun 27 07:42:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jqb_36563/06_2025/8jqb_36563.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jqb_36563/06_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_36563/06_2025/8jqb_36563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jqb_36563/06_2025/8jqb_36563.map" model { file = "/net/cci-nas-00/data/ceres_data/8jqb_36563/06_2025/8jqb_36563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jqb_36563/06_2025/8jqb_36563.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.63, per 1000 atoms: 0.56 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: 6.66 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 3.51 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: 11.52 Time building geometry restraints manager: 8.06 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: 0.04 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: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.330 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 65.110 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (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 TRP 0.021 0.003 TRP F 204 HIS 0.016 0.001 HIS F 459 PHE 0.042 0.002 PHE H 112 TYR 0.018 0.001 TYR G 202 ARG 0.019 0.001 ARG F 232 Details of bonding type rmsd hydrogen bonds : bond 0.17055 ( 1238) hydrogen bonds : angle 7.23261 ( 3477) covalent geometry : bond 0.00494 (32152) covalent geometry : angle 1.15602 (43276) *********************** 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 : 3.493 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: 0.4089 time to fit residues: 202.9033 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 : 3.664 ------------------------------------------------------------------------------- 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 320 optimal weight: 6.9990 chunk 288 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.2980 chunk 153 optimal weight: 4.9990 chunk 297 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 221 optimal weight: 0.0570 chunk 345 optimal weight: 0.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 ASN A 563 HIS B 10 ASN ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN B 563 HIS D 10 ASN ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 226 HIS ** G 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.231810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.165004 restraints weight = 42036.344| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.25 r_work: 0.3430 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 32152 Z= 0.133 Angle : 0.662 9.227 43276 Z= 0.351 Chirality : 0.046 0.191 4840 Planarity : 0.004 0.040 5532 Dihedral : 5.271 50.100 4194 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.36 % Favored : 91.91 % Rotamer: Outliers : 2.38 % Allowed : 30.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.12), residues: 3844 helix: -1.14 (0.12), residues: 1536 sheet: -0.48 (0.21), residues: 572 loop : -2.36 (0.13), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 204 HIS 0.007 0.001 HIS G 459 PHE 0.009 0.001 PHE B 413 TYR 0.025 0.001 TYR E 202 ARG 0.004 0.000 ARG G 232 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 1238) hydrogen bonds : angle 5.20157 ( 3477) covalent geometry : bond 0.00283 (32152) covalent geometry : angle 0.66249 (43276) *********************** 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 380 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 296 time to evaluate : 3.383 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 42 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8603 (mm) REVERT: A 42 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8605 (mm) REVERT: A 511 ASP cc_start: 0.7934 (t0) cc_final: 0.7547 (t0) REVERT: B 42 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8589 (mm) REVERT: B 511 ASP cc_start: 0.7916 (t0) cc_final: 0.7509 (t0) REVERT: D 15 GLU cc_start: 0.7690 (tp30) cc_final: 0.7448 (mm-30) REVERT: E 439 ASN cc_start: 0.8973 (m110) cc_final: 0.8568 (t0) REVERT: F 174 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7855 (pmtt) REVERT: F 268 MET cc_start: 0.3157 (pp-130) cc_final: 0.2861 (pp-130) REVERT: F 307 LEU cc_start: 0.7489 (mm) cc_final: 0.6772 (pt) REVERT: F 439 ASN cc_start: 0.9107 (m110) cc_final: 0.8773 (t0) REVERT: G 474 MET cc_start: 0.5578 (pmm) cc_final: 0.5208 (pmm) REVERT: H 108 PHE cc_start: 0.8477 (m-10) cc_final: 0.8276 (m-10) REVERT: H 167 ASP cc_start: 0.7714 (t0) cc_final: 0.7446 (t0) REVERT: H 188 LYS cc_start: 0.8474 (mmmt) cc_final: 0.8142 (mmmt) REVERT: H 268 MET cc_start: 0.3137 (pp-130) cc_final: 0.2879 (pp-130) REVERT: H 293 LEU cc_start: 0.7497 (tp) cc_final: 0.7290 (mt) REVERT: H 439 ASN cc_start: 0.9031 (m110) cc_final: 0.8645 (t0) REVERT: H 471 ILE cc_start: 0.8226 (mp) cc_final: 0.7359 (mp) REVERT: H 474 MET cc_start: 0.6205 (pmm) cc_final: 0.5935 (pmm) outliers start: 84 outliers final: 28 residues processed: 371 average time/residue: 0.4419 time to fit residues: 263.4022 Evaluate side-chains 285 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 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 484 GLU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 64 ASP 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 B residue 42 LEU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS 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 174 LYS Chi-restraints excluded: chain F residue 431 HIS Chi-restraints excluded: chain G residue 349 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 154 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 349 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 chunk 214 optimal weight: 50.0000 chunk 95 optimal weight: 1.9990 chunk 212 optimal weight: 30.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN C 363 ASN A 563 HIS B 10 ASN ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS D 10 ASN ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN E 213 ASN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS F 213 ASN ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 GLN G 459 HIS ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.230640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3937 r_free = 0.3937 target = 0.161074 restraints weight = 42185.636| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.98 r_work: 0.3427 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32152 Z= 0.154 Angle : 0.650 8.682 43276 Z= 0.342 Chirality : 0.046 0.185 4840 Planarity : 0.003 0.036 5532 Dihedral : 4.960 23.326 4180 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.80 % Favored : 91.49 % Rotamer: Outliers : 3.60 % Allowed : 29.00 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.13), residues: 3844 helix: -0.58 (0.13), residues: 1504 sheet: -0.59 (0.21), residues: 540 loop : -2.17 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 204 HIS 0.007 0.001 HIS H 459 PHE 0.014 0.001 PHE H 405 TYR 0.025 0.001 TYR G 202 ARG 0.006 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 1238) hydrogen bonds : angle 4.94898 ( 3477) covalent geometry : bond 0.00348 (32152) covalent geometry : angle 0.65030 (43276) *********************** 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 418 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 291 time to evaluate : 3.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8626 (mm) REVERT: C 309 GLN cc_start: 0.8189 (tt0) cc_final: 0.7947 (tt0) REVERT: C 520 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8459 (pp) REVERT: A 42 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8627 (mm) REVERT: A 511 ASP cc_start: 0.8151 (t0) cc_final: 0.7777 (t0) REVERT: A 520 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8422 (pp) REVERT: A 535 HIS cc_start: 0.8830 (t-90) cc_final: 0.8472 (t-90) REVERT: B 42 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8613 (mm) REVERT: B 511 ASP cc_start: 0.8109 (t0) cc_final: 0.7723 (t0) REVERT: B 520 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8451 (pp) REVERT: D 42 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8623 (mm) REVERT: D 520 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8396 (pp) REVERT: E 167 ASP cc_start: 0.7875 (t0) cc_final: 0.7574 (m-30) REVERT: E 439 ASN cc_start: 0.9191 (m110) cc_final: 0.8689 (t0) REVERT: F 204 TRP cc_start: 0.6995 (OUTLIER) cc_final: 0.6792 (t-100) REVERT: F 268 MET cc_start: 0.3849 (pp-130) cc_final: 0.3638 (pp-130) REVERT: F 307 LEU cc_start: 0.7562 (mm) cc_final: 0.6931 (pt) REVERT: F 439 ASN cc_start: 0.9307 (m110) cc_final: 0.8880 (t0) REVERT: G 471 ILE cc_start: 0.8462 (mm) cc_final: 0.8124 (tp) REVERT: G 474 MET cc_start: 0.6255 (pmm) cc_final: 0.5895 (pmm) REVERT: H 293 LEU cc_start: 0.7991 (tp) cc_final: 0.7645 (mt) REVERT: H 439 ASN cc_start: 0.9224 (m110) cc_final: 0.8738 (t0) REVERT: H 474 MET cc_start: 0.6324 (pmm) cc_final: 0.5968 (pmm) REVERT: H 487 MET cc_start: -0.0308 (pp-130) cc_final: -0.0574 (pp-130) outliers start: 127 outliers final: 51 residues processed: 405 average time/residue: 0.4261 time to fit residues: 278.4309 Evaluate side-chains 326 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 266 time to evaluate : 3.621 ------------------------------------------------------------------------------- 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 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 426 THR 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 67 LYS Chi-restraints excluded: chain A residue 132 ASN 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 426 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 520 ILE 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 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 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 520 ILE 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 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 329 ASP 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 520 ILE Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 443 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 349 LEU Chi-restraints excluded: chain H residue 405 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 230 optimal weight: 50.0000 chunk 330 optimal weight: 6.9990 chunk 341 optimal weight: 20.0000 chunk 295 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 374 optimal weight: 50.0000 chunk 174 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN ** A 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN ** E 260 ASN ** 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 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 = 0.4582 r_free = 0.4582 target = 0.226023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3893 r_free = 0.3893 target = 0.157463 restraints weight = 41779.520| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.99 r_work: 0.3327 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 32152 Z= 0.323 Angle : 0.778 9.413 43276 Z= 0.404 Chirality : 0.050 0.181 4840 Planarity : 0.005 0.070 5532 Dihedral : 5.365 25.813 4180 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.53 % Favored : 90.84 % Rotamer: Outliers : 4.62 % Allowed : 28.85 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.13), residues: 3844 helix: -0.68 (0.13), residues: 1528 sheet: -0.91 (0.21), residues: 536 loop : -2.15 (0.13), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 126 HIS 0.007 0.002 HIS C 415 PHE 0.025 0.002 PHE A 413 TYR 0.021 0.002 TYR E 202 ARG 0.007 0.001 ARG D 485 Details of bonding type rmsd hydrogen bonds : bond 0.05501 ( 1238) hydrogen bonds : angle 5.10233 ( 3477) covalent geometry : bond 0.00789 (32152) covalent geometry : angle 0.77802 (43276) *********************** 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 467 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 304 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8680 (mm) REVERT: C 485 ARG cc_start: 0.8901 (tpt90) cc_final: 0.8631 (tpp80) REVERT: A 42 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8688 (mm) REVERT: A 67 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8408 (ptpt) REVERT: A 309 GLN cc_start: 0.8117 (tt0) cc_final: 0.7916 (tt0) REVERT: A 483 ASN cc_start: 0.8635 (m-40) cc_final: 0.8398 (m-40) REVERT: B 42 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8698 (mm) REVERT: B 67 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8331 (ptpt) REVERT: B 483 ASN cc_start: 0.8704 (m-40) cc_final: 0.8479 (m-40) REVERT: D 42 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8716 (mm) REVERT: D 67 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8338 (ptpt) REVERT: D 129 GLU cc_start: 0.8232 (mp0) cc_final: 0.8010 (mp0) REVERT: D 483 ASN cc_start: 0.8703 (m-40) cc_final: 0.8470 (m-40) REVERT: E 167 ASP cc_start: 0.8115 (t0) cc_final: 0.7590 (m-30) REVERT: E 439 ASN cc_start: 0.9270 (m110) cc_final: 0.8738 (t0) REVERT: F 174 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7886 (pmtt) REVERT: F 204 TRP cc_start: 0.7194 (OUTLIER) cc_final: 0.6858 (t-100) REVERT: F 292 ILE cc_start: 0.8942 (mp) cc_final: 0.8685 (mm) REVERT: F 307 LEU cc_start: 0.7486 (mm) cc_final: 0.6840 (pt) REVERT: F 439 ASN cc_start: 0.9387 (m110) cc_final: 0.8903 (t0) REVERT: F 440 GLN cc_start: 0.8400 (mt0) cc_final: 0.8018 (mt0) REVERT: G 167 ASP cc_start: 0.8033 (t0) cc_final: 0.7704 (t70) REVERT: G 474 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.5795 (pmm) REVERT: H 106 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6296 (tm-30) REVERT: H 268 MET cc_start: 0.4278 (pp-130) cc_final: 0.3826 (pp-130) REVERT: H 293 LEU cc_start: 0.8341 (tp) cc_final: 0.7973 (mt) REVERT: H 439 ASN cc_start: 0.9331 (m110) cc_final: 0.8801 (t0) REVERT: H 474 MET cc_start: 0.6337 (OUTLIER) cc_final: 0.6031 (pmm) REVERT: H 487 MET cc_start: -0.0333 (pp-130) cc_final: -0.0546 (pp-130) outliers start: 163 outliers final: 84 residues processed: 442 average time/residue: 0.4379 time to fit residues: 307.0214 Evaluate side-chains 368 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 272 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 132 ASN 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 407 GLU Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 527 ILE 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 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 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 407 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 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 407 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 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 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 407 GLU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 447 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 268 MET 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 174 LYS 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 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 431 HIS 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 199 optimal weight: 1.9990 chunk 366 optimal weight: 20.0000 chunk 308 optimal weight: 4.9990 chunk 254 optimal weight: 10.0000 chunk 249 optimal weight: 1.9990 chunk 225 optimal weight: 0.2980 chunk 378 optimal weight: 50.0000 chunk 146 optimal weight: 0.9990 chunk 373 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 340 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 309 GLN ** A 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 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 125 GLN ** H 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.230395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.166789 restraints weight = 42220.317| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.29 r_work: 0.3379 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32152 Z= 0.140 Angle : 0.653 9.210 43276 Z= 0.341 Chirality : 0.046 0.176 4840 Planarity : 0.004 0.064 5532 Dihedral : 5.019 25.371 4180 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.62 % Favored : 91.75 % Rotamer: Outliers : 3.09 % Allowed : 30.16 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.13), residues: 3844 helix: -0.43 (0.13), residues: 1556 sheet: -0.88 (0.21), residues: 556 loop : -2.06 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 204 HIS 0.007 0.001 HIS F 459 PHE 0.013 0.001 PHE H 108 TYR 0.026 0.001 TYR G 202 ARG 0.006 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 1238) hydrogen bonds : angle 4.80727 ( 3477) covalent geometry : bond 0.00314 (32152) covalent geometry : angle 0.65264 (43276) *********************** 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 400 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 291 time to evaluate : 3.997 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: A 42 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8624 (mm) REVERT: A 48 LYS cc_start: 0.8647 (ttpt) cc_final: 0.8418 (ttpp) REVERT: A 483 ASN cc_start: 0.8544 (m-40) cc_final: 0.8337 (m-40) REVERT: A 511 ASP cc_start: 0.8035 (t0) cc_final: 0.7635 (t0) REVERT: B 511 ASP cc_start: 0.8007 (t0) cc_final: 0.7601 (t0) REVERT: D 42 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8594 (mm) REVERT: E 108 PHE cc_start: 0.8423 (m-10) cc_final: 0.8202 (m-10) REVERT: E 167 ASP cc_start: 0.8058 (t0) cc_final: 0.7526 (m-30) REVERT: E 439 ASN cc_start: 0.8796 (m110) cc_final: 0.8562 (t0) REVERT: F 204 TRP cc_start: 0.6857 (OUTLIER) cc_final: 0.6626 (t-100) REVERT: F 268 MET cc_start: 0.2796 (pp-130) cc_final: 0.2411 (pp-130) REVERT: F 292 ILE cc_start: 0.8380 (mp) cc_final: 0.8144 (mm) REVERT: F 307 LEU cc_start: 0.7426 (mm) cc_final: 0.6796 (pt) REVERT: G 474 MET cc_start: 0.6251 (OUTLIER) cc_final: 0.5936 (pmm) REVERT: H 167 ASP cc_start: 0.7915 (t0) cc_final: 0.7467 (m-30) REVERT: H 268 MET cc_start: 0.2903 (pp-130) cc_final: 0.2388 (pp-130) REVERT: H 293 LEU cc_start: 0.7462 (tp) cc_final: 0.7181 (mt) REVERT: H 474 MET cc_start: 0.6521 (OUTLIER) cc_final: 0.6240 (pmm) outliers start: 109 outliers final: 56 residues processed: 388 average time/residue: 0.4546 time to fit residues: 282.0907 Evaluate side-chains 329 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 268 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 132 ASN 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 373 GLU Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 132 ASN 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 555 LYS 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 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 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 67 LYS Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 324 LEU 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 555 LYS Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 268 MET 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 431 HIS 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 54 PHE Chi-restraints excluded: chain H residue 315 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 138 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 312 optimal weight: 9.9990 chunk 140 optimal weight: 0.6980 chunk 141 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 370 optimal weight: 30.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN ** A 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** 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 = 0.4593 r_free = 0.4593 target = 0.228615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.166721 restraints weight = 42455.150| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.44 r_work: 0.3332 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 32152 Z= 0.231 Angle : 0.704 9.806 43276 Z= 0.366 Chirality : 0.048 0.172 4840 Planarity : 0.004 0.059 5532 Dihedral : 5.116 26.325 4180 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.69 % Favored : 90.69 % Rotamer: Outliers : 4.05 % Allowed : 29.48 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.13), residues: 3844 helix: -0.45 (0.13), residues: 1552 sheet: -0.94 (0.20), residues: 588 loop : -2.04 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 204 HIS 0.007 0.001 HIS F 459 PHE 0.018 0.002 PHE A 413 TYR 0.023 0.001 TYR H 202 ARG 0.007 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.04615 ( 1238) hydrogen bonds : angle 4.84095 ( 3477) covalent geometry : bond 0.00559 (32152) covalent geometry : angle 0.70428 (43276) *********************** 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 428 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 285 time to evaluate : 5.849 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: 0.9062 (OUTLIER) cc_final: 0.8660 (mm) REVERT: A 42 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8683 (mm) REVERT: A 48 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8480 (ttpp) REVERT: A 483 ASN cc_start: 0.8662 (m-40) cc_final: 0.8430 (m-40) REVERT: A 511 ASP cc_start: 0.8184 (t0) cc_final: 0.7778 (t0) REVERT: B 42 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8643 (mm) REVERT: B 483 ASN cc_start: 0.8524 (m-40) cc_final: 0.8317 (m-40) REVERT: D 42 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8666 (mm) REVERT: E 108 PHE cc_start: 0.8438 (m-10) cc_final: 0.8218 (m-10) REVERT: E 167 ASP cc_start: 0.8259 (t0) cc_final: 0.7929 (m-30) REVERT: F 268 MET cc_start: 0.2806 (pp-130) cc_final: 0.2138 (pp-130) REVERT: F 292 ILE cc_start: 0.8309 (mp) cc_final: 0.8086 (mm) REVERT: F 307 LEU cc_start: 0.7412 (mm) cc_final: 0.6931 (pt) REVERT: G 167 ASP cc_start: 0.7998 (t0) cc_final: 0.7692 (t70) REVERT: G 474 MET cc_start: 0.6346 (OUTLIER) cc_final: 0.6043 (pmm) REVERT: H 106 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6430 (tm-30) REVERT: H 167 ASP cc_start: 0.7981 (t0) cc_final: 0.7506 (m-30) REVERT: H 268 MET cc_start: 0.2926 (pp-130) cc_final: 0.2471 (pp-130) REVERT: H 293 LEU cc_start: 0.7374 (tp) cc_final: 0.7069 (mt) REVERT: H 474 MET cc_start: 0.6566 (OUTLIER) cc_final: 0.6277 (pmm) outliers start: 143 outliers final: 97 residues processed: 412 average time/residue: 0.6224 time to fit residues: 408.1947 Evaluate side-chains 365 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 261 time to evaluate : 3.929 ------------------------------------------------------------------------------- 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 128 SER Chi-restraints excluded: chain C residue 132 ASN 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 A residue 9 LYS 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 426 THR Chi-restraints excluded: chain A residue 447 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 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 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 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 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 309 GLN 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 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 163 LYS Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 268 MET 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 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 326 THR 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 191 LEU Chi-restraints excluded: chain H residue 315 ILE Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 431 HIS 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 240 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 360 optimal weight: 50.0000 chunk 235 optimal weight: 7.9990 chunk 206 optimal weight: 10.0000 chunk 260 optimal weight: 20.0000 chunk 192 optimal weight: 0.0670 chunk 40 optimal weight: 3.9990 chunk 268 optimal weight: 0.4980 chunk 366 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN A 155 ASN A 309 GLN B 155 ASN B 309 GLN ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.229858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3941 r_free = 0.3941 target = 0.161786 restraints weight = 41756.130| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.05 r_work: 0.3405 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32152 Z= 0.134 Angle : 0.657 9.977 43276 Z= 0.341 Chirality : 0.046 0.172 4840 Planarity : 0.004 0.065 5532 Dihedral : 4.896 27.831 4180 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.01 % Favored : 91.36 % Rotamer: Outliers : 3.49 % Allowed : 30.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 3844 helix: -0.25 (0.13), residues: 1556 sheet: -0.90 (0.20), residues: 596 loop : -1.99 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 204 HIS 0.008 0.001 HIS F 459 PHE 0.015 0.001 PHE H 108 TYR 0.029 0.001 TYR G 202 ARG 0.006 0.000 ARG H 232 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 1238) hydrogen bonds : angle 4.68795 ( 3477) covalent geometry : bond 0.00297 (32152) covalent geometry : angle 0.65667 (43276) *********************** 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 403 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 280 time to evaluate : 3.747 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: 0.9033 (OUTLIER) cc_final: 0.8617 (mm) REVERT: A 42 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8610 (mm) REVERT: A 48 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8468 (ttpp) REVERT: B 42 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8601 (mm) REVERT: D 42 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8607 (mm) REVERT: E 108 PHE cc_start: 0.8611 (m-10) cc_final: 0.8332 (m-10) REVERT: F 268 MET cc_start: 0.3663 (pp-130) cc_final: 0.2976 (pp-130) REVERT: F 292 ILE cc_start: 0.8736 (mp) cc_final: 0.8504 (mm) REVERT: F 307 LEU cc_start: 0.7527 (mm) cc_final: 0.7040 (pt) REVERT: G 474 MET cc_start: 0.6374 (OUTLIER) cc_final: 0.6007 (pmm) REVERT: H 106 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6473 (tm-30) REVERT: H 167 ASP cc_start: 0.7994 (t0) cc_final: 0.7544 (m-30) REVERT: H 268 MET cc_start: 0.4089 (pp-130) cc_final: 0.3639 (pp-130) REVERT: H 293 LEU cc_start: 0.7969 (tp) cc_final: 0.7536 (mt) outliers start: 123 outliers final: 84 residues processed: 393 average time/residue: 0.4690 time to fit residues: 294.2035 Evaluate side-chains 352 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 262 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 132 ASN 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 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 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 450 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 309 GLN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 324 LEU 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 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 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 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 555 LYS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 268 MET 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 191 LEU Chi-restraints excluded: chain F residue 431 HIS 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 474 MET Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 54 PHE Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 315 ILE Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 431 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 134 optimal weight: 5.9990 chunk 374 optimal weight: 7.9990 chunk 216 optimal weight: 0.0070 chunk 205 optimal weight: 10.0000 chunk 275 optimal weight: 50.0000 chunk 193 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 373 optimal weight: 0.8980 chunk 348 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 324 optimal weight: 30.0000 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN B 309 GLN ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.229116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.167394 restraints weight = 42057.754| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.32 r_work: 0.3378 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32152 Z= 0.171 Angle : 0.677 12.165 43276 Z= 0.350 Chirality : 0.046 0.240 4840 Planarity : 0.004 0.059 5532 Dihedral : 4.909 30.490 4180 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.66 % Favored : 90.71 % Rotamer: Outliers : 3.20 % Allowed : 30.30 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.13), residues: 3844 helix: -0.24 (0.13), residues: 1560 sheet: -0.87 (0.20), residues: 596 loop : -2.01 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 204 HIS 0.008 0.001 HIS F 459 PHE 0.015 0.001 PHE H 108 TYR 0.024 0.001 TYR E 202 ARG 0.010 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 1238) hydrogen bonds : angle 4.69606 ( 3477) covalent geometry : bond 0.00402 (32152) covalent geometry : angle 0.67734 (43276) *********************** 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 390 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 277 time to evaluate : 3.338 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: 0.9021 (OUTLIER) cc_final: 0.8605 (mm) REVERT: A 42 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8602 (mm) REVERT: A 48 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8413 (ttpp) REVERT: B 42 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8582 (mm) REVERT: D 42 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8602 (mm) REVERT: E 108 PHE cc_start: 0.8406 (m-10) cc_final: 0.8182 (m-10) REVERT: F 232 ARG cc_start: 0.5620 (mtt180) cc_final: 0.5240 (mmt90) REVERT: F 268 MET cc_start: 0.2705 (pp-130) cc_final: 0.1916 (pp-130) REVERT: F 292 ILE cc_start: 0.8350 (mp) cc_final: 0.8123 (mm) REVERT: F 307 LEU cc_start: 0.7409 (mm) cc_final: 0.6990 (pt) REVERT: G 167 ASP cc_start: 0.7968 (t0) cc_final: 0.7642 (t70) REVERT: G 474 MET cc_start: 0.6260 (OUTLIER) cc_final: 0.5989 (pmm) REVERT: H 106 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6547 (tm-30) REVERT: H 167 ASP cc_start: 0.7936 (t0) cc_final: 0.7532 (m-30) REVERT: H 268 MET cc_start: 0.3046 (pp-130) cc_final: 0.2752 (pp-130) REVERT: H 293 LEU cc_start: 0.7330 (tp) cc_final: 0.7001 (mt) outliers start: 113 outliers final: 93 residues processed: 381 average time/residue: 0.4381 time to fit residues: 263.3918 Evaluate side-chains 368 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 269 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU 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 9 LYS 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 309 GLN 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 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 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 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 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 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 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 555 LYS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 268 MET 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 442 ILE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 431 HIS 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 44 LYS 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 191 LEU 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 471 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 12 optimal weight: 0.6980 chunk 252 optimal weight: 3.9990 chunk 324 optimal weight: 30.0000 chunk 203 optimal weight: 6.9990 chunk 348 optimal weight: 0.9980 chunk 302 optimal weight: 30.0000 chunk 240 optimal weight: 7.9990 chunk 169 optimal weight: 2.9990 chunk 378 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 290 optimal weight: 0.0470 overall best weight: 1.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** 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 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 = 0.4596 r_free = 0.4596 target = 0.228897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.167594 restraints weight = 42055.916| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.41 r_work: 0.3357 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32152 Z= 0.186 Angle : 0.690 10.711 43276 Z= 0.358 Chirality : 0.047 0.187 4840 Planarity : 0.004 0.057 5532 Dihedral : 4.957 32.890 4180 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.74 % Favored : 90.61 % Rotamer: Outliers : 3.46 % Allowed : 30.39 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.13), residues: 3844 helix: -0.25 (0.13), residues: 1560 sheet: -0.87 (0.20), residues: 596 loop : -1.98 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 204 HIS 0.008 0.001 HIS F 459 PHE 0.017 0.001 PHE H 108 TYR 0.028 0.001 TYR G 202 ARG 0.011 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 1238) hydrogen bonds : angle 4.73886 ( 3477) covalent geometry : bond 0.00443 (32152) covalent geometry : angle 0.69031 (43276) *********************** 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 407 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 285 time to evaluate : 3.457 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 42 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8615 (mm) REVERT: C 483 ASN cc_start: 0.8439 (m-40) cc_final: 0.8218 (m-40) REVERT: A 42 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8613 (mm) REVERT: A 48 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8450 (ttpp) REVERT: B 42 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8598 (mm) REVERT: D 42 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8617 (mm) REVERT: E 108 PHE cc_start: 0.8476 (m-10) cc_final: 0.8264 (m-10) REVERT: F 232 ARG cc_start: 0.5526 (mtt180) cc_final: 0.5061 (mmt90) REVERT: F 268 MET cc_start: 0.2702 (pp-130) cc_final: 0.2004 (pp-130) REVERT: F 292 ILE cc_start: 0.8338 (mp) cc_final: 0.8108 (mm) REVERT: F 307 LEU cc_start: 0.7416 (mm) cc_final: 0.7027 (pt) REVERT: G 167 ASP cc_start: 0.8010 (t0) cc_final: 0.7693 (t70) REVERT: G 474 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.5937 (pmm) REVERT: H 106 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6564 (tm-30) REVERT: H 167 ASP cc_start: 0.7947 (t0) cc_final: 0.7551 (m-30) REVERT: H 268 MET cc_start: 0.2966 (pp-130) cc_final: 0.2751 (pp-130) REVERT: H 293 LEU cc_start: 0.7272 (tp) cc_final: 0.6903 (mt) outliers start: 122 outliers final: 101 residues processed: 394 average time/residue: 0.4456 time to fit residues: 279.6521 Evaluate side-chains 379 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 272 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU 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 9 LYS 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 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 450 LEU Chi-restraints excluded: chain A residue 524 MET 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 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 456 LEU 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 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 306 LEU Chi-restraints excluded: chain D residue 309 GLN 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 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 268 MET 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 442 ILE 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 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 44 LYS Chi-restraints excluded: chain H residue 54 PHE 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 191 LEU 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 471 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 349 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 211 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 208 optimal weight: 0.0060 chunk 181 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 ASN ** 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** ** 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 = 0.4625 r_free = 0.4625 target = 0.231308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.166351 restraints weight = 42167.636| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.25 r_work: 0.3386 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32152 Z= 0.135 Angle : 0.661 9.972 43276 Z= 0.344 Chirality : 0.046 0.178 4840 Planarity : 0.004 0.056 5532 Dihedral : 4.816 36.805 4180 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.40 % Favored : 90.95 % Rotamer: Outliers : 2.98 % Allowed : 30.78 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.13), residues: 3844 helix: -0.13 (0.13), residues: 1564 sheet: -0.78 (0.20), residues: 596 loop : -1.96 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 204 HIS 0.008 0.001 HIS F 459 PHE 0.019 0.001 PHE H 108 TYR 0.021 0.001 TYR H 202 ARG 0.012 0.000 ARG D 485 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 1238) hydrogen bonds : angle 4.66504 ( 3477) covalent geometry : bond 0.00300 (32152) covalent geometry : angle 0.66125 (43276) ********************** 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 387 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 282 time to evaluate : 4.813 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 42 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8598 (mm) REVERT: C 48 LYS cc_start: 0.8695 (ttpt) cc_final: 0.8464 (ttpp) REVERT: A 42 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8605 (mm) REVERT: A 48 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8435 (ttpp) REVERT: B 42 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8581 (mm) REVERT: B 511 ASP cc_start: 0.8257 (t0) cc_final: 0.7765 (t0) REVERT: D 15 GLU cc_start: 0.8330 (tp30) cc_final: 0.8098 (mm-30) REVERT: D 42 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8566 (mm) REVERT: E 108 PHE cc_start: 0.8734 (m-10) cc_final: 0.8456 (m-10) REVERT: F 167 ASP cc_start: 0.8227 (t0) cc_final: 0.8012 (t0) REVERT: F 232 ARG cc_start: 0.6500 (mtt180) cc_final: 0.5939 (mmt90) REVERT: F 268 MET cc_start: 0.4503 (pp-130) cc_final: 0.3768 (pp-130) REVERT: F 292 ILE cc_start: 0.8905 (mp) cc_final: 0.8672 (mm) REVERT: F 307 LEU cc_start: 0.7539 (mm) cc_final: 0.7009 (pt) REVERT: G 167 ASP cc_start: 0.8077 (t0) cc_final: 0.7705 (t70) REVERT: G 474 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.5802 (pmm) REVERT: H 106 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6464 (tm-30) REVERT: H 167 ASP cc_start: 0.8063 (t0) cc_final: 0.7609 (m-30) REVERT: H 268 MET cc_start: 0.4750 (pp-130) cc_final: 0.4419 (pp-130) REVERT: H 293 LEU cc_start: 0.8391 (tp) cc_final: 0.7851 (mt) outliers start: 105 outliers final: 86 residues processed: 376 average time/residue: 0.5137 time to fit residues: 306.8515 Evaluate side-chains 361 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 269 time to evaluate : 3.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU 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 450 LEU Chi-restraints excluded: chain A residue 9 LYS 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 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 426 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 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 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 450 LEU Chi-restraints excluded: chain B residue 456 LEU 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 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 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 450 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 555 LYS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 268 MET 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 163 LYS 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 349 LEU Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain G residue 474 MET Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 54 PHE 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 191 LEU Chi-restraints excluded: chain H residue 315 ILE Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 431 HIS Chi-restraints excluded: chain H residue 471 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 300 optimal weight: 4.9990 chunk 343 optimal weight: 8.9990 chunk 321 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 279 optimal weight: 50.0000 chunk 141 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 274 optimal weight: 50.0000 chunk 330 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 213 optimal weight: 50.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 483 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 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 260 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.230011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.161939 restraints weight = 42020.424| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.23 r_work: 0.3380 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 32152 Z= 0.165 Angle : 0.755 59.088 43276 Z= 0.413 Chirality : 0.053 1.881 4840 Planarity : 0.004 0.055 5532 Dihedral : 4.800 35.450 4180 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.35 % Favored : 91.00 % Rotamer: Outliers : 2.98 % Allowed : 30.70 % Favored : 66.33 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.13), residues: 3844 helix: -0.13 (0.13), residues: 1564 sheet: -0.77 (0.20), residues: 596 loop : -1.96 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 204 HIS 0.008 0.001 HIS F 459 PHE 0.016 0.001 PHE H 108 TYR 0.019 0.001 TYR E 202 ARG 0.013 0.000 ARG B 485 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 1238) hydrogen bonds : angle 4.66620 ( 3477) covalent geometry : bond 0.00377 (32152) covalent geometry : angle 0.75507 (43276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21998.72 seconds wall clock time: 382 minutes 55.54 seconds (22975.54 seconds total)