Starting phenix.real_space_refine on Fri Mar 6 23:04:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l6i_62853/03_2026/9l6i_62853.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l6i_62853/03_2026/9l6i_62853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l6i_62853/03_2026/9l6i_62853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l6i_62853/03_2026/9l6i_62853.map" model { file = "/net/cci-nas-00/data/ceres_data/9l6i_62853/03_2026/9l6i_62853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l6i_62853/03_2026/9l6i_62853.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 22257 2.51 5 N 5844 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 25 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: 34770 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6957 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: 6957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6957 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: 6942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6942 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, '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 Chain: "D" Number of atoms: 6957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6957 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: 6957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6957 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 Time building chain proxies: 8.55, per 1000 atoms: 0.25 Number of scatterers: 34770 At special positions: 0 Unit cell: (100.43, 176.79, 202.52, 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 5844 7.00 C 22257 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: 2.85 Conformation dependent library (CDL) restraints added in 1.6 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: 206 helices and 41 sheets defined 51.2% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 27 through 34 removed outlier: 3.857A pdb=" N GLU A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 40 removed outlier: 3.916A pdb=" N TRP A 38 " --> pdb=" O ASN A 35 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP A 40 " --> pdb=" O TRP A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 52 removed outlier: 3.712A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 71 through 81 Processing helix chain 'A' and resid 81 through 100 Processing helix chain 'A' and resid 128 through 144 removed outlier: 3.706A pdb=" N MET A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 removed outlier: 4.029A pdb=" N THR A 238 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 267 Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 283 through 295 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 removed outlier: 4.123A pdb=" N HIS A 323 " --> pdb=" O PRO A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.788A pdb=" N ARG A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 366 through 374 Processing helix chain 'A' and resid 381 through 392 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 Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 510 through 520 removed outlier: 3.684A pdb=" N ARG A 514 " --> pdb=" O THR A 511 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA A 515 " --> pdb=" O TYR A 512 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N HIS A 516 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 517 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 518 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR A 520 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 530 Processing helix chain 'A' and resid 548 through 564 removed outlier: 3.657A pdb=" N ARG A 564 " --> pdb=" O GLU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 568 removed outlier: 3.682A pdb=" N LEU A 568 " --> pdb=" O PRO A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 578 through 589 removed outlier: 3.672A pdb=" N SER A 587 " --> pdb=" O ARG A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 612 removed outlier: 3.881A 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 664 through 670 removed outlier: 3.571A pdb=" N MET A 668 " --> pdb=" O ASP A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 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 709 through 741 removed outlier: 5.863A pdb=" N ASN A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU A 727 " --> pdb=" O ASN A 723 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA A 728 " --> pdb=" O ASP A 724 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 741 " --> pdb=" O SER A 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 35 removed outlier: 3.908A pdb=" N GLU B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 removed outlier: 4.257A pdb=" N TRP B 40 " --> pdb=" O MET B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 51 removed outlier: 3.655A pdb=" N ARG B 45 " --> pdb=" O ASN B 41 " (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 82 through 100 Processing helix chain 'B' and resid 128 through 145 Processing helix chain 'B' and resid 234 through 240 removed outlier: 3.519A pdb=" N ILE B 237 " --> pdb=" O ASP B 234 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR B 238 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER B 240 " --> pdb=" O ILE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 265 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.744A pdb=" N LEU B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 310 Processing helix chain 'B' and resid 319 through 323 Processing helix chain 'B' and resid 327 through 335 removed outlier: 4.127A pdb=" N TYR B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 393 through 396 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 Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 441 through 446 removed outlier: 3.651A pdb=" N TRP B 445 " --> pdb=" O ASN B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 451 Processing helix chain 'B' and resid 452 through 482 Processing helix chain 'B' and resid 485 through 493 Processing helix chain 'B' and resid 514 through 520 removed outlier: 3.623A pdb=" N LEU B 517 " --> pdb=" O ARG B 514 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 518 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 520 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 530 removed outlier: 3.579A pdb=" N LEU B 525 " --> pdb=" O ASP B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 563 Processing helix chain 'B' and resid 578 through 589 Processing helix chain 'B' and resid 605 through 613 removed outlier: 3.859A pdb=" N ASN B 613 " --> pdb=" O LLP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 629 removed outlier: 4.431A pdb=" N GLU B 627 " --> pdb=" O GLY B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 664 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 709 through 721 Processing helix chain 'B' and resid 721 through 741 removed outlier: 6.061A pdb=" N LEU B 727 " --> pdb=" O ASN B 723 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA B 728 " --> pdb=" O ASP B 724 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU B 740 " --> pdb=" O GLU B 736 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG B 741 " --> pdb=" O SER B 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 26 Processing helix chain 'C' and resid 27 through 33 removed outlier: 3.923A pdb=" N GLU C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 40 removed outlier: 3.843A pdb=" N TRP C 38 " --> pdb=" O ASN C 35 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP C 40 " --> pdb=" O TRP C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 52 removed outlier: 3.731A pdb=" N ARG C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 3.946A 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 70 Processing helix chain 'C' and resid 71 through 81 Processing helix chain 'C' and resid 81 through 100 Processing helix chain 'C' and resid 128 through 145 Processing helix chain 'C' and resid 234 through 239 removed outlier: 3.816A pdb=" N THR C 238 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR C 239 " --> pdb=" O PRO C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 267 Processing helix chain 'C' and resid 282 through 295 removed outlier: 3.938A pdb=" N LEU C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 310 Processing helix chain 'C' and resid 327 through 336 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.840A pdb=" N ARG C 341 " --> pdb=" O GLY C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 353 removed outlier: 3.946A pdb=" N GLY C 353 " --> pdb=" O PHE C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 374 Processing helix chain 'C' and resid 381 through 393 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 Processing helix chain 'C' and resid 485 through 487 No H-bonds generated for 'chain 'C' and resid 485 through 487' Processing helix chain 'C' and resid 488 through 494 Processing helix chain 'C' and resid 514 through 519 removed outlier: 3.863A pdb=" N LEU C 517 " --> pdb=" O ARG C 514 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 518 " --> pdb=" O ALA C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 530 Processing helix chain 'C' and resid 549 through 563 Processing helix chain 'C' and resid 578 through 589 Processing helix chain 'C' and resid 605 through 613 removed outlier: 3.989A pdb=" N MET C 612 " --> pdb=" O GLU C 608 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN C 613 " --> pdb=" O LLP C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 629 Processing helix chain 'C' and resid 645 through 664 Processing helix chain 'C' and resid 664 through 671 removed outlier: 3.536A pdb=" N MET C 668 " --> pdb=" O ASP C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 692 Processing helix chain 'C' and resid 693 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: 5.414A pdb=" N LEU C 727 " --> pdb=" O ASN C 723 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA C 728 " --> pdb=" O ASP C 724 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU C 740 " --> pdb=" O GLU C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.631A pdb=" N LEU C 755 " --> pdb=" O ASP C 752 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA C 757 " --> pdb=" O MET C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 794 removed outlier: 3.638A pdb=" N GLY C 793 " --> pdb=" O PRO C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 845 removed outlier: 3.593A pdb=" N PHE C 845 " --> pdb=" O ARG C 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.551A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 40 removed outlier: 4.057A pdb=" N TRP D 38 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TRP D 40 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 52 removed outlier: 3.789A pdb=" N ARG D 45 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 59 Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 71 through 80 Processing helix chain 'D' and resid 81 through 100 Processing helix chain 'D' and resid 128 through 145 removed outlier: 3.727A pdb=" N MET D 132 " --> pdb=" O GLY D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 239 removed outlier: 4.242A pdb=" N THR D 238 " --> pdb=" O ARG D 235 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR D 239 " --> pdb=" O PRO D 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 235 through 239' Processing helix chain 'D' and resid 245 through 267 Processing helix chain 'D' and resid 283 through 297 removed outlier: 3.625A pdb=" N GLY D 297 " --> pdb=" O ILE D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 310 Processing helix chain 'D' and resid 319 through 323 Processing helix chain 'D' and resid 327 through 336 removed outlier: 4.320A pdb=" N LYS D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 343 removed outlier: 3.899A 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 432 through 439 removed outlier: 4.520A pdb=" N MET D 436 " --> pdb=" O LYS D 433 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN D 437 " --> pdb=" O ASN D 434 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN D 439 " --> pdb=" O MET D 436 " (cutoff:3.500A) 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 488 through 495 removed outlier: 3.613A pdb=" N ARG D 495 " --> pdb=" O SER D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 520 removed outlier: 3.523A pdb=" N THR D 520 " --> pdb=" O LEU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 530 removed outlier: 3.593A pdb=" N LEU D 525 " --> pdb=" O ASP D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 564 removed outlier: 3.505A pdb=" N ARG D 564 " --> pdb=" O GLU D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 589 removed outlier: 3.798A pdb=" N SER D 587 " --> pdb=" O ARG D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 612 removed outlier: 3.708A pdb=" N MET D 612 " --> pdb=" O GLU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 629 removed outlier: 4.540A pdb=" N GLU D 627 " --> pdb=" O GLY D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 664 Processing helix chain 'D' and resid 664 through 671 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 742 removed outlier: 6.368A pdb=" N ASN D 723 " --> pdb=" O LYS D 719 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP D 724 " --> pdb=" O LEU D 720 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LEU D 727 " --> pdb=" O ASN D 723 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA D 728 " --> pdb=" O ASP D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 756 Processing helix chain 'E' and resid 23 through 26 Processing helix chain 'E' and resid 27 through 35 removed outlier: 4.404A pdb=" N GLU E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 52 removed outlier: 3.647A pdb=" N ARG E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 3.923A 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 69 Processing helix chain 'E' and resid 71 through 81 removed outlier: 3.942A pdb=" N VAL E 79 " --> pdb=" O LYS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 100 Processing helix chain 'E' and resid 128 through 144 Processing helix chain 'E' and resid 234 through 239 removed outlier: 3.693A pdb=" N ILE E 237 " --> pdb=" O ASP E 234 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR E 238 " --> pdb=" O ARG E 235 " (cutoff:3.500A) removed outlier: 3.839A 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 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: 4.146A pdb=" N LEU E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 310 Processing helix chain 'E' and resid 319 through 323 Processing helix chain 'E' and resid 327 through 336 removed outlier: 3.551A pdb=" N TYR E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.533A pdb=" N ARG E 341 " --> pdb=" O GLY E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 353 removed outlier: 4.051A pdb=" N GLY E 353 " --> pdb=" O PHE E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 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 434 through 438 Processing helix chain 'E' and resid 441 through 446 removed outlier: 3.503A pdb=" N TRP E 445 " --> pdb=" O ASN E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 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 514 through 519 removed outlier: 3.510A pdb=" N LEU E 517 " --> pdb=" O ARG E 514 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU E 518 " --> pdb=" O ALA E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 530 Processing helix chain 'E' and resid 548 through 563 Processing helix chain 'E' and resid 578 through 589 Processing helix chain 'E' and resid 605 through 612 removed outlier: 3.824A pdb=" N MET E 612 " --> pdb=" O GLU E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 623 through 629 removed outlier: 4.442A pdb=" N GLU E 627 " --> pdb=" O GLY E 623 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 664 Processing helix chain 'E' and resid 664 through 670 removed outlier: 3.676A 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 725 through 741 Processing helix chain 'E' and resid 742 through 745 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 758 through 759 removed outlier: 4.486A pdb=" N ALA B 758 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N SER B 825 " --> pdb=" O GLU B 788 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU B 788 " --> pdb=" O SER B 825 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B 785 " --> pdb=" O TYR B 797 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN B 795 " --> pdb=" O LYS B 787 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 758 through 759 removed outlier: 4.486A pdb=" N ALA B 758 " --> pdb=" O THR A 17 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 186 Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 186 removed outlier: 7.252A pdb=" N MET A 148 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N TYR A 221 " --> pdb=" O MET A 148 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA A 150 " --> pdb=" O TYR A 221 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU A 223 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY A 152 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 376 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 377 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 161 through 164 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.669A pdb=" N PHE A 364 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 571 through 574 removed outlier: 8.381A pdb=" N ILE A 572 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE A 538 " --> pdb=" O ILE A 572 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU A 574 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE A 540 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU A 501 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE A 539 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 503 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER A 541 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE A 505 " --> pdb=" O SER A 541 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N CYS A 506 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ASN A 617 " --> pdb=" O TRP A 635 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU A 637 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N SER A 619 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 746 through 750 removed outlier: 7.297A pdb=" N VAL A 769 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LYS A 750 " --> pdb=" O GLN A 767 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN A 767 " --> pdb=" O LYS A 750 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 806 " --> pdb=" O THR A 813 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 800 through 801 Processing sheet with id=AB2, first strand: chain 'A' and resid 800 through 801 removed outlier: 3.576A pdb=" N PHE A 826 " --> pdb=" O THR E 16 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 786 through 791 removed outlier: 7.355A pdb=" N GLN A 795 " --> pdb=" O LYS A 787 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 14 through 18 removed outlier: 3.670A pdb=" N GLU C 782 " --> pdb=" O ARG C 831 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LYS C 787 " --> pdb=" O VAL C 796 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL C 796 " --> pdb=" O LYS C 787 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 185 through 186 Processing sheet with id=AB6, first strand: chain 'B' and resid 185 through 186 removed outlier: 7.300A pdb=" N MET B 148 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N TYR B 221 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA B 150 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LEU B 223 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY B 152 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 377 " --> pdb=" O GLY B 407 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 162 through 164 Processing sheet with id=AB8, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AB9, first strand: chain 'B' and resid 571 through 574 removed outlier: 8.415A pdb=" N ILE B 572 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE B 538 " --> pdb=" O ILE B 572 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU B 574 " --> pdb=" O PHE B 538 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE B 540 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU B 501 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE B 539 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 503 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N SER B 541 " --> pdb=" O ILE B 503 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE B 505 " --> pdb=" O SER B 541 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N CYS B 506 " --> pdb=" O MET B 593 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TRP B 592 " --> pdb=" O LEU B 618 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL B 620 " --> pdb=" O TRP B 592 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASN B 594 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASN B 617 " --> pdb=" O TRP B 635 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU B 637 " --> pdb=" O ASN B 617 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N SER B 619 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 746 through 751 removed outlier: 5.733A pdb=" N VAL B 747 " --> pdb=" O ASP B 771 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP B 771 " --> pdb=" O VAL B 747 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN B 811 " --> pdb=" O GLU B 808 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY B 806 " --> pdb=" O THR B 813 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU B 815 " --> pdb=" O MET B 804 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N MET B 804 " --> pdb=" O GLU B 815 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AC3, first strand: chain 'D' and resid 746 through 751 removed outlier: 6.058A pdb=" N VAL D 747 " --> pdb=" O ASP D 771 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASP D 771 " --> pdb=" O VAL D 747 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D 749 " --> pdb=" O VAL D 769 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASN D 811 " --> pdb=" O HIS D 807 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N HIS D 807 " --> pdb=" O ASN D 811 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR D 813 " --> pdb=" O VAL D 805 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLU D 817 " --> pdb=" O PRO D 801 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LYS D 794 " --> pdb=" O GLN D 789 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLN D 789 " --> pdb=" O LYS D 794 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL D 796 " --> pdb=" O LYS D 787 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS D 787 " --> pdb=" O VAL D 796 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 781 " --> pdb=" O PHE D 802 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N MET D 804 " --> pdb=" O VAL D 779 " (cutoff:3.500A) removed outlier: 11.908A pdb=" N VAL D 779 " --> pdb=" O MET D 804 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU D 788 " --> pdb=" O SER D 825 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N SER D 825 " --> pdb=" O GLU D 788 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA D 758 " --> pdb=" O LYS C 19 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 746 through 751 removed outlier: 6.058A pdb=" N VAL D 747 " --> pdb=" O ASP D 771 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASP D 771 " --> pdb=" O VAL D 747 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D 749 " --> pdb=" O VAL D 769 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASN D 811 " --> pdb=" O HIS D 807 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N HIS D 807 " --> pdb=" O ASN D 811 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR D 813 " --> pdb=" O VAL D 805 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLU D 817 " --> pdb=" O PRO D 801 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LYS D 794 " --> pdb=" O GLN D 789 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLN D 789 " --> pdb=" O LYS D 794 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL D 796 " --> pdb=" O LYS D 787 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS D 787 " --> pdb=" O VAL D 796 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 781 " --> pdb=" O PHE D 802 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N MET D 804 " --> pdb=" O VAL D 779 " (cutoff:3.500A) removed outlier: 11.908A pdb=" N VAL D 779 " --> pdb=" O MET D 804 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU D 788 " --> pdb=" O SER D 825 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N SER D 825 " --> pdb=" O GLU D 788 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL D 830 " --> pdb=" O LEU D 851 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 185 through 186 removed outlier: 3.717A pdb=" N TYR C 204 " --> pdb=" O TYR C 201 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 185 through 186 removed outlier: 4.569A pdb=" N LYS C 219 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 110 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER C 109 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N HIS C 275 " --> pdb=" O SER C 109 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 111 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR C 274 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR C 314 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N CYS C 276 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AC8, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AC9, first strand: chain 'C' and resid 571 through 574 removed outlier: 8.260A pdb=" N ILE C 572 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE C 538 " --> pdb=" O ILE C 572 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU C 574 " --> pdb=" O PHE C 538 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE C 540 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER C 541 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 746 through 751 removed outlier: 3.670A pdb=" N HIS C 746 " --> pdb=" O ASP C 771 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL C 769 " --> pdb=" O VAL C 748 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS C 750 " --> pdb=" O GLN C 767 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N GLN C 767 " --> pdb=" O LYS C 750 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASN C 811 " --> pdb=" O HIS C 807 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N HIS C 807 " --> pdb=" O ASN C 811 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR C 813 " --> pdb=" O VAL C 805 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 17 through 18 removed outlier: 7.757A pdb=" N SER E 825 " --> pdb=" O GLU E 788 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU E 788 " --> pdb=" O SER E 825 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LYS E 787 " --> pdb=" O VAL E 796 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL E 796 " --> pdb=" O LYS E 787 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLN E 789 " --> pdb=" O LYS E 794 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LYS E 794 " --> pdb=" O GLN E 789 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 17 through 18 Processing sheet with id=AD4, first strand: chain 'D' and resid 185 through 186 Processing sheet with id=AD5, first strand: chain 'D' and resid 185 through 186 removed outlier: 4.266A pdb=" N LYS D 219 " --> pdb=" O MET D 148 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL D 110 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL D 151 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR D 112 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N PHE D 153 " --> pdb=" O TYR D 112 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU D 376 " --> pdb=" O SER D 311 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL D 377 " --> pdb=" O GLY D 407 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 162 through 164 Processing sheet with id=AD7, first strand: chain 'D' and resid 325 through 326 Processing sheet with id=AD8, first strand: chain 'D' and resid 571 through 574 removed outlier: 8.369A pdb=" N ILE D 572 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE D 538 " --> pdb=" O ILE D 572 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU D 574 " --> pdb=" O PHE D 538 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE D 540 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU D 501 " --> pdb=" O LEU D 537 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE D 539 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE D 503 " --> pdb=" O PHE D 539 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N SER D 541 " --> pdb=" O ILE D 503 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE D 505 " --> pdb=" O SER D 541 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N CYS D 506 " --> pdb=" O MET D 593 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASN D 617 " --> pdb=" O TRP D 635 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LEU D 637 " --> pdb=" O ASN D 617 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER D 619 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 185 through 186 Processing sheet with id=AE1, first strand: chain 'E' and resid 185 through 186 removed outlier: 7.389A pdb=" N MET E 148 " --> pdb=" O LYS E 219 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N TYR E 221 " --> pdb=" O MET E 148 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA E 150 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU E 223 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY E 152 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR E 274 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR E 314 " --> pdb=" O TYR E 274 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS E 276 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU E 376 " --> pdb=" O SER E 311 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL E 377 " --> pdb=" O GLY E 407 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 161 through 164 Processing sheet with id=AE3, first strand: chain 'E' and resid 325 through 326 removed outlier: 3.663A pdb=" N PHE E 364 " --> pdb=" O PHE E 326 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 571 through 574 removed outlier: 3.583A pdb=" N SER E 541 " --> pdb=" O PHE E 505 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N CYS E 506 " --> pdb=" O MET E 593 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASN E 617 " --> pdb=" O TRP E 635 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LEU E 637 " --> pdb=" O ASN E 617 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER E 619 " --> pdb=" O LEU E 637 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 746 through 751 removed outlier: 6.251A pdb=" N VAL E 747 " --> pdb=" O ASP E 771 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP E 771 " --> pdb=" O VAL E 747 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER E 749 " --> pdb=" O VAL E 769 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN E 811 " --> pdb=" O HIS E 807 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N HIS E 807 " --> pdb=" O ASN E 811 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR E 813 " --> pdb=" O VAL E 805 " (cutoff:3.500A) 1693 hydrogen bonds defined for protein. 4716 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.15 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10606 1.33 - 1.46: 6836 1.46 - 1.58: 17893 1.58 - 1.70: 4 1.70 - 1.82: 325 Bond restraints: 35664 Sorted by residual: bond pdb=" OP4 LLP E 609 " pdb=" P LLP E 609 " ideal model delta sigma weight residual 1.726 1.612 0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" OP4 LLP D 609 " pdb=" P LLP D 609 " ideal model delta sigma weight residual 1.726 1.613 0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" OP4 LLP A 609 " pdb=" P LLP A 609 " ideal model delta sigma weight residual 1.726 1.614 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" OP4 LLP B 609 " pdb=" P LLP B 609 " ideal model delta sigma weight residual 1.726 1.614 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" N LEU B 256 " pdb=" CA LEU B 256 " ideal model delta sigma weight residual 1.457 1.504 -0.046 1.29e-02 6.01e+03 1.29e+01 ... (remaining 35659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 47476 2.25 - 4.50: 695 4.50 - 6.75: 95 6.75 - 8.99: 12 8.99 - 11.24: 3 Bond angle restraints: 48281 Sorted by residual: angle pdb=" N LEU B 267 " pdb=" CA LEU B 267 " pdb=" C LEU B 267 " ideal model delta sigma weight residual 114.31 107.21 7.10 1.29e+00 6.01e-01 3.03e+01 angle pdb=" N LEU B 264 " pdb=" CA LEU B 264 " pdb=" C LEU B 264 " ideal model delta sigma weight residual 111.36 105.85 5.51 1.09e+00 8.42e-01 2.56e+01 angle pdb=" N LEU C 755 " pdb=" CA LEU C 755 " pdb=" C LEU C 755 " ideal model delta sigma weight residual 112.97 107.89 5.08 1.06e+00 8.90e-01 2.30e+01 angle pdb=" N LYS B 265 " pdb=" CA LYS B 265 " pdb=" C LYS B 265 " ideal model delta sigma weight residual 110.35 104.06 6.29 1.38e+00 5.25e-01 2.08e+01 angle pdb=" N LYS D 513 " pdb=" CA LYS D 513 " pdb=" C LYS D 513 " ideal model delta sigma weight residual 113.20 107.74 5.46 1.21e+00 6.83e-01 2.03e+01 ... (remaining 48276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.26: 19282 26.26 - 52.52: 1569 52.52 - 78.79: 222 78.79 - 105.05: 27 105.05 - 131.31: 1 Dihedral angle restraints: 21101 sinusoidal: 8646 harmonic: 12455 Sorted by residual: dihedral pdb=" CD LLP B 609 " pdb=" CE LLP B 609 " pdb=" NZ LLP B 609 " pdb=" C4' LLP B 609 " ideal model delta sinusoidal sigma weight residual 249.72 118.41 131.31 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" CA LEU C 618 " pdb=" C LEU C 618 " pdb=" N SER C 619 " pdb=" CA SER C 619 " ideal model delta harmonic sigma weight residual -180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LEU B 492 " pdb=" C LEU B 492 " pdb=" N LEU B 493 " pdb=" CA LEU B 493 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 21098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3697 0.047 - 0.095: 1000 0.095 - 0.142: 272 0.142 - 0.190: 16 0.190 - 0.237: 5 Chirality restraints: 4990 Sorted by residual: chirality pdb=" CA PHE B 845 " pdb=" N PHE B 845 " pdb=" C PHE B 845 " pdb=" CB PHE B 845 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA LLP E 609 " pdb=" N LLP E 609 " pdb=" C LLP E 609 " pdb=" CB LLP E 609 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE B 261 " pdb=" N ILE B 261 " pdb=" C ILE B 261 " pdb=" CB ILE B 261 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 4987 not shown) Planarity restraints: 6243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP B 609 " -0.074 2.00e-02 2.50e+03 2.53e-01 6.42e+02 pdb=" NZ LLP B 609 " 0.308 2.00e-02 2.50e+03 pdb=" C4 LLP B 609 " 0.137 2.00e-02 2.50e+03 pdb=" C4' LLP B 609 " -0.371 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP E 609 " -0.174 2.00e-02 2.50e+03 2.47e-01 6.12e+02 pdb=" NZ LLP E 609 " 0.056 2.00e-02 2.50e+03 pdb=" C4 LLP E 609 " -0.261 2.00e-02 2.50e+03 pdb=" C4' LLP E 609 " 0.379 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP D 609 " 0.050 2.00e-02 2.50e+03 5.20e-02 2.71e+01 pdb=" NZ LLP D 609 " -0.045 2.00e-02 2.50e+03 pdb=" C4 LLP D 609 " 0.053 2.00e-02 2.50e+03 pdb=" C4' LLP D 609 " -0.059 2.00e-02 2.50e+03 ... (remaining 6240 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 574 2.65 - 3.22: 31750 3.22 - 3.78: 55218 3.78 - 4.34: 78472 4.34 - 4.90: 130349 Nonbonded interactions: 296363 Sorted by model distance: nonbonded pdb=" O LEU B 518 " pdb=" OH TYR B 658 " model vdw 2.093 3.040 nonbonded pdb=" O LEU D 518 " pdb=" OH TYR D 658 " model vdw 2.118 3.040 nonbonded pdb=" OH TYR A 112 " pdb=" ND2 ASN A 277 " model vdw 2.195 3.120 nonbonded pdb=" O GLY E 259 " pdb=" OG1 THR E 263 " model vdw 2.196 3.040 nonbonded pdb=" OE1 GLN A 121 " pdb=" OG1 THR A 580 " model vdw 2.197 3.040 ... (remaining 296358 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 34.900 Find NCS groups from input model: 0.690 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: 0.000 Load rotamer database and sin/cos tables:7.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.006 0.114 35664 Z= 0.283 Angle : 0.672 11.243 48281 Z= 0.380 Chirality : 0.046 0.237 4990 Planarity : 0.006 0.253 6243 Dihedral : 18.139 131.310 13151 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.60 % Favored : 94.36 % Rotamer: Outliers : 3.96 % Allowed : 25.05 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.23 (0.13), residues: 4235 helix: 1.07 (0.13), residues: 1736 sheet: -0.12 (0.20), residues: 613 loop : -1.33 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 741 TYR 0.028 0.002 TYR D 696 PHE 0.031 0.002 PHE E 160 TRP 0.035 0.002 TRP C 396 HIS 0.005 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00612 (35664) covalent geometry : angle 0.67184 (48281) hydrogen bonds : bond 0.16988 ( 1641) hydrogen bonds : angle 6.93857 ( 4716) *********************** 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 521 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 375 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.7080 (tppt) cc_final: 0.6718 (ttmt) REVERT: A 15 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7199 (tt0) REVERT: A 57 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7703 (mm-30) REVERT: A 76 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.6863 (tp30) REVERT: A 102 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7693 (mptt) REVERT: A 294 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: A 759 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.6735 (tm-30) REVERT: A 803 LYS cc_start: 0.7678 (tptp) cc_final: 0.7268 (tppt) REVERT: A 811 ASN cc_start: 0.6046 (m-40) cc_final: 0.5664 (p0) REVERT: A 815 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6838 (tm-30) REVERT: A 817 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7259 (tm-30) REVERT: B 24 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7314 (mmmm) REVERT: B 49 LYS cc_start: 0.7588 (tttp) cc_final: 0.7040 (tmmt) REVERT: B 57 GLU cc_start: 0.7455 (mp0) cc_final: 0.7155 (mp0) REVERT: B 69 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.5508 (mmt90) REVERT: B 157 TYR cc_start: 0.7895 (m-80) cc_final: 0.7522 (m-10) REVERT: B 220 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8292 (tp) REVERT: B 789 GLN cc_start: 0.7821 (tp-100) cc_final: 0.7116 (pm20) REVERT: C 57 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7199 (pt0) REVERT: C 58 LYS cc_start: 0.7220 (pptt) cc_final: 0.6760 (mmtt) REVERT: C 85 MET cc_start: 0.7265 (mmm) cc_final: 0.6875 (mmp) REVERT: C 116 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.8330 (pm20) REVERT: C 119 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8930 (mm) REVERT: C 121 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: C 229 MET cc_start: 0.6626 (ptp) cc_final: 0.6313 (ptp) REVERT: C 294 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: C 443 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8533 (mp0) REVERT: C 508 ARG cc_start: 0.6054 (pmt-80) cc_final: 0.5069 (ttm-80) REVERT: C 509 PHE cc_start: 0.6373 (p90) cc_final: 0.6145 (p90) REVERT: C 593 MET cc_start: 0.8037 (mtp) cc_final: 0.7341 (ttp) REVERT: C 618 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7601 (tt) REVERT: C 727 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7523 (mp) REVERT: C 791 GLU cc_start: 0.7046 (tt0) cc_final: 0.6732 (pp20) REVERT: C 817 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: D 7 TYR cc_start: 0.6056 (t80) cc_final: 0.5645 (t80) REVERT: D 30 ASP cc_start: 0.7330 (t0) cc_final: 0.7063 (t0) REVERT: D 57 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: D 232 GLU cc_start: 0.7463 (mm-30) cc_final: 0.6727 (tp30) REVERT: D 239 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7182 (t80) REVERT: D 247 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7353 (mm-30) REVERT: D 335 MET cc_start: 0.8622 (mmm) cc_final: 0.8347 (mtp) REVERT: D 350 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7381 (tp) REVERT: D 443 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8158 (tp30) REVERT: D 651 GLN cc_start: 0.8418 (mt0) cc_final: 0.7922 (tt0) REVERT: D 759 GLU cc_start: 0.7080 (tt0) cc_final: 0.6793 (tt0) REVERT: D 817 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7065 (pp20) REVERT: E 19 LYS cc_start: 0.7998 (mttm) cc_final: 0.7155 (mmtm) REVERT: E 24 LYS cc_start: 0.7085 (mmpt) cc_final: 0.6242 (ptmm) REVERT: E 161 LYS cc_start: 0.8766 (ttmm) cc_final: 0.8271 (tttm) REVERT: E 186 ARG cc_start: 0.8132 (tpp80) cc_final: 0.7456 (ttp-170) REVERT: E 198 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7713 (OUTLIER) REVERT: E 205 GLN cc_start: 0.7205 (mt0) cc_final: 0.6988 (mm-40) REVERT: E 246 TRP cc_start: 0.6947 (t-100) cc_final: 0.6606 (t-100) REVERT: E 287 GLN cc_start: 0.8160 (tp40) cc_final: 0.7646 (tm-30) REVERT: E 292 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.4763 (t80) REVERT: E 363 ARG cc_start: 0.6367 (mtm180) cc_final: 0.5573 (mtt180) REVERT: E 433 LYS cc_start: 0.8637 (mmtm) cc_final: 0.8286 (ptmt) REVERT: E 478 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8612 (p) REVERT: E 511 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8287 (m) REVERT: E 564 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8168 (mtt180) REVERT: E 631 GLU cc_start: 0.8389 (tt0) cc_final: 0.8130 (mt-10) REVERT: E 720 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7738 (mp) REVERT: E 756 MET cc_start: 0.7054 (pmt) cc_final: 0.6787 (pmm) REVERT: E 759 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.5988 (tm-30) REVERT: E 773 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6860 (tm-30) REVERT: E 790 PRO cc_start: 0.7546 (Cg_exo) cc_final: 0.7295 (Cg_endo) REVERT: E 795 GLN cc_start: 0.7182 (mt0) cc_final: 0.6454 (mm110) REVERT: E 815 GLU cc_start: 0.7498 (tt0) cc_final: 0.6915 (tm-30) outliers start: 146 outliers final: 86 residues processed: 494 average time/residue: 0.7477 time to fit residues: 439.5268 Evaluate side-chains 469 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 360 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 828 THR Chi-restraints excluded: chain C residue 850 TRP Chi-restraints excluded: chain C residue 852 ASN Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 740 GLU Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 204 TYR Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 292 TYR Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 511 THR Chi-restraints excluded: chain E residue 564 ARG Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 743 ASP Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 748 VAL Chi-restraints excluded: chain E residue 759 GLU Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 773 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 0.8980 chunk 424 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 659 ASN A 663 ASN A 822 ASN B 121 GLN B 248 ASN B 439 GLN B 807 HIS C 203 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** C 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 ASN D 671 ASN D 776 ASN D 852 ASN ** E 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 ASN E 649 GLN E 671 ASN ** E 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.156036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104962 restraints weight = 44525.387| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.30 r_work: 0.3108 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 35664 Z= 0.196 Angle : 0.576 13.923 48281 Z= 0.300 Chirality : 0.044 0.148 4990 Planarity : 0.004 0.051 6243 Dihedral : 8.162 80.745 4931 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.84 % Favored : 95.14 % Rotamer: Outliers : 5.62 % Allowed : 22.39 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.08 (0.13), residues: 4235 helix: 1.15 (0.12), residues: 1791 sheet: 0.00 (0.20), residues: 623 loop : -1.30 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 741 TYR 0.027 0.001 TYR D 696 PHE 0.026 0.001 PHE E 160 TRP 0.018 0.002 TRP C 734 HIS 0.004 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00466 (35664) covalent geometry : angle 0.57619 (48281) hydrogen bonds : bond 0.04777 ( 1641) hydrogen bonds : angle 5.29409 ( 4716) *********************** 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 584 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 377 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7765 (mm-30) REVERT: A 76 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6807 (tp30) REVERT: A 102 LYS cc_start: 0.8385 (mmmt) cc_final: 0.7890 (mptt) REVERT: A 277 ASN cc_start: 0.8344 (t0) cc_final: 0.8095 (t0) REVERT: A 294 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: A 433 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8601 (mmtt) REVERT: A 513 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7547 (mptp) REVERT: A 570 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.7833 (mmtm) REVERT: A 759 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.6631 (tm-30) REVERT: A 803 LYS cc_start: 0.7724 (tptp) cc_final: 0.7484 (tptp) REVERT: A 811 ASN cc_start: 0.6068 (m-40) cc_final: 0.5827 (p0) REVERT: A 815 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6794 (tm-30) REVERT: A 817 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7251 (tm-30) REVERT: A 830 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.7730 (p) REVERT: B 49 LYS cc_start: 0.7540 (tttp) cc_final: 0.7117 (tmmt) REVERT: B 57 GLU cc_start: 0.7641 (mp0) cc_final: 0.7306 (mp0) REVERT: B 157 TYR cc_start: 0.7812 (m-80) cc_final: 0.7562 (m-10) REVERT: B 220 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8377 (tp) REVERT: B 245 ASP cc_start: 0.7312 (m-30) cc_final: 0.7060 (p0) REVERT: B 363 ARG cc_start: 0.4975 (tpt-90) cc_final: 0.4758 (tpt-90) REVERT: B 608 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8216 (mt-10) REVERT: B 617 ASN cc_start: 0.9186 (OUTLIER) cc_final: 0.8910 (t0) REVERT: B 719 LYS cc_start: 0.7907 (tppp) cc_final: 0.7147 (tttm) REVERT: B 725 ASN cc_start: 0.6671 (OUTLIER) cc_final: 0.6262 (p0) REVERT: B 762 GLN cc_start: 0.7195 (tt0) cc_final: 0.6411 (pt0) REVERT: B 789 GLN cc_start: 0.7816 (tp-100) cc_final: 0.7077 (pm20) REVERT: B 838 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7114 (mmmt) REVERT: C 57 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7186 (pt0) REVERT: C 58 LYS cc_start: 0.7217 (pptt) cc_final: 0.6788 (mmtt) REVERT: C 116 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.8554 (pm20) REVERT: C 178 ASN cc_start: 0.7170 (t0) cc_final: 0.6886 (m-40) REVERT: C 194 PRO cc_start: 0.7815 (Cg_exo) cc_final: 0.7446 (Cg_endo) REVERT: C 195 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7655 (tt) REVERT: C 229 MET cc_start: 0.6803 (ptp) cc_final: 0.6595 (ptp) REVERT: C 246 TRP cc_start: 0.6490 (OUTLIER) cc_final: 0.6071 (t-100) REVERT: C 269 ILE cc_start: 0.6265 (OUTLIER) cc_final: 0.5965 (mt) REVERT: C 294 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: C 363 ARG cc_start: 0.7100 (mtm180) cc_final: 0.6353 (mtp180) REVERT: C 403 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: C 443 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8587 (mp0) REVERT: C 508 ARG cc_start: 0.6295 (OUTLIER) cc_final: 0.5084 (ttm-80) REVERT: C 509 PHE cc_start: 0.6526 (p90) cc_final: 0.6281 (p90) REVERT: C 518 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8641 (mp) REVERT: C 618 LEU cc_start: 0.7813 (tt) cc_final: 0.7597 (tp) REVERT: C 727 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7473 (mp) REVERT: C 735 LYS cc_start: 0.7265 (tptt) cc_final: 0.5914 (mtpt) REVERT: C 767 GLN cc_start: 0.6644 (OUTLIER) cc_final: 0.6087 (tm-30) REVERT: C 791 GLU cc_start: 0.7097 (tt0) cc_final: 0.6396 (pm20) REVERT: C 817 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6474 (mp0) REVERT: C 845 PHE cc_start: 0.5937 (t80) cc_final: 0.5694 (t80) REVERT: D 30 ASP cc_start: 0.7329 (t0) cc_final: 0.7085 (t0) REVERT: D 57 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: D 239 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.6985 (t80) REVERT: D 247 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7292 (mm-30) REVERT: D 335 MET cc_start: 0.8484 (mmm) cc_final: 0.8130 (mtp) REVERT: D 350 ILE cc_start: 0.7684 (tt) cc_final: 0.7408 (tp) REVERT: D 443 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8177 (tp30) REVERT: D 527 LYS cc_start: 0.8244 (mttt) cc_final: 0.7979 (mtmt) REVERT: D 651 GLN cc_start: 0.8374 (mt0) cc_final: 0.7931 (tt0) REVERT: D 759 GLU cc_start: 0.7115 (tt0) cc_final: 0.6834 (tt0) REVERT: D 817 GLU cc_start: 0.7581 (tm-30) cc_final: 0.6885 (pp20) REVERT: E 19 LYS cc_start: 0.8058 (mttm) cc_final: 0.7075 (mtpp) REVERT: E 121 GLN cc_start: 0.8785 (tt0) cc_final: 0.8560 (tt0) REVERT: E 161 LYS cc_start: 0.8686 (ttmm) cc_final: 0.8195 (tttm) REVERT: E 186 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7460 (ttp-170) REVERT: E 287 GLN cc_start: 0.8178 (tp40) cc_final: 0.7735 (tm-30) REVERT: E 363 ARG cc_start: 0.6427 (mtm180) cc_final: 0.5608 (mtt180) REVERT: E 433 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8269 (ptmt) REVERT: E 511 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8206 (m) REVERT: E 608 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: E 756 MET cc_start: 0.7179 (pmt) cc_final: 0.6881 (pmm) REVERT: E 773 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6546 (tm-30) REVERT: E 790 PRO cc_start: 0.7556 (Cg_endo) cc_final: 0.7267 (Cg_endo) REVERT: E 795 GLN cc_start: 0.7164 (mt0) cc_final: 0.6533 (mm110) REVERT: E 815 GLU cc_start: 0.7509 (tt0) cc_final: 0.6887 (tm-30) outliers start: 207 outliers final: 75 residues processed: 543 average time/residue: 0.7013 time to fit residues: 455.4267 Evaluate side-chains 449 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 346 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 725 ASN Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 246 TRP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 767 GLN Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 847 TYR Chi-restraints excluded: chain C residue 850 TRP Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 382 LYS Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 740 GLU Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 511 THR Chi-restraints excluded: chain E residue 541 SER Chi-restraints excluded: chain E residue 608 GLU Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 743 ASP Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 773 GLN Chi-restraints excluded: chain E residue 808 GLU Chi-restraints excluded: chain E residue 810 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 373 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 256 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 245 optimal weight: 30.0000 chunk 275 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 237 optimal weight: 0.9980 chunk 378 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 ASN B 545 HIS C 193 ASN C 230 ASN C 594 ASN ** C 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN D 810 ASN ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN ** E 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.155621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112123 restraints weight = 44363.069| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.32 r_work: 0.3119 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 35664 Z= 0.208 Angle : 0.569 11.689 48281 Z= 0.295 Chirality : 0.044 0.174 4990 Planarity : 0.004 0.048 6243 Dihedral : 7.217 88.381 4826 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.82 % Favored : 95.16 % Rotamer: Outliers : 5.67 % Allowed : 22.82 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.09 (0.13), residues: 4235 helix: 1.13 (0.12), residues: 1794 sheet: -0.01 (0.20), residues: 622 loop : -1.29 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 156 TYR 0.027 0.002 TYR D 696 PHE 0.028 0.001 PHE E 160 TRP 0.020 0.002 TRP C 734 HIS 0.004 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00497 (35664) covalent geometry : angle 0.56853 (48281) hydrogen bonds : bond 0.04656 ( 1641) hydrogen bonds : angle 5.11898 ( 4716) *********************** 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 584 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 375 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7796 (mm-30) REVERT: A 76 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6813 (tp30) REVERT: A 102 LYS cc_start: 0.8401 (mmmt) cc_final: 0.7902 (mptt) REVERT: A 294 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: A 513 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7625 (mptp) REVERT: A 570 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.7831 (mmtm) REVERT: A 759 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.6627 (tm-30) REVERT: A 803 LYS cc_start: 0.7717 (tptp) cc_final: 0.7352 (tppt) REVERT: A 815 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6769 (tm-30) REVERT: A 817 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7188 (tm-30) REVERT: A 830 VAL cc_start: 0.8095 (OUTLIER) cc_final: 0.7865 (p) REVERT: B 1 MET cc_start: 0.6176 (OUTLIER) cc_final: 0.5710 (ttt) REVERT: B 24 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7243 (mmmm) REVERT: B 49 LYS cc_start: 0.7656 (tttp) cc_final: 0.7210 (tmmt) REVERT: B 57 GLU cc_start: 0.7619 (mp0) cc_final: 0.7241 (mp0) REVERT: B 89 LYS cc_start: 0.7644 (mmmt) cc_final: 0.6966 (ttpp) REVERT: B 157 TYR cc_start: 0.7761 (m-80) cc_final: 0.7393 (m-10) REVERT: B 220 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8425 (tp) REVERT: B 245 ASP cc_start: 0.7275 (m-30) cc_final: 0.7056 (p0) REVERT: B 443 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8411 (mp0) REVERT: B 608 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8223 (mt-10) REVERT: B 617 ASN cc_start: 0.9195 (OUTLIER) cc_final: 0.8937 (t0) REVERT: B 719 LYS cc_start: 0.8035 (tppp) cc_final: 0.7355 (tttm) REVERT: B 725 ASN cc_start: 0.6776 (OUTLIER) cc_final: 0.6311 (p0) REVERT: B 762 GLN cc_start: 0.7231 (tt0) cc_final: 0.6454 (pt0) REVERT: B 789 GLN cc_start: 0.7859 (tp-100) cc_final: 0.7073 (pm20) REVERT: B 838 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7162 (mmmt) REVERT: C 57 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7161 (pt0) REVERT: C 58 LYS cc_start: 0.7232 (pptt) cc_final: 0.6825 (mmtt) REVERT: C 116 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.8491 (pm20) REVERT: C 178 ASN cc_start: 0.7237 (t0) cc_final: 0.7017 (m-40) REVERT: C 194 PRO cc_start: 0.7790 (Cg_exo) cc_final: 0.7419 (Cg_endo) REVERT: C 195 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7658 (tt) REVERT: C 229 MET cc_start: 0.7057 (ptp) cc_final: 0.6819 (ptp) REVERT: C 246 TRP cc_start: 0.6577 (OUTLIER) cc_final: 0.6118 (t60) REVERT: C 269 ILE cc_start: 0.6414 (OUTLIER) cc_final: 0.6129 (mt) REVERT: C 294 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: C 363 ARG cc_start: 0.7077 (mtm180) cc_final: 0.6320 (ttt180) REVERT: C 403 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: C 509 PHE cc_start: 0.6526 (p90) cc_final: 0.6272 (p90) REVERT: C 593 MET cc_start: 0.7887 (mtp) cc_final: 0.7602 (ttp) REVERT: C 618 LEU cc_start: 0.7840 (tt) cc_final: 0.7495 (tt) REVERT: C 727 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7460 (mp) REVERT: C 735 LYS cc_start: 0.7325 (tptt) cc_final: 0.6063 (mtpt) REVERT: C 767 GLN cc_start: 0.6571 (OUTLIER) cc_final: 0.6051 (tm-30) REVERT: C 791 GLU cc_start: 0.7165 (tt0) cc_final: 0.6464 (pm20) REVERT: C 817 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: C 832 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5023 (mmt) REVERT: C 847 TYR cc_start: 0.5691 (OUTLIER) cc_final: 0.4245 (t80) REVERT: D 7 TYR cc_start: 0.5999 (t80) cc_final: 0.5566 (t80) REVERT: D 30 ASP cc_start: 0.7366 (t0) cc_final: 0.7108 (t0) REVERT: D 57 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: D 247 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7299 (mm-30) REVERT: D 335 MET cc_start: 0.8465 (mmm) cc_final: 0.7964 (mmm) REVERT: D 350 ILE cc_start: 0.7724 (tt) cc_final: 0.7447 (tp) REVERT: D 361 ASN cc_start: 0.7302 (m110) cc_final: 0.6875 (p0) REVERT: D 390 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: D 443 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8171 (tp30) REVERT: D 527 LYS cc_start: 0.8248 (mttt) cc_final: 0.7990 (mtmt) REVERT: D 651 GLN cc_start: 0.8414 (mt0) cc_final: 0.7941 (tt0) REVERT: D 713 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8632 (tt0) REVERT: D 759 GLU cc_start: 0.7108 (tt0) cc_final: 0.6824 (tt0) REVERT: D 773 GLN cc_start: 0.6782 (tm-30) cc_final: 0.6407 (tm-30) REVERT: D 817 GLU cc_start: 0.7624 (tm-30) cc_final: 0.6954 (pp20) REVERT: E 19 LYS cc_start: 0.8083 (mttm) cc_final: 0.7104 (mtpp) REVERT: E 85 MET cc_start: 0.6954 (mmm) cc_final: 0.6735 (mmm) REVERT: E 121 GLN cc_start: 0.8792 (tt0) cc_final: 0.8547 (tt0) REVERT: E 161 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8222 (tttm) REVERT: E 246 TRP cc_start: 0.7017 (t-100) cc_final: 0.6770 (t-100) REVERT: E 287 GLN cc_start: 0.8237 (tp40) cc_final: 0.7801 (tm-30) REVERT: E 335 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6790 (mmt) REVERT: E 363 ARG cc_start: 0.6456 (mtm180) cc_final: 0.5713 (mtt180) REVERT: E 433 LYS cc_start: 0.8632 (mmtm) cc_final: 0.8246 (ptmt) REVERT: E 478 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8621 (m) REVERT: E 511 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8185 (m) REVERT: E 608 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: E 719 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7208 (mtpm) REVERT: E 720 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7693 (mp) REVERT: E 756 MET cc_start: 0.7150 (pmt) cc_final: 0.6866 (pmm) REVERT: E 759 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6134 (tm-30) REVERT: E 763 LYS cc_start: 0.8575 (tmmm) cc_final: 0.8321 (tmmm) REVERT: E 773 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6631 (tm-30) REVERT: E 790 PRO cc_start: 0.7566 (Cg_endo) cc_final: 0.7300 (Cg_endo) REVERT: E 795 GLN cc_start: 0.7282 (mt0) cc_final: 0.6683 (mm110) REVERT: E 815 GLU cc_start: 0.7614 (tt0) cc_final: 0.7008 (tm-30) outliers start: 209 outliers final: 85 residues processed: 538 average time/residue: 0.6979 time to fit residues: 449.4947 Evaluate side-chains 474 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 353 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 725 ASN Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 246 TRP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 767 GLN Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain C residue 847 TYR Chi-restraints excluded: chain C residue 850 TRP Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 382 LYS Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 740 GLU Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 204 TYR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 511 THR Chi-restraints excluded: chain E residue 541 SER Chi-restraints excluded: chain E residue 608 GLU Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 719 LYS Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 743 ASP Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 759 GLU Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 773 GLN Chi-restraints excluded: chain E residue 808 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 87 optimal weight: 30.0000 chunk 256 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 420 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 387 optimal weight: 5.9990 chunk 117 optimal weight: 50.0000 chunk 13 optimal weight: 3.9990 chunk 299 optimal weight: 9.9990 chunk 321 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN A 822 ASN B 545 HIS C 203 ASN C 323 HIS ** C 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN D 776 ASN D 810 ASN ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN ** E 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.156223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104109 restraints weight = 44254.783| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.34 r_work: 0.3094 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 35664 Z= 0.206 Angle : 0.563 11.122 48281 Z= 0.292 Chirality : 0.044 0.145 4990 Planarity : 0.004 0.060 6243 Dihedral : 7.092 86.225 4818 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.70 % Favored : 95.28 % Rotamer: Outliers : 5.89 % Allowed : 22.63 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.08 (0.13), residues: 4235 helix: 1.13 (0.12), residues: 1794 sheet: -0.04 (0.20), residues: 618 loop : -1.26 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 741 TYR 0.028 0.001 TYR D 696 PHE 0.027 0.001 PHE E 160 TRP 0.022 0.002 TRP C 734 HIS 0.004 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00494 (35664) covalent geometry : angle 0.56350 (48281) hydrogen bonds : bond 0.04514 ( 1641) hydrogen bonds : angle 5.03640 ( 4716) *********************** 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 589 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 372 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7791 (mm-30) REVERT: A 85 MET cc_start: 0.7193 (mmm) cc_final: 0.6896 (mmm) REVERT: A 102 LYS cc_start: 0.8370 (mmmt) cc_final: 0.7836 (mptt) REVERT: A 246 TRP cc_start: 0.7247 (t-100) cc_final: 0.6273 (t60) REVERT: A 294 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: A 333 LYS cc_start: 0.6457 (OUTLIER) cc_final: 0.6210 (tptt) REVERT: A 363 ARG cc_start: 0.6930 (mtp180) cc_final: 0.6700 (mtp180) REVERT: A 433 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8604 (mmtt) REVERT: A 570 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.7844 (mmtm) REVERT: A 759 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.6424 (tm-30) REVERT: A 803 LYS cc_start: 0.7684 (tptp) cc_final: 0.7310 (tppt) REVERT: A 815 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6676 (tm-30) REVERT: A 817 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7171 (tm-30) REVERT: A 830 VAL cc_start: 0.8059 (OUTLIER) cc_final: 0.7836 (p) REVERT: B 1 MET cc_start: 0.6232 (OUTLIER) cc_final: 0.5962 (tmt) REVERT: B 49 LYS cc_start: 0.7555 (tttp) cc_final: 0.7056 (tmmt) REVERT: B 57 GLU cc_start: 0.7603 (mp0) cc_final: 0.7192 (mp0) REVERT: B 89 LYS cc_start: 0.7600 (mmmt) cc_final: 0.6929 (ttpp) REVERT: B 157 TYR cc_start: 0.7713 (m-80) cc_final: 0.7328 (m-10) REVERT: B 220 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8387 (tp) REVERT: B 245 ASP cc_start: 0.7327 (m-30) cc_final: 0.7094 (p0) REVERT: B 443 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8434 (mp0) REVERT: B 608 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8262 (mt-10) REVERT: B 617 ASN cc_start: 0.9201 (OUTLIER) cc_final: 0.8963 (t0) REVERT: B 719 LYS cc_start: 0.7964 (tppp) cc_final: 0.7257 (tttm) REVERT: B 725 ASN cc_start: 0.6701 (OUTLIER) cc_final: 0.6230 (p0) REVERT: B 762 GLN cc_start: 0.7162 (tt0) cc_final: 0.6414 (pt0) REVERT: B 789 GLN cc_start: 0.7811 (tp-100) cc_final: 0.6982 (pm20) REVERT: B 838 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7159 (mmmt) REVERT: C 12 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7300 (tt0) REVERT: C 58 LYS cc_start: 0.7161 (pptt) cc_final: 0.6813 (mmtt) REVERT: C 116 GLU cc_start: 0.9336 (OUTLIER) cc_final: 0.8456 (pm20) REVERT: C 178 ASN cc_start: 0.7222 (t0) cc_final: 0.6893 (m-40) REVERT: C 194 PRO cc_start: 0.7766 (Cg_exo) cc_final: 0.7426 (Cg_endo) REVERT: C 195 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7584 (tt) REVERT: C 229 MET cc_start: 0.7123 (ptp) cc_final: 0.6891 (ptp) REVERT: C 269 ILE cc_start: 0.6326 (OUTLIER) cc_final: 0.6070 (mt) REVERT: C 294 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: C 403 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: C 509 PHE cc_start: 0.6583 (p90) cc_final: 0.6343 (p90) REVERT: C 727 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7431 (mp) REVERT: C 791 GLU cc_start: 0.7199 (tt0) cc_final: 0.6448 (pm20) REVERT: C 817 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: D 30 ASP cc_start: 0.7294 (t0) cc_final: 0.7039 (t0) REVERT: D 57 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: D 232 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7027 (mm-30) REVERT: D 239 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7302 (t80) REVERT: D 247 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7245 (mm-30) REVERT: D 350 ILE cc_start: 0.7578 (tt) cc_final: 0.7318 (tp) REVERT: D 361 ASN cc_start: 0.7270 (m110) cc_final: 0.6829 (p0) REVERT: D 443 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8147 (tp30) REVERT: D 527 LYS cc_start: 0.8200 (mttt) cc_final: 0.7941 (mtmt) REVERT: D 651 GLN cc_start: 0.8375 (mt0) cc_final: 0.7879 (tt0) REVERT: D 713 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8606 (tt0) REVERT: D 759 GLU cc_start: 0.7030 (tt0) cc_final: 0.6749 (tt0) REVERT: D 773 GLN cc_start: 0.6851 (tm-30) cc_final: 0.6462 (tm-30) REVERT: D 817 GLU cc_start: 0.7587 (tm-30) cc_final: 0.6865 (pp20) REVERT: E 19 LYS cc_start: 0.8007 (mttm) cc_final: 0.7194 (mtpp) REVERT: E 121 GLN cc_start: 0.8792 (tt0) cc_final: 0.8529 (tt0) REVERT: E 161 LYS cc_start: 0.8729 (ttmm) cc_final: 0.8194 (tttm) REVERT: E 246 TRP cc_start: 0.6992 (t-100) cc_final: 0.6698 (t-100) REVERT: E 287 GLN cc_start: 0.8226 (tp40) cc_final: 0.7771 (tm-30) REVERT: E 335 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6783 (mmt) REVERT: E 363 ARG cc_start: 0.6443 (mtm180) cc_final: 0.5636 (mtt180) REVERT: E 433 LYS cc_start: 0.8648 (mmtm) cc_final: 0.8224 (ptmt) REVERT: E 478 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8628 (m) REVERT: E 511 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8273 (m) REVERT: E 608 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: E 719 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7129 (mtpm) REVERT: E 720 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7598 (mp) REVERT: E 756 MET cc_start: 0.7151 (pmt) cc_final: 0.6859 (pmm) REVERT: E 759 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6200 (tm-30) REVERT: E 763 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8303 (tmmm) REVERT: E 773 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6513 (tm-30) REVERT: E 790 PRO cc_start: 0.7436 (Cg_endo) cc_final: 0.7161 (Cg_endo) REVERT: E 795 GLN cc_start: 0.7193 (mt0) cc_final: 0.6542 (mm110) REVERT: E 815 GLU cc_start: 0.7628 (tt0) cc_final: 0.6999 (tm-30) outliers start: 217 outliers final: 104 residues processed: 545 average time/residue: 0.7098 time to fit residues: 461.6904 Evaluate side-chains 487 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 349 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 725 ASN Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 850 TRP Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 382 LYS Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 740 GLU Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 204 TYR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 481 LYS Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 511 THR Chi-restraints excluded: chain E residue 541 SER Chi-restraints excluded: chain E residue 608 GLU Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 688 SER Chi-restraints excluded: chain E residue 719 LYS Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 743 ASP Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 759 GLU Chi-restraints excluded: chain E residue 763 LYS Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 773 GLN Chi-restraints excluded: chain E residue 808 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 150 optimal weight: 9.9990 chunk 354 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 chunk 287 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 333 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 224 optimal weight: 0.7980 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 795 GLN A 822 ASN B 121 GLN B 545 HIS C 214 ASN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 530 ASN D 810 ASN ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN ** E 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.155887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103790 restraints weight = 44396.798| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.33 r_work: 0.3091 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 35664 Z= 0.219 Angle : 0.576 10.827 48281 Z= 0.298 Chirality : 0.044 0.174 4990 Planarity : 0.004 0.062 6243 Dihedral : 7.064 85.855 4815 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.91 % Favored : 95.06 % Rotamer: Outliers : 5.86 % Allowed : 22.93 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.12 (0.13), residues: 4235 helix: 1.07 (0.12), residues: 1801 sheet: -0.08 (0.20), residues: 619 loop : -1.25 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 741 TYR 0.028 0.002 TYR D 696 PHE 0.028 0.002 PHE E 160 TRP 0.022 0.002 TRP C 734 HIS 0.004 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00527 (35664) covalent geometry : angle 0.57561 (48281) hydrogen bonds : bond 0.04558 ( 1641) hydrogen bonds : angle 5.02416 ( 4716) *********************** 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 584 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 368 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7771 (mm-30) REVERT: A 76 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7014 (tp30) REVERT: A 85 MET cc_start: 0.7161 (mmm) cc_final: 0.6889 (mmm) REVERT: A 102 LYS cc_start: 0.8401 (mmmt) cc_final: 0.7858 (mptt) REVERT: A 246 TRP cc_start: 0.7316 (t-100) cc_final: 0.6360 (t60) REVERT: A 277 ASN cc_start: 0.8451 (t0) cc_final: 0.8171 (t0) REVERT: A 333 LYS cc_start: 0.6422 (OUTLIER) cc_final: 0.6157 (tptt) REVERT: A 354 ARG cc_start: 0.7944 (ttp-170) cc_final: 0.7703 (ttp-170) REVERT: A 433 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8567 (mmtt) REVERT: A 513 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7578 (mptp) REVERT: A 533 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8253 (mm-30) REVERT: A 570 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.7860 (mmtm) REVERT: A 759 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.6528 (tm-30) REVERT: A 803 LYS cc_start: 0.7692 (tptp) cc_final: 0.7422 (tptp) REVERT: A 815 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6870 (tm-30) REVERT: A 830 VAL cc_start: 0.8087 (OUTLIER) cc_final: 0.7862 (p) REVERT: B 24 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7188 (mmmm) REVERT: B 49 LYS cc_start: 0.7556 (tttp) cc_final: 0.6857 (tmmt) REVERT: B 89 LYS cc_start: 0.7603 (mmmt) cc_final: 0.6928 (ttpp) REVERT: B 121 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7429 (mm110) REVERT: B 157 TYR cc_start: 0.7690 (m-80) cc_final: 0.7358 (m-10) REVERT: B 220 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8415 (tp) REVERT: B 245 ASP cc_start: 0.7324 (m-30) cc_final: 0.7108 (p0) REVERT: B 443 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: B 608 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8261 (mt-10) REVERT: B 617 ASN cc_start: 0.9208 (OUTLIER) cc_final: 0.8977 (t0) REVERT: B 719 LYS cc_start: 0.7984 (tppp) cc_final: 0.7263 (tttm) REVERT: B 762 GLN cc_start: 0.7163 (tt0) cc_final: 0.6433 (pt0) REVERT: B 789 GLN cc_start: 0.7820 (tp-100) cc_final: 0.6987 (pm20) REVERT: B 838 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7222 (mmmt) REVERT: C 12 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7300 (tt0) REVERT: C 58 LYS cc_start: 0.7169 (pptt) cc_final: 0.6819 (mmtt) REVERT: C 74 ARG cc_start: 0.6954 (tpt170) cc_final: 0.6180 (mmm160) REVERT: C 116 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.8569 (pm20) REVERT: C 121 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: C 194 PRO cc_start: 0.7786 (Cg_exo) cc_final: 0.7444 (Cg_endo) REVERT: C 195 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7529 (tt) REVERT: C 229 MET cc_start: 0.7141 (ptp) cc_final: 0.6906 (ptp) REVERT: C 269 ILE cc_start: 0.6314 (OUTLIER) cc_final: 0.6071 (mt) REVERT: C 294 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: C 363 ARG cc_start: 0.7044 (mtm180) cc_final: 0.6251 (mtt180) REVERT: C 509 PHE cc_start: 0.6519 (p90) cc_final: 0.6301 (p90) REVERT: C 518 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8675 (mp) REVERT: C 727 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7432 (mp) REVERT: C 791 GLU cc_start: 0.7223 (tt0) cc_final: 0.6488 (pm20) REVERT: C 817 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: D 7 TYR cc_start: 0.5984 (t80) cc_final: 0.5556 (t80) REVERT: D 30 ASP cc_start: 0.7324 (t0) cc_final: 0.7072 (t0) REVERT: D 57 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: D 217 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7863 (mtt180) REVERT: D 232 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6964 (mm-30) REVERT: D 239 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.7256 (t80) REVERT: D 247 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7241 (mm-30) REVERT: D 335 MET cc_start: 0.8488 (mmm) cc_final: 0.8186 (mtp) REVERT: D 350 ILE cc_start: 0.7601 (tt) cc_final: 0.7351 (tp) REVERT: D 361 ASN cc_start: 0.7331 (m110) cc_final: 0.6890 (p0) REVERT: D 443 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8181 (tp30) REVERT: D 527 LYS cc_start: 0.8206 (mttt) cc_final: 0.7946 (mtmt) REVERT: D 651 GLN cc_start: 0.8392 (mt0) cc_final: 0.7911 (tt0) REVERT: D 713 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8635 (tt0) REVERT: D 759 GLU cc_start: 0.7092 (tt0) cc_final: 0.6821 (tt0) REVERT: D 773 GLN cc_start: 0.6892 (tm-30) cc_final: 0.6520 (tm-30) REVERT: D 817 GLU cc_start: 0.7645 (tm-30) cc_final: 0.6865 (pp20) REVERT: E 19 LYS cc_start: 0.8023 (mttm) cc_final: 0.7224 (mtpp) REVERT: E 121 GLN cc_start: 0.8801 (tt0) cc_final: 0.8542 (tt0) REVERT: E 161 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8188 (tttm) REVERT: E 186 ARG cc_start: 0.8236 (tpp80) cc_final: 0.7468 (ttp-170) REVERT: E 246 TRP cc_start: 0.6988 (t-100) cc_final: 0.6683 (t-100) REVERT: E 287 GLN cc_start: 0.8239 (tp40) cc_final: 0.7785 (tm-30) REVERT: E 335 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6915 (mmt) REVERT: E 354 ARG cc_start: 0.8075 (mtt90) cc_final: 0.7022 (mmt90) REVERT: E 363 ARG cc_start: 0.6462 (mtm180) cc_final: 0.5534 (mtt180) REVERT: E 433 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8249 (ptmt) REVERT: E 478 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8642 (m) REVERT: E 608 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: E 719 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.7127 (mtpm) REVERT: E 720 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7608 (mp) REVERT: E 756 MET cc_start: 0.7214 (pmt) cc_final: 0.6869 (pmm) REVERT: E 759 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6166 (tm-30) REVERT: E 763 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8292 (tmmm) REVERT: E 773 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6479 (tm-30) REVERT: E 790 PRO cc_start: 0.7434 (Cg_endo) cc_final: 0.7152 (Cg_endo) REVERT: E 795 GLN cc_start: 0.7222 (mt0) cc_final: 0.6568 (mm110) REVERT: E 815 GLU cc_start: 0.7635 (tt0) cc_final: 0.7005 (tm-30) outliers start: 216 outliers final: 111 residues processed: 540 average time/residue: 0.6950 time to fit residues: 449.0286 Evaluate side-chains 502 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 354 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 850 TRP Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 382 LYS Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 606 SER Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 740 GLU Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 204 TYR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 541 SER Chi-restraints excluded: chain E residue 608 GLU Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 688 SER Chi-restraints excluded: chain E residue 719 LYS Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 743 ASP Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 759 GLU Chi-restraints excluded: chain E residue 763 LYS Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 773 GLN Chi-restraints excluded: chain E residue 805 VAL Chi-restraints excluded: chain E residue 808 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 97 optimal weight: 9.9990 chunk 269 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 173 optimal weight: 9.9990 chunk 348 optimal weight: 9.9990 chunk 302 optimal weight: 2.9990 chunk 414 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN B 545 HIS ** B 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 767 GLN D 810 ASN D 811 ASN ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN ** E 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.156732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105889 restraints weight = 44173.828| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.41 r_work: 0.3100 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 35664 Z= 0.177 Angle : 0.553 9.838 48281 Z= 0.286 Chirality : 0.043 0.169 4990 Planarity : 0.004 0.057 6243 Dihedral : 6.922 82.852 4809 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.70 % Favored : 95.28 % Rotamer: Outliers : 5.37 % Allowed : 23.88 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.01 (0.13), residues: 4235 helix: 1.21 (0.12), residues: 1783 sheet: -0.03 (0.20), residues: 618 loop : -1.21 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 741 TYR 0.026 0.001 TYR D 696 PHE 0.024 0.001 PHE E 160 TRP 0.024 0.002 TRP C 734 HIS 0.004 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00424 (35664) covalent geometry : angle 0.55262 (48281) hydrogen bonds : bond 0.04267 ( 1641) hydrogen bonds : angle 4.94226 ( 4716) *********************** 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 579 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 381 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7780 (mm-30) REVERT: A 76 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7012 (tp30) REVERT: A 102 LYS cc_start: 0.8414 (mmmt) cc_final: 0.7889 (mptt) REVERT: A 246 TRP cc_start: 0.7338 (t-100) cc_final: 0.6434 (t60) REVERT: A 277 ASN cc_start: 0.8351 (t0) cc_final: 0.8050 (t0) REVERT: A 333 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.6242 (tptt) REVERT: A 513 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7592 (mptp) REVERT: A 570 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.7859 (mmtm) REVERT: A 759 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.6526 (tm-30) REVERT: A 803 LYS cc_start: 0.7695 (tptp) cc_final: 0.6619 (ttpt) REVERT: A 815 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6870 (tm-30) REVERT: A 830 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7854 (p) REVERT: B 24 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7224 (mmmm) REVERT: B 49 LYS cc_start: 0.7388 (tttp) cc_final: 0.6885 (tmmt) REVERT: B 72 TYR cc_start: 0.7646 (t80) cc_final: 0.7331 (t80) REVERT: B 89 LYS cc_start: 0.7599 (mmmt) cc_final: 0.6922 (ttpp) REVERT: B 157 TYR cc_start: 0.7645 (m-80) cc_final: 0.7323 (m-10) REVERT: B 245 ASP cc_start: 0.7324 (m-30) cc_final: 0.7090 (p0) REVERT: B 443 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8473 (mp0) REVERT: B 608 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8265 (mt-10) REVERT: B 617 ASN cc_start: 0.9173 (OUTLIER) cc_final: 0.8927 (t0) REVERT: B 674 LYS cc_start: 0.8064 (mmmm) cc_final: 0.7777 (pmmt) REVERT: B 719 LYS cc_start: 0.7995 (tppp) cc_final: 0.7268 (tttm) REVERT: B 762 GLN cc_start: 0.7120 (tt0) cc_final: 0.6399 (pt0) REVERT: B 789 GLN cc_start: 0.7837 (tp-100) cc_final: 0.7011 (pm20) REVERT: B 803 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7329 (tmtt) REVERT: B 838 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7278 (mmmt) REVERT: C 58 LYS cc_start: 0.7199 (pptt) cc_final: 0.6858 (mmtt) REVERT: C 72 TYR cc_start: 0.6076 (m-80) cc_final: 0.5740 (m-80) REVERT: C 74 ARG cc_start: 0.6938 (tpt170) cc_final: 0.6192 (mmm160) REVERT: C 116 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.8495 (pm20) REVERT: C 121 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8083 (tt0) REVERT: C 194 PRO cc_start: 0.7812 (Cg_exo) cc_final: 0.7461 (Cg_endo) REVERT: C 229 MET cc_start: 0.7214 (ptp) cc_final: 0.6988 (ptp) REVERT: C 269 ILE cc_start: 0.6356 (OUTLIER) cc_final: 0.6121 (mt) REVERT: C 294 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: C 363 ARG cc_start: 0.6985 (mtm180) cc_final: 0.6190 (mtp180) REVERT: C 403 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7844 (mt-10) REVERT: C 509 PHE cc_start: 0.6629 (p90) cc_final: 0.6428 (p90) REVERT: C 593 MET cc_start: 0.8015 (mtp) cc_final: 0.7723 (ttp) REVERT: C 618 LEU cc_start: 0.7912 (tt) cc_final: 0.7581 (tt) REVERT: C 727 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7430 (mp) REVERT: C 781 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6718 (mm) REVERT: C 791 GLU cc_start: 0.7202 (tt0) cc_final: 0.6492 (pm20) REVERT: C 817 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6419 (mp0) REVERT: D 7 TYR cc_start: 0.5880 (t80) cc_final: 0.5366 (t80) REVERT: D 30 ASP cc_start: 0.7303 (t0) cc_final: 0.7055 (t0) REVERT: D 57 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: D 217 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7794 (mtt180) REVERT: D 239 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.7279 (t80) REVERT: D 247 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7327 (mm-30) REVERT: D 335 MET cc_start: 0.8460 (mmm) cc_final: 0.8122 (mtp) REVERT: D 350 ILE cc_start: 0.7575 (tt) cc_final: 0.7329 (tp) REVERT: D 361 ASN cc_start: 0.7346 (m110) cc_final: 0.6891 (p0) REVERT: D 443 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8190 (tp30) REVERT: D 527 LYS cc_start: 0.8205 (mttt) cc_final: 0.7960 (mtmt) REVERT: D 651 GLN cc_start: 0.8419 (mt0) cc_final: 0.7931 (tt0) REVERT: D 713 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8650 (tt0) REVERT: D 719 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7234 (mmpt) REVERT: D 759 GLU cc_start: 0.7115 (tt0) cc_final: 0.6829 (tt0) REVERT: D 773 GLN cc_start: 0.6765 (tm-30) cc_final: 0.6478 (tm-30) REVERT: D 817 GLU cc_start: 0.7646 (tm-30) cc_final: 0.6934 (pp20) REVERT: E 19 LYS cc_start: 0.8085 (mttm) cc_final: 0.7270 (mtpp) REVERT: E 85 MET cc_start: 0.7022 (mmm) cc_final: 0.6782 (mmm) REVERT: E 121 GLN cc_start: 0.8791 (tt0) cc_final: 0.8563 (tt0) REVERT: E 161 LYS cc_start: 0.8737 (ttmm) cc_final: 0.8213 (tttm) REVERT: E 186 ARG cc_start: 0.8190 (tpp80) cc_final: 0.7438 (ttp-170) REVERT: E 246 TRP cc_start: 0.7008 (t-100) cc_final: 0.6731 (t-100) REVERT: E 287 GLN cc_start: 0.8242 (tp40) cc_final: 0.7800 (tm-30) REVERT: E 354 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7013 (mmt90) REVERT: E 363 ARG cc_start: 0.6482 (mtm180) cc_final: 0.5502 (mmm160) REVERT: E 433 LYS cc_start: 0.8661 (mmtm) cc_final: 0.8266 (ptmt) REVERT: E 478 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8662 (m) REVERT: E 608 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: E 719 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7163 (mtpm) REVERT: E 720 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7634 (mp) REVERT: E 756 MET cc_start: 0.7194 (pmt) cc_final: 0.6843 (pmm) REVERT: E 759 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6209 (tm-30) REVERT: E 763 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8303 (tmmm) REVERT: E 773 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6454 (tm-30) REVERT: E 790 PRO cc_start: 0.7424 (Cg_endo) cc_final: 0.7140 (Cg_endo) REVERT: E 791 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6640 (pp20) REVERT: E 795 GLN cc_start: 0.7178 (mt0) cc_final: 0.6515 (mm110) REVERT: E 815 GLU cc_start: 0.7652 (tt0) cc_final: 0.7029 (tm-30) outliers start: 198 outliers final: 104 residues processed: 534 average time/residue: 0.7337 time to fit residues: 467.6289 Evaluate side-chains 491 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 355 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 803 LYS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain C residue 850 TRP Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 382 LYS Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 606 SER Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 740 GLU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 541 SER Chi-restraints excluded: chain E residue 608 GLU Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 688 SER Chi-restraints excluded: chain E residue 719 LYS Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 759 GLU Chi-restraints excluded: chain E residue 763 LYS Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 773 GLN Chi-restraints excluded: chain E residue 791 GLU Chi-restraints excluded: chain E residue 805 VAL Chi-restraints excluded: chain E residue 808 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 331 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 322 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 365 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 chunk 258 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN B 121 GLN B 169 GLN B 545 HIS ** B 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 214 ASN C 687 ASN D 35 ASN D 671 ASN D 810 ASN ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN ** E 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.153759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.102311 restraints weight = 44555.980| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.29 r_work: 0.3066 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 35664 Z= 0.342 Angle : 0.672 12.433 48281 Z= 0.346 Chirality : 0.048 0.170 4990 Planarity : 0.005 0.068 6243 Dihedral : 7.043 86.410 4797 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.71 % Favored : 94.26 % Rotamer: Outliers : 6.00 % Allowed : 23.69 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.86 (0.12), residues: 1777 sheet: -0.20 (0.20), residues: 616 loop : -1.36 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 741 TYR 0.036 0.002 TYR D 696 PHE 0.037 0.002 PHE E 160 TRP 0.025 0.002 TRP C 734 HIS 0.006 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00829 (35664) covalent geometry : angle 0.67196 (48281) hydrogen bonds : bond 0.05266 ( 1641) hydrogen bonds : angle 5.19226 ( 4716) *********************** 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 570 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 349 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7818 (mm-30) REVERT: A 76 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7056 (tp30) REVERT: A 85 MET cc_start: 0.7379 (mmm) cc_final: 0.7007 (mmm) REVERT: A 102 LYS cc_start: 0.8426 (mmmt) cc_final: 0.7937 (mptt) REVERT: A 246 TRP cc_start: 0.7372 (t-100) cc_final: 0.6420 (t60) REVERT: A 277 ASN cc_start: 0.8682 (t0) cc_final: 0.8447 (t0) REVERT: A 333 LYS cc_start: 0.6566 (OUTLIER) cc_final: 0.6266 (tptt) REVERT: A 363 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7338 (mtp180) REVERT: A 433 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8606 (mmtt) REVERT: A 513 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.7658 (mptp) REVERT: A 570 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.7932 (mmtm) REVERT: A 608 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8572 (mt-10) REVERT: A 759 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.6624 (tm-30) REVERT: A 815 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6180 (tp30) REVERT: B 49 LYS cc_start: 0.7406 (tttp) cc_final: 0.6880 (tmmt) REVERT: B 72 TYR cc_start: 0.7634 (t80) cc_final: 0.7297 (t80) REVERT: B 89 LYS cc_start: 0.7625 (mmmt) cc_final: 0.6933 (ttpp) REVERT: B 121 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7399 (mm-40) REVERT: B 157 TYR cc_start: 0.7705 (m-80) cc_final: 0.7372 (m-10) REVERT: B 220 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8439 (tp) REVERT: B 245 ASP cc_start: 0.7369 (m-30) cc_final: 0.7116 (p0) REVERT: B 443 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8446 (mp0) REVERT: B 608 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8271 (mt-10) REVERT: B 617 ASN cc_start: 0.9222 (OUTLIER) cc_final: 0.8986 (t0) REVERT: B 641 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7514 (mtp180) REVERT: B 719 LYS cc_start: 0.7956 (tppp) cc_final: 0.7228 (tttm) REVERT: B 762 GLN cc_start: 0.7221 (tt0) cc_final: 0.6499 (pt0) REVERT: B 789 GLN cc_start: 0.7852 (tp-100) cc_final: 0.7033 (pm20) REVERT: B 803 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7375 (tmtt) REVERT: B 838 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7323 (mmmt) REVERT: C 58 LYS cc_start: 0.7246 (pptt) cc_final: 0.6886 (mmtt) REVERT: C 74 ARG cc_start: 0.6957 (tpt170) cc_final: 0.6718 (tpt170) REVERT: C 92 TYR cc_start: 0.6739 (t80) cc_final: 0.6473 (t80) REVERT: C 116 GLU cc_start: 0.9376 (OUTLIER) cc_final: 0.8533 (pm20) REVERT: C 121 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: C 229 MET cc_start: 0.7252 (ptp) cc_final: 0.6942 (ptp) REVERT: C 269 ILE cc_start: 0.6373 (OUTLIER) cc_final: 0.6125 (mt) REVERT: C 294 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: C 494 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7303 (pp20) REVERT: C 727 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7505 (mp) REVERT: C 791 GLU cc_start: 0.7189 (tt0) cc_final: 0.6459 (pm20) REVERT: C 817 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6460 (mp0) REVERT: D 7 TYR cc_start: 0.5837 (t80) cc_final: 0.5493 (t80) REVERT: D 30 ASP cc_start: 0.7392 (t0) cc_final: 0.7141 (t0) REVERT: D 57 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: D 217 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7923 (mtt180) REVERT: D 229 MET cc_start: 0.6373 (OUTLIER) cc_final: 0.5988 (ptt) REVERT: D 232 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: D 239 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7279 (t80) REVERT: D 247 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7292 (mm-30) REVERT: D 335 MET cc_start: 0.8492 (mmm) cc_final: 0.8113 (mtp) REVERT: D 350 ILE cc_start: 0.7633 (tt) cc_final: 0.7375 (tp) REVERT: D 361 ASN cc_start: 0.7370 (m110) cc_final: 0.6918 (p0) REVERT: D 390 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7115 (mp10) REVERT: D 443 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8220 (tp30) REVERT: D 527 LYS cc_start: 0.8209 (mttt) cc_final: 0.7996 (mtmt) REVERT: D 651 GLN cc_start: 0.8478 (mt0) cc_final: 0.7990 (tt0) REVERT: D 713 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8710 (tt0) REVERT: D 719 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7061 (mmpt) REVERT: D 759 GLU cc_start: 0.7158 (tt0) cc_final: 0.6859 (tt0) REVERT: D 773 GLN cc_start: 0.6925 (tm-30) cc_final: 0.6618 (tm-30) REVERT: D 817 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7450 (tm-30) REVERT: E 19 LYS cc_start: 0.8030 (mttm) cc_final: 0.7243 (mtpp) REVERT: E 121 GLN cc_start: 0.8827 (tt0) cc_final: 0.8511 (tt0) REVERT: E 161 LYS cc_start: 0.8750 (ttmm) cc_final: 0.8228 (tttm) REVERT: E 186 ARG cc_start: 0.8289 (tpp80) cc_final: 0.7517 (ttp-170) REVERT: E 246 TRP cc_start: 0.7114 (t-100) cc_final: 0.6823 (t-100) REVERT: E 287 GLN cc_start: 0.8223 (tp40) cc_final: 0.7798 (tm-30) REVERT: E 354 ARG cc_start: 0.8139 (mtt90) cc_final: 0.7429 (mtt90) REVERT: E 363 ARG cc_start: 0.6391 (mtm180) cc_final: 0.5558 (mmm160) REVERT: E 433 LYS cc_start: 0.8691 (mmtm) cc_final: 0.8259 (ptmt) REVERT: E 608 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8263 (mp0) REVERT: E 720 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7663 (mp) REVERT: E 756 MET cc_start: 0.7302 (pmt) cc_final: 0.6894 (pmm) REVERT: E 763 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8282 (tmmm) REVERT: E 773 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: E 790 PRO cc_start: 0.7444 (Cg_endo) cc_final: 0.7173 (Cg_endo) REVERT: E 795 GLN cc_start: 0.7296 (mt0) cc_final: 0.6684 (mm110) REVERT: E 804 MET cc_start: 0.6572 (OUTLIER) cc_final: 0.5799 (tpt) REVERT: E 815 GLU cc_start: 0.7651 (tt0) cc_final: 0.7047 (tm-30) outliers start: 221 outliers final: 119 residues processed: 528 average time/residue: 0.7627 time to fit residues: 478.2488 Evaluate side-chains 496 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 341 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 505 PHE Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 803 LYS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain C residue 850 TRP Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 382 LYS Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 606 SER Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 725 ASN Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 740 GLU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 204 TYR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 466 LYS Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 481 LYS Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 541 SER Chi-restraints excluded: chain E residue 608 GLU Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 688 SER Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 763 LYS Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 773 GLN Chi-restraints excluded: chain E residue 804 MET Chi-restraints excluded: chain E residue 808 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 368 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 108 optimal weight: 0.3980 chunk 355 optimal weight: 5.9990 chunk 347 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 795 GLN B 725 ASN C 205 GLN C 340 GLN C 552 GLN C 687 ASN D 671 ASN E 277 ASN E 356 ASN ** E 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.157969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106765 restraints weight = 44213.410| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.30 r_work: 0.3128 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35664 Z= 0.130 Angle : 0.538 9.639 48281 Z= 0.278 Chirality : 0.042 0.167 4990 Planarity : 0.004 0.055 6243 Dihedral : 6.742 82.254 4795 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.16 % Favored : 95.82 % Rotamer: Outliers : 4.02 % Allowed : 25.92 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.01 (0.13), residues: 4235 helix: 1.18 (0.12), residues: 1794 sheet: -0.06 (0.20), residues: 618 loop : -1.19 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 741 TYR 0.022 0.001 TYR A 696 PHE 0.018 0.001 PHE E 160 TRP 0.028 0.001 TRP C 734 HIS 0.006 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00300 (35664) covalent geometry : angle 0.53753 (48281) hydrogen bonds : bond 0.03986 ( 1641) hydrogen bonds : angle 4.90509 ( 4716) *********************** 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 525 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 377 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7633 (mmtt) REVERT: A 57 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7791 (mm-30) REVERT: A 76 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7007 (tp30) REVERT: A 85 MET cc_start: 0.7469 (mmm) cc_final: 0.7246 (mmm) REVERT: A 102 LYS cc_start: 0.8406 (mmmt) cc_final: 0.7867 (mptt) REVERT: A 246 TRP cc_start: 0.7311 (t-100) cc_final: 0.6428 (t60) REVERT: A 277 ASN cc_start: 0.8254 (t0) cc_final: 0.7951 (t0) REVERT: A 294 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6549 (mp0) REVERT: A 333 LYS cc_start: 0.6535 (OUTLIER) cc_final: 0.6256 (tptt) REVERT: A 348 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6891 (mt-10) REVERT: A 513 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7567 (mptp) REVERT: A 554 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8720 (tt) REVERT: A 570 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7836 (mmtm) REVERT: A 759 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.6590 (tm-30) REVERT: A 815 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6177 (tp30) REVERT: B 24 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7287 (mmmm) REVERT: B 49 LYS cc_start: 0.7352 (tttp) cc_final: 0.6835 (tmmt) REVERT: B 72 TYR cc_start: 0.7678 (t80) cc_final: 0.7385 (t80) REVERT: B 74 ARG cc_start: 0.7297 (mmm160) cc_final: 0.7095 (mmm160) REVERT: B 89 LYS cc_start: 0.7568 (mmmt) cc_final: 0.6865 (ttpp) REVERT: B 157 TYR cc_start: 0.7544 (m-80) cc_final: 0.7193 (m-10) REVERT: B 220 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8373 (tp) REVERT: B 443 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8465 (mp0) REVERT: B 608 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: B 674 LYS cc_start: 0.8059 (mmmm) cc_final: 0.7776 (pmmt) REVERT: B 719 LYS cc_start: 0.7944 (tppp) cc_final: 0.7227 (tttm) REVERT: B 725 ASN cc_start: 0.6700 (OUTLIER) cc_final: 0.6310 (p0) REVERT: B 762 GLN cc_start: 0.7075 (tt0) cc_final: 0.6354 (pt0) REVERT: B 789 GLN cc_start: 0.7812 (tp-100) cc_final: 0.6977 (pm20) REVERT: B 803 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7395 (tmtt) REVERT: B 838 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7271 (mmmt) REVERT: C 58 LYS cc_start: 0.7168 (pptt) cc_final: 0.6870 (mmtt) REVERT: C 60 ASN cc_start: 0.6727 (m-40) cc_final: 0.6320 (p0) REVERT: C 85 MET cc_start: 0.7271 (mmm) cc_final: 0.6992 (mmp) REVERT: C 92 TYR cc_start: 0.6737 (t80) cc_final: 0.6502 (t80) REVERT: C 178 ASN cc_start: 0.7191 (t0) cc_final: 0.6913 (m-40) REVERT: C 194 PRO cc_start: 0.7850 (Cg_exo) cc_final: 0.7524 (Cg_endo) REVERT: C 229 MET cc_start: 0.7244 (ptp) cc_final: 0.7021 (ptp) REVERT: C 294 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: C 363 ARG cc_start: 0.7008 (mtm180) cc_final: 0.6205 (mtt180) REVERT: C 593 MET cc_start: 0.7947 (mtp) cc_final: 0.7573 (ttp) REVERT: C 727 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7496 (mp) REVERT: C 791 GLU cc_start: 0.7167 (tt0) cc_final: 0.6465 (pm20) REVERT: C 817 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6394 (mp0) REVERT: D 7 TYR cc_start: 0.5751 (t80) cc_final: 0.5429 (t80) REVERT: D 57 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: D 232 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6764 (tp30) REVERT: D 239 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7250 (t80) REVERT: D 247 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7318 (mm-30) REVERT: D 335 MET cc_start: 0.8467 (mmm) cc_final: 0.8111 (mtp) REVERT: D 350 ILE cc_start: 0.7510 (tt) cc_final: 0.7267 (tp) REVERT: D 361 ASN cc_start: 0.7341 (m110) cc_final: 0.6883 (p0) REVERT: D 443 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8197 (tp30) REVERT: D 461 MET cc_start: 0.8313 (mmm) cc_final: 0.7997 (mmm) REVERT: D 527 LYS cc_start: 0.8191 (mttt) cc_final: 0.7948 (mtmt) REVERT: D 651 GLN cc_start: 0.8357 (mt0) cc_final: 0.7884 (tt0) REVERT: D 713 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8606 (tt0) REVERT: D 719 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7206 (mmpt) REVERT: D 759 GLU cc_start: 0.7162 (tt0) cc_final: 0.6889 (tt0) REVERT: D 773 GLN cc_start: 0.6878 (tm-30) cc_final: 0.6601 (tm-30) REVERT: D 817 GLU cc_start: 0.7673 (tm-30) cc_final: 0.6893 (pp20) REVERT: E 19 LYS cc_start: 0.8098 (mttm) cc_final: 0.7264 (mtpp) REVERT: E 161 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8198 (tttm) REVERT: E 186 ARG cc_start: 0.8192 (tpp80) cc_final: 0.7452 (ttp-170) REVERT: E 246 TRP cc_start: 0.7063 (t-100) cc_final: 0.6755 (t-100) REVERT: E 287 GLN cc_start: 0.8180 (tp40) cc_final: 0.7779 (tm-30) REVERT: E 354 ARG cc_start: 0.8038 (mtt90) cc_final: 0.7006 (mmt90) REVERT: E 363 ARG cc_start: 0.6435 (mtm180) cc_final: 0.5475 (mmm160) REVERT: E 433 LYS cc_start: 0.8673 (mmtm) cc_final: 0.8284 (ptmt) REVERT: E 608 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: E 756 MET cc_start: 0.7224 (pmt) cc_final: 0.6823 (pmm) REVERT: E 759 GLU cc_start: 0.7565 (tt0) cc_final: 0.7026 (tm-30) REVERT: E 773 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6605 (tm-30) REVERT: E 790 PRO cc_start: 0.7471 (Cg_endo) cc_final: 0.7222 (Cg_endo) REVERT: E 791 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6653 (pp20) REVERT: E 795 GLN cc_start: 0.7206 (mt0) cc_final: 0.6501 (mm110) REVERT: E 815 GLU cc_start: 0.7538 (tt0) cc_final: 0.6968 (tm-30) outliers start: 148 outliers final: 80 residues processed: 488 average time/residue: 0.7521 time to fit residues: 436.7957 Evaluate side-chains 461 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 356 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 725 ASN Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 803 LYS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 850 TRP Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 725 ASN Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 740 GLU Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 541 SER Chi-restraints excluded: chain E residue 608 GLU Chi-restraints excluded: chain E residue 688 SER Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 773 GLN Chi-restraints excluded: chain E residue 791 GLU Chi-restraints excluded: chain E residue 808 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 417 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 242 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 263 optimal weight: 0.9990 chunk 317 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 325 optimal weight: 5.9990 chunk 282 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 chunk 319 optimal weight: 8.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN B 545 HIS ** B 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 687 ASN E 356 ASN ** E 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.156706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105351 restraints weight = 44176.741| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.29 r_work: 0.3108 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 35664 Z= 0.190 Angle : 0.573 10.078 48281 Z= 0.295 Chirality : 0.044 0.168 4990 Planarity : 0.004 0.059 6243 Dihedral : 6.691 85.017 4790 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.70 % Favored : 95.28 % Rotamer: Outliers : 3.72 % Allowed : 26.38 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.03 (0.13), residues: 4235 helix: 1.16 (0.12), residues: 1792 sheet: -0.06 (0.20), residues: 618 loop : -1.19 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 741 TYR 0.027 0.001 TYR D 696 PHE 0.027 0.001 PHE E 160 TRP 0.028 0.002 TRP C 734 HIS 0.004 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00456 (35664) covalent geometry : angle 0.57323 (48281) hydrogen bonds : bond 0.04322 ( 1641) hydrogen bonds : angle 4.94337 ( 4716) *********************** 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 501 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 364 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7603 (mmtt) REVERT: A 57 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7793 (mm-30) REVERT: A 76 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7024 (tp30) REVERT: A 85 MET cc_start: 0.7481 (mmm) cc_final: 0.7250 (mmm) REVERT: A 102 LYS cc_start: 0.8390 (mmmt) cc_final: 0.7883 (mptt) REVERT: A 246 TRP cc_start: 0.7323 (t-100) cc_final: 0.6448 (t60) REVERT: A 277 ASN cc_start: 0.8436 (t0) cc_final: 0.8138 (t0) REVERT: A 294 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6469 (mp0) REVERT: A 333 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.6246 (tptt) REVERT: A 513 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7600 (mptp) REVERT: A 554 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8766 (tt) REVERT: A 570 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.7843 (mmtm) REVERT: A 759 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.6615 (tm-30) REVERT: A 815 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6164 (tp30) REVERT: B 49 LYS cc_start: 0.7314 (tttp) cc_final: 0.6794 (ttpt) REVERT: B 72 TYR cc_start: 0.7683 (t80) cc_final: 0.7373 (t80) REVERT: B 89 LYS cc_start: 0.7594 (mmmt) cc_final: 0.6888 (ttpp) REVERT: B 157 TYR cc_start: 0.7580 (m-80) cc_final: 0.7247 (m-10) REVERT: B 220 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8388 (tp) REVERT: B 443 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8494 (mp0) REVERT: B 608 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8062 (mt-10) REVERT: B 674 LYS cc_start: 0.8048 (mmmm) cc_final: 0.7756 (pmmt) REVERT: B 719 LYS cc_start: 0.7941 (tppp) cc_final: 0.7225 (tttm) REVERT: B 762 GLN cc_start: 0.7089 (tt0) cc_final: 0.6366 (pt0) REVERT: B 789 GLN cc_start: 0.7811 (tp-100) cc_final: 0.6975 (pm20) REVERT: B 803 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7466 (tmtt) REVERT: B 838 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7309 (mmmt) REVERT: C 58 LYS cc_start: 0.7190 (pptt) cc_final: 0.6850 (mmtt) REVERT: C 92 TYR cc_start: 0.6733 (t80) cc_final: 0.6495 (t80) REVERT: C 116 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.8534 (pm20) REVERT: C 121 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: C 194 PRO cc_start: 0.7852 (Cg_exo) cc_final: 0.7524 (Cg_endo) REVERT: C 229 MET cc_start: 0.7243 (ptp) cc_final: 0.7024 (ptp) REVERT: C 294 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: C 363 ARG cc_start: 0.7049 (mtm180) cc_final: 0.6230 (mtt180) REVERT: C 593 MET cc_start: 0.7993 (mtp) cc_final: 0.7637 (ttp) REVERT: C 727 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7485 (mp) REVERT: C 791 GLU cc_start: 0.7165 (tt0) cc_final: 0.6452 (pm20) REVERT: D 7 TYR cc_start: 0.5753 (t80) cc_final: 0.5436 (t80) REVERT: D 57 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: D 232 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6781 (tp30) REVERT: D 239 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.7280 (t80) REVERT: D 247 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7353 (mm-30) REVERT: D 335 MET cc_start: 0.8454 (mmm) cc_final: 0.8110 (mtp) REVERT: D 350 ILE cc_start: 0.7541 (tt) cc_final: 0.7306 (tp) REVERT: D 361 ASN cc_start: 0.7394 (m110) cc_final: 0.6888 (p0) REVERT: D 443 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8205 (tp30) REVERT: D 527 LYS cc_start: 0.8177 (mttt) cc_final: 0.7958 (mtmt) REVERT: D 651 GLN cc_start: 0.8390 (mt0) cc_final: 0.7918 (tt0) REVERT: D 713 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8647 (tt0) REVERT: D 719 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7066 (mmpt) REVERT: D 759 GLU cc_start: 0.7205 (tt0) cc_final: 0.6914 (tt0) REVERT: D 773 GLN cc_start: 0.6918 (tm-30) cc_final: 0.6635 (tm-30) REVERT: D 817 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7467 (tm-30) REVERT: E 19 LYS cc_start: 0.8106 (mttm) cc_final: 0.7275 (mtpp) REVERT: E 85 MET cc_start: 0.7044 (mmm) cc_final: 0.6724 (mmm) REVERT: E 161 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8203 (tttm) REVERT: E 241 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8038 (mm) REVERT: E 246 TRP cc_start: 0.7070 (t-100) cc_final: 0.6757 (t-100) REVERT: E 287 GLN cc_start: 0.8212 (tp40) cc_final: 0.7798 (tm-30) REVERT: E 354 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7517 (mtt90) REVERT: E 363 ARG cc_start: 0.6428 (mtm180) cc_final: 0.5580 (mmm160) REVERT: E 433 LYS cc_start: 0.8658 (mmtm) cc_final: 0.8267 (ptmt) REVERT: E 608 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: E 720 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7670 (mp) REVERT: E 756 MET cc_start: 0.7262 (pmt) cc_final: 0.6868 (pmm) REVERT: E 759 GLU cc_start: 0.7539 (tt0) cc_final: 0.6932 (tm-30) REVERT: E 773 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.6636 (tm-30) REVERT: E 795 GLN cc_start: 0.7187 (mt0) cc_final: 0.6494 (mm110) REVERT: E 815 GLU cc_start: 0.7651 (tt0) cc_final: 0.7032 (tm-30) outliers start: 137 outliers final: 90 residues processed: 467 average time/residue: 0.7301 time to fit residues: 405.4993 Evaluate side-chains 466 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 351 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 803 LYS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain C residue 850 TRP Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 725 ASN Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 740 GLU Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 352 MET Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 541 SER Chi-restraints excluded: chain E residue 608 GLU Chi-restraints excluded: chain E residue 688 SER Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 773 GLN Chi-restraints excluded: chain E residue 808 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 6 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 310 optimal weight: 9.9990 chunk 274 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 chunk 405 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN B 545 HIS B 725 ASN C 205 GLN C 687 ASN D 671 ASN D 810 ASN E 356 ASN ** E 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.157118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105247 restraints weight = 44445.575| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.32 r_work: 0.3106 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 35664 Z= 0.193 Angle : 0.578 10.618 48281 Z= 0.297 Chirality : 0.044 0.180 4990 Planarity : 0.004 0.062 6243 Dihedral : 6.674 85.093 4787 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.77 % Allowed : 26.35 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.03 (0.13), residues: 4235 helix: 1.16 (0.12), residues: 1792 sheet: -0.04 (0.20), residues: 618 loop : -1.19 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 741 TYR 0.034 0.001 TYR E 209 PHE 0.026 0.001 PHE E 160 TRP 0.029 0.002 TRP C 734 HIS 0.004 0.001 HIS B 545 Details of bonding type rmsd covalent geometry : bond 0.00464 (35664) covalent geometry : angle 0.57772 (48281) hydrogen bonds : bond 0.04333 ( 1641) hydrogen bonds : angle 4.94950 ( 4716) ********************** 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 492 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 353 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7602 (mmtt) REVERT: A 57 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7809 (mm-30) REVERT: A 73 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7525 (p0) REVERT: A 76 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7028 (tp30) REVERT: A 85 MET cc_start: 0.7386 (mmm) cc_final: 0.7148 (mmm) REVERT: A 102 LYS cc_start: 0.8381 (mmmt) cc_final: 0.7877 (mptt) REVERT: A 246 TRP cc_start: 0.7357 (t-100) cc_final: 0.6463 (t60) REVERT: A 277 ASN cc_start: 0.8445 (t0) cc_final: 0.8145 (t0) REVERT: A 294 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6466 (mp0) REVERT: A 513 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7592 (mptp) REVERT: A 554 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8767 (tt) REVERT: A 570 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.7851 (mmtm) REVERT: A 759 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.6639 (tm-30) REVERT: A 815 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6150 (tp30) REVERT: A 830 VAL cc_start: 0.8046 (OUTLIER) cc_final: 0.7831 (p) REVERT: B 49 LYS cc_start: 0.7310 (tttp) cc_final: 0.6797 (ttpt) REVERT: B 69 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.5284 (mpt-90) REVERT: B 72 TYR cc_start: 0.7698 (t80) cc_final: 0.7398 (t80) REVERT: B 89 LYS cc_start: 0.7579 (mmmt) cc_final: 0.6866 (ttpp) REVERT: B 157 TYR cc_start: 0.7589 (m-80) cc_final: 0.7258 (m-10) REVERT: B 220 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8402 (tp) REVERT: B 443 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8485 (mp0) REVERT: B 608 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: B 674 LYS cc_start: 0.8038 (mmmm) cc_final: 0.7774 (pmmt) REVERT: B 719 LYS cc_start: 0.7911 (tppp) cc_final: 0.7195 (tttm) REVERT: B 762 GLN cc_start: 0.7108 (tt0) cc_final: 0.6384 (pt0) REVERT: B 789 GLN cc_start: 0.7819 (tp-100) cc_final: 0.6981 (pm20) REVERT: B 803 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7455 (tmtt) REVERT: B 838 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7257 (mmmt) REVERT: C 58 LYS cc_start: 0.7177 (pptt) cc_final: 0.6884 (mmtt) REVERT: C 60 ASN cc_start: 0.6794 (m-40) cc_final: 0.6352 (p0) REVERT: C 85 MET cc_start: 0.7064 (mmm) cc_final: 0.6752 (mmp) REVERT: C 116 GLU cc_start: 0.9336 (OUTLIER) cc_final: 0.8543 (pm20) REVERT: C 121 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: C 194 PRO cc_start: 0.7859 (Cg_exo) cc_final: 0.7533 (Cg_endo) REVERT: C 229 MET cc_start: 0.7239 (ptp) cc_final: 0.7024 (ptp) REVERT: C 294 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: C 363 ARG cc_start: 0.7057 (mtm180) cc_final: 0.6238 (mtt180) REVERT: C 430 TYR cc_start: 0.7365 (m-10) cc_final: 0.7141 (m-10) REVERT: C 593 MET cc_start: 0.7977 (mtp) cc_final: 0.7626 (ttp) REVERT: C 727 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7458 (mp) REVERT: C 791 GLU cc_start: 0.7169 (tt0) cc_final: 0.6449 (pm20) REVERT: D 7 TYR cc_start: 0.5713 (t80) cc_final: 0.5445 (t80) REVERT: D 57 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: D 232 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.6764 (tp30) REVERT: D 239 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.7300 (t80) REVERT: D 247 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7354 (mm-30) REVERT: D 335 MET cc_start: 0.8450 (mmm) cc_final: 0.8110 (mtp) REVERT: D 350 ILE cc_start: 0.7458 (tt) cc_final: 0.7226 (tp) REVERT: D 361 ASN cc_start: 0.7355 (m110) cc_final: 0.6856 (p0) REVERT: D 443 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8201 (tp30) REVERT: D 527 LYS cc_start: 0.8181 (mttt) cc_final: 0.7963 (mtmt) REVERT: D 651 GLN cc_start: 0.8394 (mt0) cc_final: 0.7918 (tt0) REVERT: D 713 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8626 (tt0) REVERT: D 719 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7061 (mmpt) REVERT: D 759 GLU cc_start: 0.7134 (tt0) cc_final: 0.6843 (tt0) REVERT: D 773 GLN cc_start: 0.6914 (tm-30) cc_final: 0.6639 (tm-30) REVERT: D 817 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7465 (tm-30) REVERT: E 19 LYS cc_start: 0.8090 (mttm) cc_final: 0.7253 (mtpp) REVERT: E 85 MET cc_start: 0.7017 (mmm) cc_final: 0.6708 (mmm) REVERT: E 161 LYS cc_start: 0.8724 (ttmm) cc_final: 0.8204 (tttm) REVERT: E 241 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8210 (mm) REVERT: E 246 TRP cc_start: 0.7070 (t-100) cc_final: 0.6749 (t-100) REVERT: E 287 GLN cc_start: 0.8196 (tp40) cc_final: 0.7786 (tm-30) REVERT: E 354 ARG cc_start: 0.8062 (mtt90) cc_final: 0.7493 (mtt90) REVERT: E 363 ARG cc_start: 0.6422 (mtm180) cc_final: 0.5576 (mmm160) REVERT: E 433 LYS cc_start: 0.8664 (mmtm) cc_final: 0.8271 (ptmt) REVERT: E 608 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: E 720 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7673 (mp) REVERT: E 756 MET cc_start: 0.7255 (pmt) cc_final: 0.6862 (pmm) REVERT: E 759 GLU cc_start: 0.7493 (tt0) cc_final: 0.6882 (tm-30) REVERT: E 773 GLN cc_start: 0.6971 (OUTLIER) cc_final: 0.6651 (tm-30) REVERT: E 790 PRO cc_start: 0.7497 (Cg_endo) cc_final: 0.7216 (Cg_endo) REVERT: E 791 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6666 (pp20) REVERT: E 795 GLN cc_start: 0.7176 (mt0) cc_final: 0.6483 (mm110) REVERT: E 815 GLU cc_start: 0.7640 (tt0) cc_final: 0.7014 (tm-30) outliers start: 139 outliers final: 93 residues processed: 464 average time/residue: 0.7544 time to fit residues: 416.4417 Evaluate side-chains 472 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 351 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 803 LYS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 850 TRP Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 606 SER Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 725 ASN Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 740 GLU Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 352 MET Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 541 SER Chi-restraints excluded: chain E residue 608 GLU Chi-restraints excluded: chain E residue 688 SER Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 773 GLN Chi-restraints excluded: chain E residue 791 GLU Chi-restraints excluded: chain E residue 808 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 156 optimal weight: 0.9990 chunk 338 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 228 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 330 optimal weight: 0.3980 chunk 91 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 322 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN B 545 HIS B 725 ASN C 205 GLN C 687 ASN D 671 ASN D 810 ASN E 356 ASN ** E 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.158314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.106425 restraints weight = 44097.074| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.33 r_work: 0.3121 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35664 Z= 0.153 Angle : 0.551 10.303 48281 Z= 0.284 Chirality : 0.043 0.178 4990 Planarity : 0.004 0.056 6243 Dihedral : 6.611 85.306 4787 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.45 % Allowed : 26.76 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.08 (0.13), residues: 4235 helix: 1.25 (0.12), residues: 1794 sheet: 0.05 (0.20), residues: 618 loop : -1.15 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 741 TYR 0.025 0.001 TYR D 696 PHE 0.025 0.001 PHE E 349 TRP 0.030 0.002 TRP C 734 HIS 0.004 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00363 (35664) covalent geometry : angle 0.55147 (48281) hydrogen bonds : bond 0.04068 ( 1641) hydrogen bonds : angle 4.87555 ( 4716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13898.53 seconds wall clock time: 237 minutes 12.14 seconds (14232.14 seconds total)