Starting phenix.real_space_refine on Sat Mar 7 00:11:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/20yr_67417/03_2026/20yr_67417.cif Found real_map, /net/cci-nas-00/data/ceres_data/20yr_67417/03_2026/20yr_67417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/20yr_67417/03_2026/20yr_67417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/20yr_67417/03_2026/20yr_67417.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/20yr_67417/03_2026/20yr_67417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/20yr_67417/03_2026/20yr_67417.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 195 5.16 5 C 22242 2.51 5 N 5829 2.21 5 O 6470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34740 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6951 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 820} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 6951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6951 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 820} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 6951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6951 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 820} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 6951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6951 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 820} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 6936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6936 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 820} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'LLP:plan-1': 1, 'LLP:plan-2': 1, 'LLP:plan-3': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 7.82, per 1000 atoms: 0.23 Number of scatterers: 34740 At special positions: 0 Unit cell: (104.58, 179.28, 203.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 195 16.00 P 4 15.00 O 6470 8.00 N 5829 7.00 C 22242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.5 seconds 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7950 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 40 sheets defined 49.7% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 23 through 27 removed outlier: 3.782A pdb=" N LYS A 27 " --> pdb=" O LYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 52 removed outlier: 3.697A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.832A pdb=" N GLU A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 71 through 80 Processing helix chain 'A' and resid 81 through 100 removed outlier: 3.696A pdb=" N MET A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 144 Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.840A pdb=" N LEU A 182 " --> pdb=" O PHE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 267 Processing helix chain 'A' and resid 282 through 297 removed outlier: 3.976A pdb=" N LEU A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 309 removed outlier: 3.590A pdb=" N ALA A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 323 Processing helix chain 'A' and resid 328 through 335 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 345 through 353 removed outlier: 4.042A pdb=" N GLY A 353 " --> pdb=" O PHE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 373 Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.891A pdb=" N LYS A 397 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 420 through 431 Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 452 through 482 removed outlier: 3.554A pdb=" N TYR A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 488 through 494 removed outlier: 3.758A pdb=" N GLU A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 Processing helix chain 'A' and resid 516 through 520 Processing helix chain 'A' and resid 521 through 530 Processing helix chain 'A' and resid 549 through 563 Processing helix chain 'A' and resid 578 through 589 removed outlier: 3.525A pdb=" N SER A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 612 removed outlier: 3.912A pdb=" N MET A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 629 Processing helix chain 'A' and resid 645 through 664 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 680 through 692 Processing helix chain 'A' and resid 693 through 696 Processing helix chain 'A' and resid 697 through 709 Processing helix chain 'A' and resid 710 through 741 removed outlier: 3.995A pdb=" N ARG A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASN A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU A 727 " --> pdb=" O ASN A 723 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA A 728 " --> pdb=" O ASP A 724 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 741 " --> pdb=" O SER A 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 27 through 35 removed outlier: 3.802A pdb=" N GLU B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.693A pdb=" N TRP B 40 " --> pdb=" O TRP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 removed outlier: 3.631A pdb=" N ARG B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 59 Processing helix chain 'B' and resid 62 through 69 Processing helix chain 'B' and resid 71 through 81 Processing helix chain 'B' and resid 81 through 100 Processing helix chain 'B' and resid 128 through 145 Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 245 through 256 Processing helix chain 'B' and resid 257 through 266 Processing helix chain 'B' and resid 279 through 282 removed outlier: 3.724A pdb=" N ALA B 282 " --> pdb=" O GLY B 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 279 through 282' Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'B' and resid 299 through 310 removed outlier: 5.036A pdb=" N GLU B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU B 306 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 323 Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 366 through 374 Processing helix chain 'B' and resid 381 through 392 removed outlier: 3.540A pdb=" N GLN B 389 " --> pdb=" O GLY B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 420 through 431 removed outlier: 3.553A pdb=" N LEU B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 3.579A pdb=" N TRP B 445 " --> pdb=" O ASN B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 450 Processing helix chain 'B' and resid 452 through 482 removed outlier: 3.575A pdb=" N ILE B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 487 No H-bonds generated for 'chain 'B' and resid 485 through 487' Processing helix chain 'B' and resid 488 through 493 Processing helix chain 'B' and resid 510 through 514 removed outlier: 3.574A pdb=" N ARG B 514 " --> pdb=" O THR B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 520 removed outlier: 3.553A pdb=" N THR B 520 " --> pdb=" O LEU B 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 517 through 520' Processing helix chain 'B' and resid 521 through 530 Processing helix chain 'B' and resid 549 through 563 Processing helix chain 'B' and resid 584 through 589 Processing helix chain 'B' and resid 605 through 613 removed outlier: 3.857A pdb=" N MET B 612 " --> pdb=" O GLU B 608 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASN B 613 " --> pdb=" O LLP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 629 Processing helix chain 'B' and resid 648 through 665 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 678 through 692 Processing helix chain 'B' and resid 693 through 696 Processing helix chain 'B' and resid 697 through 709 Processing helix chain 'B' and resid 712 through 721 removed outlier: 3.537A pdb=" N ARG B 716 " --> pdb=" O LYS B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 741 removed outlier: 6.066A pdb=" N LEU B 727 " --> pdb=" O ASN B 723 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA B 728 " --> pdb=" O ASP B 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 33 Processing helix chain 'D' and resid 35 through 40 removed outlier: 4.088A pdb=" N TRP D 38 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TRP D 40 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 52 removed outlier: 3.847A pdb=" N ARG D 45 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 58 Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'D' and resid 71 through 81 Processing helix chain 'D' and resid 81 through 99 removed outlier: 3.552A pdb=" N MET D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 145 Processing helix chain 'D' and resid 234 through 239 removed outlier: 3.583A pdb=" N ILE D 237 " --> pdb=" O ASP D 234 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR D 238 " --> pdb=" O ARG D 235 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR D 239 " --> pdb=" O PRO D 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 234 through 239' Processing helix chain 'D' and resid 245 through 267 Processing helix chain 'D' and resid 282 through 297 removed outlier: 4.084A pdb=" N LEU D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY D 297 " --> pdb=" O ILE D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 310 removed outlier: 3.638A pdb=" N SER D 310 " --> pdb=" O LEU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 336 removed outlier: 4.371A pdb=" N LYS D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 343 removed outlier: 3.523A pdb=" N ARG D 341 " --> pdb=" O GLY D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 352 Processing helix chain 'D' and resid 366 through 374 Processing helix chain 'D' and resid 381 through 392 Processing helix chain 'D' and resid 400 through 404 Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 434 through 438 Processing helix chain 'D' and resid 441 through 446 Processing helix chain 'D' and resid 447 through 451 Processing helix chain 'D' and resid 452 through 482 Processing helix chain 'D' and resid 485 through 487 No H-bonds generated for 'chain 'D' and resid 485 through 487' Processing helix chain 'D' and resid 488 through 494 Processing helix chain 'D' and resid 514 through 520 removed outlier: 3.647A pdb=" N LEU D 517 " --> pdb=" O ARG D 514 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU D 518 " --> pdb=" O ALA D 515 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR D 520 " --> pdb=" O LEU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 530 removed outlier: 3.863A pdb=" N LEU D 525 " --> pdb=" O ASP D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 563 removed outlier: 3.557A pdb=" N GLN D 552 " --> pdb=" O ASP D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 589 removed outlier: 3.690A pdb=" N SER D 587 " --> pdb=" O ALA D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 612 removed outlier: 3.759A pdb=" N MET D 612 " --> pdb=" O GLU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 629 Processing helix chain 'D' and resid 645 through 664 Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 678 through 692 Processing helix chain 'D' and resid 693 through 696 Processing helix chain 'D' and resid 697 through 709 Processing helix chain 'D' and resid 709 through 741 removed outlier: 3.601A pdb=" N GLU D 713 " --> pdb=" O PHE D 709 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ASN D 723 " --> pdb=" O LYS D 719 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP D 724 " --> pdb=" O LEU D 720 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU D 727 " --> pdb=" O ASN D 723 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA D 728 " --> pdb=" O ASP D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 757 removed outlier: 3.687A pdb=" N MET D 756 " --> pdb=" O ASP D 752 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA D 757 " --> pdb=" O CYS D 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 752 through 757' Processing helix chain 'E' and resid 26 through 34 removed outlier: 4.181A pdb=" N ASP E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 40 removed outlier: 3.568A pdb=" N TRP E 40 " --> pdb=" O TRP E 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 37 through 40' Processing helix chain 'E' and resid 41 through 52 removed outlier: 3.698A pdb=" N ARG E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP E 52 " --> pdb=" O PHE E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 59 Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 71 through 81 Processing helix chain 'E' and resid 82 through 100 Processing helix chain 'E' and resid 128 through 145 Processing helix chain 'E' and resid 234 through 239 removed outlier: 3.566A pdb=" N ILE E 237 " --> pdb=" O ASP E 234 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR E 238 " --> pdb=" O ARG E 235 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR E 239 " --> pdb=" O PRO E 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 234 through 239' Processing helix chain 'E' and resid 245 through 267 removed outlier: 3.813A pdb=" N LEU E 250 " --> pdb=" O TRP E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 281 No H-bonds generated for 'chain 'E' and resid 279 through 281' Processing helix chain 'E' and resid 282 through 297 removed outlier: 4.091A pdb=" N LEU E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 310 removed outlier: 3.521A pdb=" N ALA E 303 " --> pdb=" O ASN E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 323 Processing helix chain 'E' and resid 327 through 336 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 345 through 353 removed outlier: 4.246A pdb=" N GLY E 353 " --> pdb=" O PHE E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 374 Processing helix chain 'E' and resid 381 through 392 Processing helix chain 'E' and resid 393 through 396 Processing helix chain 'E' and resid 400 through 404 Processing helix chain 'E' and resid 414 through 419 Processing helix chain 'E' and resid 420 through 431 Processing helix chain 'E' and resid 441 through 446 removed outlier: 3.527A pdb=" N TRP E 445 " --> pdb=" O ASN E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 removed outlier: 3.570A pdb=" N LYS E 450 " --> pdb=" O ALA E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 482 Processing helix chain 'E' and resid 485 through 487 No H-bonds generated for 'chain 'E' and resid 485 through 487' Processing helix chain 'E' and resid 488 through 494 Processing helix chain 'E' and resid 510 through 520 removed outlier: 3.670A pdb=" N LYS E 513 " --> pdb=" O ALA E 510 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG E 514 " --> pdb=" O THR E 511 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA E 515 " --> pdb=" O TYR E 512 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N HIS E 516 " --> pdb=" O LYS E 513 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU E 518 " --> pdb=" O ALA E 515 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR E 520 " --> pdb=" O LEU E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 530 Processing helix chain 'E' and resid 548 through 563 removed outlier: 3.916A pdb=" N GLN E 552 " --> pdb=" O ASP E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 589 Processing helix chain 'E' and resid 605 through 612 Processing helix chain 'E' and resid 623 through 629 removed outlier: 4.490A pdb=" N GLU E 627 " --> pdb=" O GLY E 623 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 664 removed outlier: 3.605A pdb=" N GLN E 649 " --> pdb=" O ASN E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 670 removed outlier: 3.567A pdb=" N MET E 668 " --> pdb=" O ASP E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 692 Processing helix chain 'E' and resid 693 through 696 Processing helix chain 'E' and resid 697 through 709 Processing helix chain 'E' and resid 709 through 721 Processing helix chain 'E' and resid 721 through 741 removed outlier: 5.758A pdb=" N LEU E 727 " --> pdb=" O ASN E 723 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA E 728 " --> pdb=" O ASP E 724 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG E 741 " --> pdb=" O SER E 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 35 removed outlier: 3.700A pdb=" N ASP C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.653A pdb=" N TRP C 40 " --> pdb=" O TRP C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 52 removed outlier: 3.995A pdb=" N ARG C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 59 Processing helix chain 'C' and resid 62 through 69 Processing helix chain 'C' and resid 71 through 80 Processing helix chain 'C' and resid 82 through 100 Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'C' and resid 245 through 268 Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.921A pdb=" N ALA C 282 " --> pdb=" O GLY C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 295 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 319 through 323 removed outlier: 3.527A pdb=" N HIS C 323 " --> pdb=" O PRO C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 335 removed outlier: 3.561A pdb=" N PHE C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 346 through 354 removed outlier: 4.165A pdb=" N GLY C 353 " --> pdb=" O PHE C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 374 Processing helix chain 'C' and resid 381 through 392 Processing helix chain 'C' and resid 400 through 404 Processing helix chain 'C' and resid 414 through 419 Processing helix chain 'C' and resid 420 through 431 Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 447 through 451 Processing helix chain 'C' and resid 452 through 482 removed outlier: 3.698A pdb=" N ILE C 456 " --> pdb=" O SER C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 495 removed outlier: 3.929A pdb=" N ARG C 495 " --> pdb=" O SER C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 520 removed outlier: 3.607A pdb=" N LEU C 518 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 520 " --> pdb=" O LEU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 530 Processing helix chain 'C' and resid 549 through 564 Processing helix chain 'C' and resid 578 through 589 Processing helix chain 'C' and resid 605 through 612 removed outlier: 4.045A pdb=" N MET C 612 " --> pdb=" O GLU C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 627 Processing helix chain 'C' and resid 632 through 636 removed outlier: 3.706A pdb=" N TRP C 635 " --> pdb=" O GLY C 632 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 636 " --> pdb=" O ALA C 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 632 through 636' Processing helix chain 'C' and resid 645 through 664 Processing helix chain 'C' and resid 664 through 670 Processing helix chain 'C' and resid 678 through 691 Processing helix chain 'C' and resid 692 through 696 Processing helix chain 'C' and resid 697 through 709 Processing helix chain 'C' and resid 709 through 721 Processing helix chain 'C' and resid 721 through 742 removed outlier: 5.779A pdb=" N LEU C 727 " --> pdb=" O ASN C 723 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA C 728 " --> pdb=" O ASP C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 745 No H-bonds generated for 'chain 'C' and resid 743 through 745' Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 6.066A pdb=" N TYR A 7 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TRP B 850 " --> pdb=" O TYR A 7 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR B 847 " --> pdb=" O PRO B 834 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA B 758 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 19 " --> pdb=" O ALA B 758 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 6 through 8 removed outlier: 6.066A pdb=" N TYR A 7 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TRP B 850 " --> pdb=" O TYR A 7 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR B 847 " --> pdb=" O PRO B 834 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 186 Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 186 removed outlier: 4.562A pdb=" N LYS A 219 " --> pdb=" O MET A 148 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA A 111 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 377 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 161 through 164 Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 571 through 574 removed outlier: 6.318A pdb=" N LEU A 501 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE A 539 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE A 503 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER A 541 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE A 505 " --> pdb=" O SER A 541 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N CYS A 506 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASN A 617 " --> pdb=" O TRP A 635 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU A 637 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N SER A 619 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 746 through 750 removed outlier: 3.611A pdb=" N HIS A 746 " --> pdb=" O ASP A 771 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 769 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LYS A 750 " --> pdb=" O GLN A 767 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLN A 767 " --> pdb=" O LYS A 750 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY A 806 " --> pdb=" O THR A 813 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU A 815 " --> pdb=" O MET A 804 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N MET A 804 " --> pdb=" O GLU A 815 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 758 through 759 removed outlier: 6.884A pdb=" N ALA A 758 " --> pdb=" O LYS E 19 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N SER A 825 " --> pdb=" O GLU A 788 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 788 " --> pdb=" O SER A 825 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS A 827 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS A 787 " --> pdb=" O VAL A 796 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL A 796 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN A 789 " --> pdb=" O LYS A 794 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS A 794 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 846 through 848 Processing sheet with id=AB2, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.563A pdb=" N ILE B 18 " --> pdb=" O GLY C 824 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY C 824 " --> pdb=" O ILE B 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 149 through 153 removed outlier: 6.427A pdb=" N ALA B 150 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LEU B 223 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLY B 152 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP B 224 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AB5, first strand: chain 'B' and resid 275 through 277 removed outlier: 6.858A pdb=" N VAL B 377 " --> pdb=" O GLY B 407 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AB7, first strand: chain 'B' and resid 571 through 574 removed outlier: 8.744A pdb=" N ILE B 572 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE B 538 " --> pdb=" O ILE B 572 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU B 574 " --> pdb=" O PHE B 538 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE B 540 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU B 501 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N PHE B 539 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE B 503 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N SER B 541 " --> pdb=" O ILE B 503 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE B 505 " --> pdb=" O SER B 541 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N CYS B 506 " --> pdb=" O MET B 593 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN B 617 " --> pdb=" O TRP B 635 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU B 637 " --> pdb=" O ASN B 617 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N SER B 619 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 746 through 750 removed outlier: 3.660A pdb=" N HIS B 746 " --> pdb=" O ASP B 771 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL B 769 " --> pdb=" O VAL B 748 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 7 through 8 removed outlier: 6.288A pdb=" N TYR D 7 " --> pdb=" O VAL E 848 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N TRP E 850 " --> pdb=" O TYR D 7 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TYR E 847 " --> pdb=" O PRO E 834 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA E 758 " --> pdb=" O THR D 17 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 7 through 8 removed outlier: 6.288A pdb=" N TYR D 7 " --> pdb=" O VAL E 848 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N TRP E 850 " --> pdb=" O TYR D 7 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TYR E 847 " --> pdb=" O PRO E 834 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N SER E 825 " --> pdb=" O GLU E 788 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU E 788 " --> pdb=" O SER E 825 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU E 782 " --> pdb=" O ARG E 831 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LYS E 787 " --> pdb=" O VAL E 796 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL E 796 " --> pdb=" O LYS E 787 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN E 789 " --> pdb=" O LYS E 794 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LYS E 794 " --> pdb=" O GLN E 789 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 185 through 186 removed outlier: 3.738A pdb=" N TYR D 204 " --> pdb=" O TYR D 201 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 185 through 186 removed outlier: 7.272A pdb=" N MET D 148 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N TYR D 221 " --> pdb=" O MET D 148 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA D 150 " --> pdb=" O TYR D 221 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU D 223 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLY D 152 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER D 109 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N HIS D 275 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA D 111 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ASN D 277 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE D 113 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU D 376 " --> pdb=" O SER D 311 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL D 377 " --> pdb=" O GLY D 407 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 161 through 164 removed outlier: 3.533A pdb=" N LYS D 161 " --> pdb=" O ASN D 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN D 173 " --> pdb=" O LYS D 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 325 through 326 Processing sheet with id=AC6, first strand: chain 'D' and resid 571 through 574 removed outlier: 8.490A pdb=" N ILE D 572 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE D 538 " --> pdb=" O ILE D 572 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU D 574 " --> pdb=" O PHE D 538 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE D 540 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU D 501 " --> pdb=" O LEU D 537 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE D 539 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE D 503 " --> pdb=" O PHE D 539 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N SER D 541 " --> pdb=" O ILE D 503 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE D 505 " --> pdb=" O SER D 541 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N MET D 502 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N MET D 593 " --> pdb=" O MET D 502 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY D 504 " --> pdb=" O MET D 593 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASN D 617 " --> pdb=" O TRP D 635 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU D 637 " --> pdb=" O ASN D 617 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N SER D 619 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 746 through 751 removed outlier: 6.636A pdb=" N VAL D 769 " --> pdb=" O VAL D 748 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LYS D 750 " --> pdb=" O GLN D 767 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLN D 767 " --> pdb=" O LYS D 750 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL D 766 " --> pdb=" O ALA D 816 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA D 816 " --> pdb=" O VAL D 766 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR D 768 " --> pdb=" O PHE D 814 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN D 811 " --> pdb=" O HIS D 807 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N HIS D 807 " --> pdb=" O ASN D 811 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THR D 813 " --> pdb=" O VAL D 805 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU D 817 " --> pdb=" O PRO D 801 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LEU D 781 " --> pdb=" O PHE D 802 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET D 804 " --> pdb=" O VAL D 779 " (cutoff:3.500A) removed outlier: 12.259A pdb=" N VAL D 779 " --> pdb=" O MET D 804 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU D 782 " --> pdb=" O ARG D 831 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 831 " --> pdb=" O GLU D 782 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR D 828 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C 14 " --> pdb=" O THR D 828 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA D 758 " --> pdb=" O LYS C 19 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 746 through 751 removed outlier: 6.636A pdb=" N VAL D 769 " --> pdb=" O VAL D 748 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LYS D 750 " --> pdb=" O GLN D 767 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLN D 767 " --> pdb=" O LYS D 750 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL D 766 " --> pdb=" O ALA D 816 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA D 816 " --> pdb=" O VAL D 766 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR D 768 " --> pdb=" O PHE D 814 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN D 811 " --> pdb=" O HIS D 807 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N HIS D 807 " --> pdb=" O ASN D 811 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THR D 813 " --> pdb=" O VAL D 805 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU D 817 " --> pdb=" O PRO D 801 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LEU D 781 " --> pdb=" O PHE D 802 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET D 804 " --> pdb=" O VAL D 779 " (cutoff:3.500A) removed outlier: 12.259A pdb=" N VAL D 779 " --> pdb=" O MET D 804 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU D 782 " --> pdb=" O ARG D 831 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 831 " --> pdb=" O GLU D 782 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS D 849 " --> pdb=" O MET D 832 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 846 through 847 removed outlier: 6.754A pdb=" N CYS D 846 " --> pdb=" O TYR C 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 185 through 186 Processing sheet with id=AD2, first strand: chain 'E' and resid 185 through 186 removed outlier: 7.289A pdb=" N MET E 148 " --> pdb=" O LYS E 219 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N TYR E 221 " --> pdb=" O MET E 148 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA E 150 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU E 223 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY E 152 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU E 376 " --> pdb=" O SER E 311 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL E 377 " --> pdb=" O GLY E 407 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 161 through 164 Processing sheet with id=AD4, first strand: chain 'E' and resid 571 through 574 removed outlier: 8.427A pdb=" N ILE E 572 " --> pdb=" O VAL E 536 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE E 538 " --> pdb=" O ILE E 572 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU E 574 " --> pdb=" O PHE E 538 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE E 540 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU E 501 " --> pdb=" O LEU E 537 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE E 539 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE E 503 " --> pdb=" O PHE E 539 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N SER E 541 " --> pdb=" O ILE E 503 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE E 505 " --> pdb=" O SER E 541 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N CYS E 506 " --> pdb=" O MET E 593 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASN E 617 " --> pdb=" O TRP E 635 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU E 637 " --> pdb=" O ASN E 617 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N SER E 619 " --> pdb=" O LEU E 637 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 764 through 771 removed outlier: 6.789A pdb=" N ASN E 811 " --> pdb=" O HIS E 807 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N HIS E 807 " --> pdb=" O ASN E 811 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR E 813 " --> pdb=" O VAL E 805 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 185 through 186 removed outlier: 3.854A pdb=" N VAL C 206 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA C 208 " --> pdb=" O VAL C 197 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 185 through 186 removed outlier: 7.423A pdb=" N MET C 148 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N TYR C 221 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA C 150 " --> pdb=" O TYR C 221 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LEU C 223 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N GLY C 152 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA C 111 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AD9, first strand: chain 'C' and resid 378 through 379 Processing sheet with id=AE1, first strand: chain 'C' and resid 571 through 574 removed outlier: 8.380A pdb=" N ILE C 572 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE C 538 " --> pdb=" O ILE C 572 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU C 574 " --> pdb=" O PHE C 538 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE C 540 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU C 501 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE C 539 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE C 503 " --> pdb=" O PHE C 539 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N SER C 541 " --> pdb=" O ILE C 503 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 746 through 747 removed outlier: 3.977A pdb=" N HIS C 746 " --> pdb=" O ASP C 771 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 794 through 796 removed outlier: 7.023A pdb=" N VAL C 796 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLN C 789 " --> pdb=" O VAL C 796 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU C 782 " --> pdb=" O ARG C 831 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG C 831 " --> pdb=" O GLU C 782 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL C 784 " --> pdb=" O GLY C 829 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C 829 " --> pdb=" O VAL C 784 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 803 through 804 removed outlier: 3.642A pdb=" N LYS C 803 " --> pdb=" O GLU C 815 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU C 815 " --> pdb=" O LYS C 803 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 1554 hydrogen bonds defined for protein. 4335 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: 8.49 Time building geometry restraints manager: 3.77 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: 11080 1.34 - 1.45: 5578 1.45 - 1.57: 18647 1.57 - 1.69: 4 1.69 - 1.81: 325 Bond restraints: 35634 Sorted by residual: bond pdb=" OP4 LLP A 609 " pdb=" P LLP A 609 " ideal model delta sigma weight residual 1.726 1.543 0.183 2.00e-02 2.50e+03 8.36e+01 bond pdb=" OP4 LLP D 609 " pdb=" P LLP D 609 " ideal model delta sigma weight residual 1.726 1.543 0.183 2.00e-02 2.50e+03 8.36e+01 bond pdb=" OP4 LLP B 609 " pdb=" P LLP B 609 " ideal model delta sigma weight residual 1.726 1.543 0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" OP4 LLP E 609 " pdb=" P LLP E 609 " ideal model delta sigma weight residual 1.726 1.544 0.182 2.00e-02 2.50e+03 8.25e+01 bond pdb=" NZ LLP D 609 " pdb=" C4' LLP D 609 " ideal model delta sigma weight residual 1.273 1.428 -0.155 2.00e-02 2.50e+03 6.04e+01 ... (remaining 35629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 47916 2.78 - 5.56: 293 5.56 - 8.33: 22 8.33 - 11.11: 12 11.11 - 13.89: 3 Bond angle restraints: 48246 Sorted by residual: angle pdb=" C VAL A 101 " pdb=" N LYS A 102 " pdb=" CA LYS A 102 " ideal model delta sigma weight residual 120.69 134.58 -13.89 2.95e+00 1.15e-01 2.22e+01 angle pdb=" NZ LLP B 609 " pdb=" C4' LLP B 609 " pdb=" C4 LLP B 609 " ideal model delta sigma weight residual 120.09 108.88 11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CE LLP D 609 " pdb=" NZ LLP D 609 " pdb=" C4' LLP D 609 " ideal model delta sigma weight residual 119.26 108.18 11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" CE LLP A 609 " pdb=" NZ LLP A 609 " pdb=" C4' LLP A 609 " ideal model delta sigma weight residual 119.26 108.23 11.03 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N GLU E 305 " pdb=" CA GLU E 305 " pdb=" CB GLU E 305 " ideal model delta sigma weight residual 110.12 115.51 -5.39 1.47e+00 4.63e-01 1.35e+01 ... (remaining 48241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 19108 17.78 - 35.55: 1602 35.55 - 53.33: 275 53.33 - 71.11: 67 71.11 - 88.88: 24 Dihedral angle restraints: 21076 sinusoidal: 8621 harmonic: 12455 Sorted by residual: dihedral pdb=" CA LEU B 256 " pdb=" C LEU B 256 " pdb=" N GLY B 257 " pdb=" CA GLY B 257 " ideal model delta harmonic sigma weight residual -180.00 -155.37 -24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA PRO B 667 " pdb=" C PRO B 667 " pdb=" N MET B 668 " pdb=" CA MET B 668 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU B 581 " pdb=" C LEU B 581 " pdb=" N ALA B 582 " pdb=" CA ALA B 582 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 21073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3840 0.046 - 0.093: 871 0.093 - 0.139: 272 0.139 - 0.185: 6 0.185 - 0.231: 1 Chirality restraints: 4990 Sorted by residual: chirality pdb=" CB ILE B 344 " pdb=" CA ILE B 344 " pdb=" CG1 ILE B 344 " pdb=" CG2 ILE B 344 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA LEU D 493 " pdb=" N LEU D 493 " pdb=" C LEU D 493 " pdb=" CB LEU D 493 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA GLU E 305 " pdb=" N GLU E 305 " pdb=" C GLU E 305 " pdb=" CB GLU E 305 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.07e-01 ... (remaining 4987 not shown) Planarity restraints: 6238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP E 609 " -0.048 2.00e-02 2.50e+03 4.60e-02 2.11e+01 pdb=" NZ LLP E 609 " 0.046 2.00e-02 2.50e+03 pdb=" C4 LLP E 609 " -0.044 2.00e-02 2.50e+03 pdb=" C4' LLP E 609 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 531 " -0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO D 532 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO D 532 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 532 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CE LLP D 609 " -0.036 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" NZ LLP D 609 " 0.034 2.00e-02 2.50e+03 pdb=" C4 LLP D 609 " -0.033 2.00e-02 2.50e+03 pdb=" C4' LLP D 609 " 0.034 2.00e-02 2.50e+03 ... (remaining 6235 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 811 2.70 - 3.25: 33441 3.25 - 3.80: 55006 3.80 - 4.35: 74765 4.35 - 4.90: 126416 Nonbonded interactions: 290439 Sorted by model distance: nonbonded pdb=" O CYS C 365 " pdb=" OG1 THR C 368 " model vdw 2.148 3.040 nonbonded pdb=" OE2 GLU A 759 " pdb=" OG SER E 21 " model vdw 2.163 3.040 nonbonded pdb=" O THR A 760 " pdb=" OG SER E 21 " model vdw 2.170 3.040 nonbonded pdb=" O LEU A 518 " pdb=" OH TYR A 658 " model vdw 2.176 3.040 nonbonded pdb=" O GLY C 353 " pdb=" OG1 THR C 368 " model vdw 2.179 3.040 ... (remaining 290434 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 608 or (resid 609 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )) or resid \ 610 through 852)) selection = (chain 'B' and (resid 1 through 608 or (resid 609 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )) or resid \ 610 through 852)) selection = chain 'C' selection = (chain 'D' and (resid 1 through 608 or (resid 609 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )) or resid \ 610 through 852)) selection = (chain 'E' and (resid 1 through 608 or (resid 609 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )) or resid \ 610 through 852)) } 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: 10.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.120 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 0.183 35634 Z= 0.222 Angle : 0.595 13.888 48246 Z= 0.305 Chirality : 0.042 0.231 4990 Planarity : 0.004 0.090 6238 Dihedral : 13.786 88.882 13126 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.03 % Allowed : 0.03 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.13), residues: 4235 helix: 0.77 (0.13), residues: 1716 sheet: -0.20 (0.22), residues: 607 loop : -1.33 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 842 TYR 0.025 0.001 TYR D 239 PHE 0.018 0.001 PHE E 160 TRP 0.024 0.001 TRP D 734 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00469 (35634) covalent geometry : angle 0.59473 (48246) hydrogen bonds : bond 0.17086 ( 1522) hydrogen bonds : angle 7.11137 ( 4335) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 439 time to evaluate : 1.211 Fit side-chains REVERT: A 72 TYR cc_start: 0.7251 (t80) cc_final: 0.6852 (t80) REVERT: B 42 TYR cc_start: 0.7910 (p90) cc_final: 0.7491 (p90) REVERT: D 302 GLN cc_start: 0.6934 (mt0) cc_final: 0.6247 (mt0) REVERT: D 815 GLU cc_start: 0.6081 (mm-30) cc_final: 0.5119 (tt0) REVERT: E 651 GLN cc_start: 0.7481 (mp10) cc_final: 0.7223 (mp10) outliers start: 1 outliers final: 0 residues processed: 440 average time/residue: 0.8061 time to fit residues: 415.2091 Evaluate side-chains 309 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 810 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN B 723 ASN B 773 GLN D 104 ASN D 725 ASN D 762 GLN D 810 ASN E 646 GLN E 723 ASN C 212 GLN C 302 GLN C 645 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.152090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119644 restraints weight = 45853.165| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.16 r_work: 0.3044 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35634 Z= 0.157 Angle : 0.560 9.201 48246 Z= 0.295 Chirality : 0.043 0.169 4990 Planarity : 0.004 0.061 6238 Dihedral : 4.946 77.324 4711 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.55 % Allowed : 7.72 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.13), residues: 4235 helix: 0.93 (0.13), residues: 1755 sheet: -0.00 (0.21), residues: 631 loop : -1.40 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 341 TYR 0.026 0.001 TYR A 696 PHE 0.017 0.001 PHE A 160 TRP 0.018 0.001 TRP E 246 HIS 0.007 0.001 HIS C 746 Details of bonding type rmsd covalent geometry : bond 0.00370 (35634) covalent geometry : angle 0.56002 (48246) hydrogen bonds : bond 0.04663 ( 1522) hydrogen bonds : angle 5.30551 ( 4335) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 344 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: A 72 TYR cc_start: 0.7368 (t80) cc_final: 0.7093 (t80) REVERT: A 81 ASP cc_start: 0.8080 (t0) cc_final: 0.7867 (t0) REVERT: A 363 ARG cc_start: 0.7516 (ptt180) cc_final: 0.7176 (ptm160) REVERT: B 36 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8127 (mtt) REVERT: B 42 TYR cc_start: 0.7995 (p90) cc_final: 0.7544 (p90) REVERT: B 171 ILE cc_start: 0.8924 (mt) cc_final: 0.8586 (mm) REVERT: B 821 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7659 (pp) REVERT: D 57 GLU cc_start: 0.7651 (pp20) cc_final: 0.7342 (pp20) REVERT: D 296 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7151 (m-30) REVERT: E 49 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8230 (ttpt) REVERT: E 355 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: E 813 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7726 (m) REVERT: C 19 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7333 (ptpt) REVERT: C 213 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.7195 (ttp) REVERT: C 436 MET cc_start: 0.7230 (mmt) cc_final: 0.6907 (mmm) REVERT: C 629 TYR cc_start: 0.4346 (p90) cc_final: 0.3982 (p90) REVERT: C 756 MET cc_start: 0.3232 (pp-130) cc_final: 0.2748 (pp-130) REVERT: C 832 MET cc_start: 0.6860 (mmt) cc_final: 0.6532 (mmt) REVERT: C 849 LYS cc_start: 0.5647 (mmmt) cc_final: 0.5291 (mmmt) outliers start: 57 outliers final: 14 residues processed: 366 average time/residue: 0.7334 time to fit residues: 318.2361 Evaluate side-chains 326 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 304 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 679 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 6 optimal weight: 0.4980 chunk 118 optimal weight: 0.3980 chunk 424 optimal weight: 6.9990 chunk 247 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 264 optimal weight: 3.9990 chunk 402 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 412 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 277 ASN A 360 HIS ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 ASN D 390 GLN D 671 ASN D 725 ASN D 810 ASN E 723 ASN E 762 GLN C 121 GLN C 212 GLN C 302 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.151922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.119049 restraints weight = 45797.399| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.12 r_work: 0.3043 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35634 Z= 0.144 Angle : 0.530 8.991 48246 Z= 0.278 Chirality : 0.042 0.166 4990 Planarity : 0.004 0.055 6238 Dihedral : 4.842 73.654 4711 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.88 % Allowed : 10.11 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.13), residues: 4235 helix: 0.97 (0.13), residues: 1767 sheet: 0.01 (0.21), residues: 643 loop : -1.38 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 341 TYR 0.025 0.001 TYR E 209 PHE 0.018 0.001 PHE E 160 TRP 0.023 0.001 TRP E 246 HIS 0.005 0.001 HIS C 746 Details of bonding type rmsd covalent geometry : bond 0.00341 (35634) covalent geometry : angle 0.53012 (48246) hydrogen bonds : bond 0.04208 ( 1522) hydrogen bonds : angle 5.02195 ( 4335) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 333 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: A 72 TYR cc_start: 0.7391 (t80) cc_final: 0.7094 (t80) REVERT: A 81 ASP cc_start: 0.8133 (t0) cc_final: 0.7844 (t0) REVERT: A 363 ARG cc_start: 0.7709 (ptt180) cc_final: 0.7499 (ptm160) REVERT: B 36 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8078 (mtt) REVERT: B 42 TYR cc_start: 0.7980 (p90) cc_final: 0.7508 (p90) REVERT: B 171 ILE cc_start: 0.8906 (mt) cc_final: 0.8637 (mm) REVERT: B 352 MET cc_start: 0.7976 (mtm) cc_final: 0.7775 (mtp) REVERT: B 533 GLU cc_start: 0.6809 (tp30) cc_final: 0.6417 (tp30) REVERT: B 821 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7623 (pp) REVERT: D 57 GLU cc_start: 0.7689 (pp20) cc_final: 0.7327 (pp20) REVERT: D 287 GLN cc_start: 0.8363 (tp40) cc_final: 0.7840 (tp-100) REVERT: D 296 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7146 (m-30) REVERT: D 430 TYR cc_start: 0.7106 (m-80) cc_final: 0.6808 (m-80) REVERT: D 810 ASN cc_start: 0.6957 (OUTLIER) cc_final: 0.6472 (t0) REVERT: E 49 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8265 (ttpt) REVERT: E 352 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8312 (mtp) REVERT: E 355 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: E 813 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7731 (m) REVERT: E 817 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6914 (tp30) REVERT: C 7 TYR cc_start: 0.7406 (t80) cc_final: 0.7030 (t80) REVERT: C 19 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7401 (ptpt) REVERT: C 267 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7558 (tt) REVERT: C 397 LYS cc_start: 0.6278 (mmtm) cc_final: 0.5915 (pmmt) REVERT: C 629 TYR cc_start: 0.4348 (p90) cc_final: 0.3994 (p90) REVERT: C 804 MET cc_start: 0.4802 (OUTLIER) cc_final: 0.4110 (tmt) REVERT: C 817 GLU cc_start: 0.5541 (mm-30) cc_final: 0.5180 (tp30) REVERT: C 849 LYS cc_start: 0.5876 (mmmt) cc_final: 0.5506 (mmmt) outliers start: 69 outliers final: 18 residues processed: 369 average time/residue: 0.7435 time to fit residues: 323.6221 Evaluate side-chains 334 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 304 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 804 MET Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 352 MET Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 817 GLU Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 679 LYS Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 804 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 323 optimal weight: 0.6980 chunk 312 optimal weight: 0.6980 chunk 287 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 300 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS A 810 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 ASN D 207 HIS D 725 ASN E 646 GLN E 723 ASN C 121 GLN C 212 GLN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 GLN C 617 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.153443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120737 restraints weight = 45497.003| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.05 r_work: 0.3077 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35634 Z= 0.112 Angle : 0.497 8.842 48246 Z= 0.261 Chirality : 0.041 0.159 4990 Planarity : 0.004 0.054 6238 Dihedral : 4.670 72.673 4711 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.85 % Allowed : 11.60 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 4235 helix: 1.14 (0.13), residues: 1768 sheet: 0.09 (0.21), residues: 641 loop : -1.36 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 341 TYR 0.024 0.001 TYR E 209 PHE 0.016 0.001 PHE E 160 TRP 0.024 0.001 TRP E 246 HIS 0.004 0.001 HIS C 746 Details of bonding type rmsd covalent geometry : bond 0.00258 (35634) covalent geometry : angle 0.49708 (48246) hydrogen bonds : bond 0.03780 ( 1522) hydrogen bonds : angle 4.82762 ( 4335) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 327 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: A 72 TYR cc_start: 0.7364 (t80) cc_final: 0.7035 (t80) REVERT: A 81 ASP cc_start: 0.8056 (t0) cc_final: 0.7833 (t0) REVERT: A 391 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8791 (ptt) REVERT: B 36 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8016 (mtt) REVERT: B 42 TYR cc_start: 0.7886 (p90) cc_final: 0.7432 (p90) REVERT: B 96 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7338 (tpm170) REVERT: B 169 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7655 (tp-100) REVERT: B 239 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7564 (m-80) REVERT: B 352 MET cc_start: 0.7963 (mtm) cc_final: 0.7739 (mtp) REVERT: B 533 GLU cc_start: 0.6725 (tp30) cc_final: 0.6508 (tp30) REVERT: B 821 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7600 (pp) REVERT: D 57 GLU cc_start: 0.7572 (pp20) cc_final: 0.7120 (tp30) REVERT: D 287 GLN cc_start: 0.8317 (tp40) cc_final: 0.7809 (tp-100) REVERT: D 296 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.7141 (m-30) REVERT: D 430 TYR cc_start: 0.7128 (m-80) cc_final: 0.6840 (m-80) REVERT: D 804 MET cc_start: 0.6255 (tpt) cc_final: 0.6016 (tpt) REVERT: D 810 ASN cc_start: 0.7149 (m-40) cc_final: 0.6709 (t0) REVERT: E 49 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8275 (ttpt) REVERT: E 355 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: C 7 TYR cc_start: 0.7430 (t80) cc_final: 0.7050 (t80) REVERT: C 19 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7463 (ptpt) REVERT: C 267 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7569 (tt) REVERT: C 397 LYS cc_start: 0.6267 (mmtm) cc_final: 0.5809 (pmmt) REVERT: C 629 TYR cc_start: 0.4368 (p90) cc_final: 0.4007 (p90) REVERT: C 804 MET cc_start: 0.4863 (OUTLIER) cc_final: 0.4126 (tpt) REVERT: C 817 GLU cc_start: 0.5514 (mm-30) cc_final: 0.4993 (tp30) REVERT: C 849 LYS cc_start: 0.5952 (mmmt) cc_final: 0.5531 (mmmt) outliers start: 68 outliers final: 16 residues processed: 367 average time/residue: 0.7598 time to fit residues: 331.1560 Evaluate side-chains 329 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 302 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 804 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 150 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 171 optimal weight: 0.1980 chunk 276 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 379 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 277 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS A 810 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 ASN B 767 GLN D 725 ASN E 178 ASN E 646 GLN E 723 ASN C 212 GLN C 390 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.151796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119257 restraints weight = 45943.026| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.03 r_work: 0.3060 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 35634 Z= 0.156 Angle : 0.526 8.451 48246 Z= 0.275 Chirality : 0.042 0.160 4990 Planarity : 0.004 0.053 6238 Dihedral : 4.690 70.545 4711 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.20 % Allowed : 12.31 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.13), residues: 4235 helix: 1.08 (0.13), residues: 1774 sheet: 0.08 (0.20), residues: 649 loop : -1.35 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 341 TYR 0.026 0.001 TYR E 209 PHE 0.019 0.001 PHE E 160 TRP 0.026 0.001 TRP E 246 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00374 (35634) covalent geometry : angle 0.52577 (48246) hydrogen bonds : bond 0.04108 ( 1522) hydrogen bonds : angle 4.83001 ( 4335) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 318 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.7397 (t80) cc_final: 0.7108 (t80) REVERT: A 81 ASP cc_start: 0.8076 (t0) cc_final: 0.7864 (t0) REVERT: A 391 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8724 (ptt) REVERT: A 507 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7354 (mtm-85) REVERT: A 727 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8787 (tt) REVERT: A 792 ASP cc_start: 0.7224 (t0) cc_final: 0.7022 (t0) REVERT: B 42 TYR cc_start: 0.8076 (p90) cc_final: 0.7647 (p90) REVERT: B 96 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7459 (tpm170) REVERT: B 169 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7784 (tp-100) REVERT: B 239 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.7642 (m-80) REVERT: B 352 MET cc_start: 0.8105 (mtm) cc_final: 0.7897 (mtp) REVERT: B 821 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7563 (pp) REVERT: D 57 GLU cc_start: 0.7659 (pp20) cc_final: 0.7225 (tp30) REVERT: D 287 GLN cc_start: 0.8456 (tp40) cc_final: 0.7999 (tp-100) REVERT: D 296 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7241 (m-30) REVERT: D 430 TYR cc_start: 0.7248 (m-80) cc_final: 0.6934 (m-80) REVERT: D 804 MET cc_start: 0.6377 (tpt) cc_final: 0.6089 (tpt) REVERT: D 810 ASN cc_start: 0.7182 (m-40) cc_final: 0.6796 (t0) REVERT: E 49 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8372 (ttpt) REVERT: E 355 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: C 7 TYR cc_start: 0.7444 (t80) cc_final: 0.7098 (t80) REVERT: C 19 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7580 (ptpt) REVERT: C 267 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7603 (tt) REVERT: C 334 TYR cc_start: 0.5252 (OUTLIER) cc_final: 0.4690 (t80) REVERT: C 390 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7874 (mt0) REVERT: C 397 LYS cc_start: 0.6419 (mmtm) cc_final: 0.6101 (mppt) REVERT: C 804 MET cc_start: 0.4750 (OUTLIER) cc_final: 0.4151 (tpt) REVERT: C 817 GLU cc_start: 0.5617 (mm-30) cc_final: 0.5279 (tp30) outliers start: 81 outliers final: 27 residues processed: 373 average time/residue: 0.7572 time to fit residues: 335.7807 Evaluate side-chains 343 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 302 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 804 MET Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 799 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 805 VAL Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 334 TYR Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 390 GLN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 804 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 58 optimal weight: 1.9990 chunk 385 optimal weight: 0.9980 chunk 293 optimal weight: 2.9990 chunk 415 optimal weight: 8.9990 chunk 422 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 358 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 416 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 277 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS A 810 ASN B 277 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 GLN D 390 GLN D 725 ASN E 646 GLN E 723 ASN E 767 GLN C 170 GLN C 212 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.149412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116350 restraints weight = 45888.603| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.03 r_work: 0.3022 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 35634 Z= 0.243 Angle : 0.592 7.863 48246 Z= 0.308 Chirality : 0.045 0.185 4990 Planarity : 0.004 0.053 6238 Dihedral : 4.883 70.198 4711 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.50 % Allowed : 13.04 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 4235 helix: 0.84 (0.13), residues: 1777 sheet: -0.08 (0.20), residues: 648 loop : -1.39 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 341 TYR 0.031 0.002 TYR E 209 PHE 0.024 0.002 PHE A 160 TRP 0.027 0.002 TRP E 246 HIS 0.006 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00593 (35634) covalent geometry : angle 0.59231 (48246) hydrogen bonds : bond 0.04735 ( 1522) hydrogen bonds : angle 4.99545 ( 4335) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 310 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: A 72 TYR cc_start: 0.7428 (t80) cc_final: 0.7167 (t80) REVERT: A 81 ASP cc_start: 0.8180 (t0) cc_final: 0.7946 (t0) REVERT: A 391 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8689 (ptt) REVERT: A 612 MET cc_start: 0.8725 (mtt) cc_final: 0.8481 (mtt) REVERT: A 727 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8792 (tt) REVERT: A 792 ASP cc_start: 0.7212 (t0) cc_final: 0.7000 (t0) REVERT: B 1 MET cc_start: 0.4577 (pmm) cc_final: 0.4280 (pmm) REVERT: B 42 TYR cc_start: 0.8171 (p90) cc_final: 0.7683 (p90) REVERT: B 239 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7549 (m-80) REVERT: B 668 MET cc_start: 0.8861 (ttp) cc_final: 0.8623 (ttm) REVERT: B 821 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7628 (pp) REVERT: D 287 GLN cc_start: 0.8503 (tp40) cc_final: 0.7934 (tp-100) REVERT: D 296 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7342 (m-30) REVERT: D 430 TYR cc_start: 0.7275 (m-80) cc_final: 0.6946 (m-80) REVERT: D 804 MET cc_start: 0.6568 (tpt) cc_final: 0.6288 (tpt) REVERT: D 810 ASN cc_start: 0.7126 (m-40) cc_final: 0.6688 (t0) REVERT: E 49 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8358 (ttpt) REVERT: E 355 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: E 803 LYS cc_start: 0.7662 (tptt) cc_final: 0.7404 (mttm) REVERT: C 7 TYR cc_start: 0.7407 (t80) cc_final: 0.7077 (t80) REVERT: C 19 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7598 (ptpt) REVERT: C 119 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8549 (mm) REVERT: C 213 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.6858 (tpp) REVERT: C 267 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7613 (tt) REVERT: C 302 GLN cc_start: 0.4768 (pt0) cc_final: 0.4473 (pt0) REVERT: C 334 TYR cc_start: 0.5493 (OUTLIER) cc_final: 0.4478 (t80) REVERT: C 390 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7225 (mt0) REVERT: C 397 LYS cc_start: 0.6527 (mmtm) cc_final: 0.6283 (mppt) REVERT: C 804 MET cc_start: 0.4837 (OUTLIER) cc_final: 0.4441 (tpt) REVERT: C 817 GLU cc_start: 0.5585 (mm-30) cc_final: 0.5242 (tp30) outliers start: 92 outliers final: 36 residues processed: 376 average time/residue: 0.7529 time to fit residues: 336.7961 Evaluate side-chains 349 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 298 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 804 MET Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 725 ASN Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 799 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 805 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 334 TYR Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 390 GLN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 804 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 313 optimal weight: 0.7980 chunk 405 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 416 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 354 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 277 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS A 810 ASN B 277 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN D 725 ASN D 746 HIS E 646 GLN E 723 ASN C 212 GLN C 530 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.150538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.117610 restraints weight = 45989.664| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.95 r_work: 0.3044 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35634 Z= 0.167 Angle : 0.543 8.421 48246 Z= 0.284 Chirality : 0.043 0.156 4990 Planarity : 0.004 0.053 6238 Dihedral : 4.775 68.387 4711 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.42 % Allowed : 13.53 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 4235 helix: 0.93 (0.13), residues: 1782 sheet: -0.07 (0.20), residues: 650 loop : -1.38 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 341 TYR 0.029 0.001 TYR E 209 PHE 0.020 0.001 PHE E 160 TRP 0.029 0.001 TRP E 246 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00403 (35634) covalent geometry : angle 0.54322 (48246) hydrogen bonds : bond 0.04226 ( 1522) hydrogen bonds : angle 4.88380 ( 4335) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 313 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.7404 (t80) cc_final: 0.7121 (t80) REVERT: A 81 ASP cc_start: 0.8146 (t0) cc_final: 0.7912 (t0) REVERT: A 391 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8646 (ptt) REVERT: A 727 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8817 (tt) REVERT: A 792 ASP cc_start: 0.7228 (t0) cc_final: 0.7019 (t0) REVERT: B 1 MET cc_start: 0.4650 (pmm) cc_final: 0.4439 (pmm) REVERT: B 42 TYR cc_start: 0.8134 (p90) cc_final: 0.7665 (p90) REVERT: B 169 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7813 (tp40) REVERT: B 239 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7603 (m-80) REVERT: B 821 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7625 (pp) REVERT: D 287 GLN cc_start: 0.8445 (tp40) cc_final: 0.7904 (tp-100) REVERT: D 296 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: D 430 TYR cc_start: 0.7158 (m-80) cc_final: 0.6830 (m-80) REVERT: D 804 MET cc_start: 0.6641 (tpt) cc_final: 0.6404 (tpt) REVERT: D 810 ASN cc_start: 0.7134 (m-40) cc_final: 0.6693 (t0) REVERT: E 49 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8343 (ttpt) REVERT: E 355 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: E 754 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.5330 (pmt) REVERT: E 803 LYS cc_start: 0.7695 (tptt) cc_final: 0.7427 (mttm) REVERT: C 7 TYR cc_start: 0.7441 (t80) cc_final: 0.7115 (t80) REVERT: C 19 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7519 (ptpt) REVERT: C 119 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8552 (mm) REVERT: C 267 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7588 (tt) REVERT: C 328 GLU cc_start: 0.6239 (tp30) cc_final: 0.6013 (tt0) REVERT: C 334 TYR cc_start: 0.5507 (OUTLIER) cc_final: 0.4495 (t80) REVERT: C 397 LYS cc_start: 0.6445 (mmtm) cc_final: 0.6106 (pmmt) REVERT: C 804 MET cc_start: 0.4924 (OUTLIER) cc_final: 0.4551 (tpt) REVERT: C 817 GLU cc_start: 0.5530 (mm-30) cc_final: 0.5218 (tp30) outliers start: 89 outliers final: 40 residues processed: 377 average time/residue: 0.7456 time to fit residues: 335.4630 Evaluate side-chains 356 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 303 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 804 MET Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 799 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain E residue 805 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 334 TYR Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 786 LEU Chi-restraints excluded: chain C residue 804 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 148 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 421 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 270 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS A 810 ASN B 277 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN D 725 ASN ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 646 GLN E 723 ASN E 725 ASN C 212 GLN C 230 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.150555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.120473 restraints weight = 46074.818| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.00 r_work: 0.3038 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35634 Z= 0.168 Angle : 0.549 9.189 48246 Z= 0.286 Chirality : 0.043 0.150 4990 Planarity : 0.004 0.053 6238 Dihedral : 4.742 67.865 4711 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.31 % Allowed : 14.21 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.13), residues: 4235 helix: 0.96 (0.13), residues: 1783 sheet: 0.01 (0.21), residues: 636 loop : -1.40 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 341 TYR 0.029 0.001 TYR E 209 PHE 0.020 0.001 PHE E 160 TRP 0.033 0.002 TRP E 246 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00404 (35634) covalent geometry : angle 0.54947 (48246) hydrogen bonds : bond 0.04210 ( 1522) hydrogen bonds : angle 4.85037 ( 4335) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 312 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.7396 (t80) cc_final: 0.7099 (t80) REVERT: A 81 ASP cc_start: 0.8157 (t0) cc_final: 0.7938 (t0) REVERT: A 241 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8771 (mt) REVERT: A 391 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8707 (ptt) REVERT: A 727 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8800 (tt) REVERT: B 1 MET cc_start: 0.4759 (pmm) cc_final: 0.4402 (pmm) REVERT: B 42 TYR cc_start: 0.8118 (p90) cc_final: 0.7638 (p90) REVERT: B 169 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7793 (tp40) REVERT: B 239 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: B 821 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7628 (pp) REVERT: D 57 GLU cc_start: 0.7687 (pp20) cc_final: 0.7144 (tp30) REVERT: D 287 GLN cc_start: 0.8426 (tp40) cc_final: 0.7944 (tp-100) REVERT: D 296 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: D 430 TYR cc_start: 0.7165 (m-80) cc_final: 0.6839 (m-80) REVERT: D 804 MET cc_start: 0.6655 (tpt) cc_final: 0.6406 (tpt) REVERT: E 19 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8587 (ttpp) REVERT: E 49 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8337 (ttpt) REVERT: E 355 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: E 754 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.5437 (pmt) REVERT: E 803 LYS cc_start: 0.7622 (tptt) cc_final: 0.7403 (mttm) REVERT: C 7 TYR cc_start: 0.7410 (t80) cc_final: 0.7088 (t80) REVERT: C 19 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7566 (ptpt) REVERT: C 213 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.6709 (tpp) REVERT: C 267 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7619 (tt) REVERT: C 328 GLU cc_start: 0.6273 (tp30) cc_final: 0.5993 (tt0) REVERT: C 333 LYS cc_start: 0.7125 (pptt) cc_final: 0.6871 (pttt) REVERT: C 397 LYS cc_start: 0.6440 (mmtm) cc_final: 0.6092 (pmmt) REVERT: C 804 MET cc_start: 0.4979 (OUTLIER) cc_final: 0.4636 (tpt) REVERT: C 817 GLU cc_start: 0.5438 (mm-30) cc_final: 0.5117 (tp30) outliers start: 85 outliers final: 41 residues processed: 375 average time/residue: 0.7216 time to fit residues: 322.4781 Evaluate side-chains 358 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 303 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 804 MET Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 725 ASN Chi-restraints excluded: chain D residue 752 ASP Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 799 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 805 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 786 LEU Chi-restraints excluded: chain C residue 804 MET Chi-restraints excluded: chain C residue 847 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 201 optimal weight: 2.9990 chunk 390 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 232 optimal weight: 0.8980 chunk 326 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 417 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS A 810 ASN B 277 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN D 725 ASN D 810 ASN E 230 ASN E 646 GLN E 723 ASN C 212 GLN C 390 GLN C 645 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.149189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.115946 restraints weight = 45971.929| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.13 r_work: 0.3011 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 35634 Z= 0.237 Angle : 0.600 9.201 48246 Z= 0.312 Chirality : 0.045 0.183 4990 Planarity : 0.004 0.053 6238 Dihedral : 4.868 68.594 4711 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.26 % Allowed : 14.51 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.13), residues: 4235 helix: 0.85 (0.13), residues: 1771 sheet: -0.05 (0.21), residues: 631 loop : -1.43 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 341 TYR 0.033 0.002 TYR E 209 PHE 0.025 0.002 PHE A 160 TRP 0.036 0.002 TRP E 246 HIS 0.006 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00579 (35634) covalent geometry : angle 0.60021 (48246) hydrogen bonds : bond 0.04660 ( 1522) hydrogen bonds : angle 4.97705 ( 4335) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 302 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.7411 (t80) cc_final: 0.7112 (t80) REVERT: A 81 ASP cc_start: 0.8223 (t0) cc_final: 0.7962 (t0) REVERT: A 241 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8783 (mt) REVERT: A 391 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8689 (ptt) REVERT: A 727 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8788 (tt) REVERT: A 759 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8269 (tm-30) REVERT: B 1 MET cc_start: 0.4673 (pmm) cc_final: 0.4339 (pmm) REVERT: B 42 TYR cc_start: 0.8185 (p90) cc_final: 0.7726 (p90) REVERT: B 169 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7858 (tp-100) REVERT: B 239 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7594 (m-80) REVERT: B 821 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7618 (pp) REVERT: D 57 GLU cc_start: 0.7665 (pp20) cc_final: 0.7105 (tp30) REVERT: D 287 GLN cc_start: 0.8464 (tp40) cc_final: 0.7884 (tp-100) REVERT: D 430 TYR cc_start: 0.7194 (m-80) cc_final: 0.6816 (m-80) REVERT: D 517 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8645 (mp) REVERT: D 804 MET cc_start: 0.6627 (tpt) cc_final: 0.6332 (tpt) REVERT: E 19 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8579 (ttpp) REVERT: E 49 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8336 (ttpt) REVERT: E 305 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6603 (mp0) REVERT: E 355 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: E 803 LYS cc_start: 0.7580 (tptt) cc_final: 0.7357 (mttm) REVERT: C 7 TYR cc_start: 0.7403 (t80) cc_final: 0.7131 (t80) REVERT: C 19 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7537 (ptpt) REVERT: C 213 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.6723 (tpp) REVERT: C 267 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7565 (tt) REVERT: C 328 GLU cc_start: 0.6239 (tp30) cc_final: 0.5933 (tt0) REVERT: C 334 TYR cc_start: 0.5614 (OUTLIER) cc_final: 0.4360 (t80) REVERT: C 397 LYS cc_start: 0.6536 (mmtm) cc_final: 0.6144 (pmmt) REVERT: C 804 MET cc_start: 0.5115 (OUTLIER) cc_final: 0.4723 (tpt) REVERT: C 817 GLU cc_start: 0.5436 (mm-30) cc_final: 0.5066 (tp30) outliers start: 83 outliers final: 41 residues processed: 366 average time/residue: 0.7612 time to fit residues: 331.2719 Evaluate side-chains 357 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 300 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 804 MET Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 725 ASN Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 799 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 805 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 334 TYR Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 786 LEU Chi-restraints excluded: chain C residue 804 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 307 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 168 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 381 optimal weight: 1.9990 chunk 145 optimal weight: 0.0770 chunk 216 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 302 GLN A 360 HIS A 810 ASN B 277 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN D 725 ASN D 810 ASN ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 646 GLN E 723 ASN C 212 GLN C 390 GLN C 645 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.152494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.122403 restraints weight = 45951.098| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.82 r_work: 0.3080 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35634 Z= 0.116 Angle : 0.523 9.447 48246 Z= 0.273 Chirality : 0.041 0.155 4990 Planarity : 0.004 0.053 6238 Dihedral : 4.663 67.173 4711 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.63 % Allowed : 15.19 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 4235 helix: 1.11 (0.13), residues: 1779 sheet: 0.13 (0.21), residues: 636 loop : -1.33 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 341 TYR 0.028 0.001 TYR E 209 PHE 0.017 0.001 PHE E 160 TRP 0.039 0.001 TRP A 246 HIS 0.003 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00267 (35634) covalent geometry : angle 0.52274 (48246) hydrogen bonds : bond 0.03734 ( 1522) hydrogen bonds : angle 4.73840 ( 4335) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 322 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8101 (t0) cc_final: 0.7877 (t0) REVERT: A 727 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8804 (tt) REVERT: A 759 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8274 (tm-30) REVERT: B 42 TYR cc_start: 0.8064 (p90) cc_final: 0.7597 (p90) REVERT: B 169 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7746 (tp-100) REVERT: B 239 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7448 (m-10) REVERT: B 821 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7631 (pp) REVERT: D 57 GLU cc_start: 0.7581 (pp20) cc_final: 0.7054 (tp30) REVERT: D 102 LYS cc_start: 0.7750 (mppt) cc_final: 0.7518 (tppt) REVERT: D 287 GLN cc_start: 0.8384 (tp40) cc_final: 0.7786 (tp-100) REVERT: D 430 TYR cc_start: 0.7133 (m-80) cc_final: 0.6778 (m-80) REVERT: D 804 MET cc_start: 0.6584 (tpt) cc_final: 0.6217 (tpt) REVERT: D 810 ASN cc_start: 0.6972 (OUTLIER) cc_final: 0.6591 (t0) REVERT: E 49 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8341 (ttpt) REVERT: E 305 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6594 (mp0) REVERT: E 363 ARG cc_start: 0.5641 (mtp180) cc_final: 0.5402 (mtt-85) REVERT: E 803 LYS cc_start: 0.7615 (tptt) cc_final: 0.7412 (mttm) REVERT: C 7 TYR cc_start: 0.7448 (t80) cc_final: 0.7146 (t80) REVERT: C 19 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7524 (ptpt) REVERT: C 267 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7558 (tt) REVERT: C 328 GLU cc_start: 0.6238 (tp30) cc_final: 0.6012 (tt0) REVERT: C 334 TYR cc_start: 0.5735 (OUTLIER) cc_final: 0.4547 (t80) REVERT: C 390 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7945 (mt0) REVERT: C 397 LYS cc_start: 0.6337 (mmtm) cc_final: 0.5981 (pmmt) REVERT: C 756 MET cc_start: 0.3284 (pp-130) cc_final: 0.2718 (pp-130) REVERT: C 804 MET cc_start: 0.5028 (OUTLIER) cc_final: 0.4686 (tpt) REVERT: C 817 GLU cc_start: 0.5420 (mm-30) cc_final: 0.5053 (tp30) outliers start: 60 outliers final: 29 residues processed: 368 average time/residue: 0.7445 time to fit residues: 327.2754 Evaluate side-chains 347 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 306 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 804 MET Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 752 ASP Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 805 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 334 TYR Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 390 GLN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 804 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 287 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 376 optimal weight: 6.9990 chunk 292 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 322 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 chunk 289 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 360 HIS A 810 ASN B 277 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 ASN B 773 GLN D 671 ASN ** D 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 810 ASN ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 646 GLN E 762 GLN C 212 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.150899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120986 restraints weight = 45982.852| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.97 r_work: 0.3045 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35634 Z= 0.165 Angle : 0.555 9.497 48246 Z= 0.289 Chirality : 0.043 0.156 4990 Planarity : 0.004 0.052 6238 Dihedral : 4.689 67.574 4711 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.41 % Allowed : 15.95 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 4235 helix: 1.09 (0.13), residues: 1775 sheet: 0.13 (0.21), residues: 636 loop : -1.35 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 341 TYR 0.030 0.001 TYR E 209 PHE 0.020 0.001 PHE E 160 TRP 0.047 0.002 TRP A 246 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00398 (35634) covalent geometry : angle 0.55510 (48246) hydrogen bonds : bond 0.04089 ( 1522) hydrogen bonds : angle 4.78839 ( 4335) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10108.71 seconds wall clock time: 173 minutes 43.67 seconds (10423.67 seconds total)