Starting phenix.real_space_refine on Fri Mar 6 23:27:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u3a_63814/03_2026/9u3a_63814.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u3a_63814/03_2026/9u3a_63814.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/9u3a_63814/03_2026/9u3a_63814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u3a_63814/03_2026/9u3a_63814.map" model { file = "/net/cci-nas-00/data/ceres_data/9u3a_63814/03_2026/9u3a_63814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u3a_63814/03_2026/9u3a_63814.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= 0.002 sd= 0.027 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 12 5.49 5 S 195 5.16 5 C 22337 2.51 5 N 5884 2.21 5 O 6526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.04s 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: 34954 Number of models: 1 Model: "" Number of chains: 9 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: {'PTRANS': 31, 'TRANS': 820} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'LLP:plan-1': 1, 'LLP:plan-2': 1, 'LLP:plan-3': 1} Unresolved non-hydrogen planarities: 13 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 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'AMP%rna2p': 1, 'AMP%rna3p': 1} Classifications: {'RNA_mixed': 2} Modifications used: {'rna2p': 1, 'rna3p': 1} Link IDs: {'rna2p': 1} Chain breaks: 1 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'AMP%rna2p': 2} Classifications: {'RNA_mixed': 2} Modifications used: {'rna2p': 2} Link IDs: {'rna2p': 1} Chain breaks: 1 Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'AMP%rna2p': 2} Classifications: {'RNA_mixed': 2} Modifications used: {'rna2p': 2} Link IDs: {'rna2p': 1} Chain breaks: 1 Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'AMP%rna2p': 2} Classifications: {'RNA_mixed': 2} Modifications used: {'rna2p': 2} Link IDs: {'rna2p': 1} Chain breaks: 1 Time building chain proxies: 7.62, per 1000 atoms: 0.22 Number of scatterers: 34954 At special positions: 0 Unit cell: (101.26, 175.96, 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 12 15.00 O 6526 8.00 N 5884 7.00 C 22337 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: 2.82 Conformation dependent library (CDL) restraints added in 1.3 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: 195 helices and 43 sheets defined 48.5% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 41 through 52 removed outlier: 3.698A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.723A 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 70 Processing helix chain 'A' and resid 71 through 80 Processing helix chain 'A' and resid 82 through 100 Processing helix chain 'A' and resid 128 through 144 Processing helix chain 'A' and resid 245 through 267 Processing helix chain 'A' and resid 282 through 297 removed outlier: 4.088A pdb=" N LEU A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 309 removed outlier: 3.786A pdb=" N ALA A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 323 Processing helix chain 'A' and resid 327 through 335 removed outlier: 3.582A pdb=" N TYR A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 366 through 373 Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 393 through 397 removed outlier: 4.199A pdb=" N LYS A 397 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 420 through 428 removed outlier: 3.673A pdb=" N LEU A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 447 through 450 Processing helix chain 'A' and resid 452 through 482 removed outlier: 3.602A pdb=" N TYR A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 516 through 520 Processing helix chain 'A' and resid 521 through 530 Processing helix chain 'A' and resid 549 through 563 Processing helix chain 'A' and resid 578 through 589 removed outlier: 3.691A pdb=" N SER A 587 " --> pdb=" O ARG A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 612 removed outlier: 3.890A pdb=" N MET A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 629 Processing helix chain 'A' and resid 645 through 664 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 680 through 692 removed outlier: 3.501A pdb=" N ILE A 689 " --> pdb=" O VAL A 685 " (cutoff:3.500A) 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: 3.751A pdb=" N ALA A 715 " --> pdb=" O ASN A 711 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU A 727 " --> pdb=" O ASN A 723 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA A 728 " --> pdb=" O ASP A 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 27 through 33 removed outlier: 3.881A pdb=" N GLU B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 40 removed outlier: 4.278A pdb=" N TRP B 38 " --> pdb=" O ASN B 35 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP B 40 " --> pdb=" O TRP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 removed outlier: 3.700A pdb=" N ARG B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 59 Processing helix chain 'B' and resid 62 through 67 Processing helix chain 'B' and resid 71 through 81 Processing helix chain 'B' and resid 81 through 101 removed outlier: 4.162A pdb=" N VAL B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 145 Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.825A pdb=" N LEU B 250 " --> pdb=" O TRP B 246 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLY B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLY B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.984A pdb=" N GLU B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU B 306 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 323 Processing helix chain 'B' and resid 327 through 336 removed outlier: 3.620A pdb=" N TYR B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY B 336 " --> pdb=" O GLY B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.755A pdb=" N ARG B 341 " --> pdb=" O GLY B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 353 removed outlier: 4.169A pdb=" N GLY B 353 " --> pdb=" O PHE B 349 " (cutoff:3.500A) 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 397 removed outlier: 4.061A pdb=" N LYS B 397 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 414 through 419 removed outlier: 3.551A pdb=" N TRP B 418 " --> pdb=" O HIS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 431 Processing helix chain 'B' and resid 441 through 446 removed outlier: 3.510A pdb=" N TRP B 445 " --> pdb=" O ASN B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 482 removed outlier: 3.576A pdb=" N TRP B 457 " --> pdb=" O ASP B 453 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 463 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 520 Processing helix chain 'B' and resid 521 through 530 Processing helix chain 'B' and resid 549 through 563 Processing helix chain 'B' and resid 584 through 589 Processing helix chain 'B' and resid 624 through 629 Processing helix chain 'B' and resid 648 through 664 Processing helix chain 'B' and resid 664 through 670 removed outlier: 3.788A pdb=" N MET B 668 " --> pdb=" O ASP B 664 " (cutoff:3.500A) 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 708 removed outlier: 3.508A pdb=" N ASP B 703 " --> pdb=" O LYS B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 721 removed outlier: 3.577A pdb=" N ALA B 715 " --> pdb=" O ASN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 740 removed outlier: 5.940A pdb=" N LEU B 727 " --> pdb=" O ASN B 723 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA B 728 " --> pdb=" O ASP B 724 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU B 740 " --> pdb=" O GLU B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 745 Processing helix chain 'B' and resid 752 through 757 removed outlier: 3.882A pdb=" N MET B 756 " --> pdb=" O ASP B 752 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA B 757 " --> pdb=" O CYS B 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 752 through 757' Processing helix chain 'C' and resid 26 through 35 removed outlier: 3.967A pdb=" N ASP C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.569A pdb=" N TRP C 40 " --> pdb=" O TRP C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 52 removed outlier: 3.802A pdb=" N ARG C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 3.961A 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 80 Processing helix chain 'C' and resid 82 through 100 Processing helix chain 'C' and resid 129 through 142 Processing helix chain 'C' and resid 245 through 267 removed outlier: 3.754A pdb=" N GLY C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 281 Processing helix chain 'C' and resid 282 through 295 removed outlier: 4.132A pdb=" N LEU C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 319 through 323 removed outlier: 3.602A pdb=" N HIS C 323 " --> pdb=" O PRO C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 335 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.766A pdb=" N ARG C 341 " --> pdb=" O GLY C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 354 removed outlier: 4.308A 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 392 Processing helix chain 'C' and resid 400 through 404 Processing helix chain 'C' and resid 414 through 419 Processing helix chain 'C' and resid 420 through 431 Processing helix chain 'C' and resid 441 through 446 removed outlier: 3.538A pdb=" N TRP C 445 " --> pdb=" O ASN C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 Processing helix chain 'C' and resid 452 through 482 Processing helix chain 'C' and resid 488 through 495 removed outlier: 3.535A pdb=" N ARG C 495 " --> pdb=" O SER C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 530 Processing helix chain 'C' and resid 548 through 563 removed outlier: 3.965A pdb=" N GLN C 552 " --> pdb=" O ASP C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 589 removed outlier: 3.545A pdb=" N SER C 587 " --> pdb=" O ARG C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 612 removed outlier: 3.755A pdb=" N GLU C 608 " --> pdb=" O GLY C 604 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET C 612 " --> pdb=" O GLU C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 627 removed outlier: 3.611A pdb=" N VAL C 626 " --> pdb=" O GLY C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 664 Processing helix chain 'C' and resid 664 through 670 Processing helix chain 'C' and resid 678 through 691 Processing helix chain 'C' and resid 692 through 696 removed outlier: 3.521A pdb=" N HIS C 695 " --> pdb=" O ILE C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 707 Processing helix chain 'C' and resid 711 through 721 Processing helix chain 'C' and resid 721 through 742 removed outlier: 5.819A pdb=" N LEU C 727 " --> pdb=" O ASN C 723 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA C 728 " --> pdb=" O ASP C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 745 No H-bonds generated for 'chain 'C' and resid 743 through 745' Processing helix chain 'C' and resid 790 through 794 removed outlier: 3.555A pdb=" N GLY C 793 " --> pdb=" O PRO C 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 35 through 40 removed outlier: 3.914A pdb=" N TRP D 38 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP D 40 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 52 removed outlier: 3.701A pdb=" N ARG D 45 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 4.289A 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 81 Processing helix chain 'D' and resid 82 through 100 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 234 through 239 removed outlier: 3.962A pdb=" N ILE D 237 " --> pdb=" O ASP D 234 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR D 238 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 267 Processing helix chain 'D' and resid 283 through 297 removed outlier: 3.557A pdb=" N ASP D 296 " --> pdb=" O TYR D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 309 Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.749A pdb=" N LYS D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 345 through 352 Processing helix chain 'D' and resid 366 through 373 Processing helix chain 'D' and resid 381 through 393 Processing helix chain 'D' and resid 400 through 404 Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 434 through 438 Processing helix chain 'D' and resid 441 through 446 removed outlier: 3.535A pdb=" N TRP D 445 " --> pdb=" O ASN D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 451 Processing helix chain 'D' and resid 452 through 482 Processing helix chain 'D' and resid 485 through 487 No H-bonds generated for 'chain 'D' and resid 485 through 487' Processing helix chain 'D' and resid 488 through 494 Processing helix chain 'D' and resid 510 through 520 removed outlier: 6.496A pdb=" N ALA D 515 " --> pdb=" O TYR D 512 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N HIS D 516 " --> pdb=" O LYS D 513 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 517 " --> pdb=" O ARG D 514 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU D 518 " --> pdb=" O ALA D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 530 removed outlier: 3.701A pdb=" N LEU D 525 " --> pdb=" O ASP D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 563 removed outlier: 3.551A pdb=" N GLN D 552 " --> pdb=" O ASP D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 589 removed outlier: 3.615A pdb=" N VAL D 589 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 613 removed outlier: 4.010A pdb=" N MET D 612 " --> pdb=" O GLU D 608 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN D 613 " --> pdb=" O LLP D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 629 Processing helix chain 'D' and resid 645 through 664 Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 678 through 692 Processing helix chain 'D' and resid 693 through 696 Processing helix chain 'D' and resid 697 through 709 Processing helix chain 'D' and resid 709 through 741 removed outlier: 3.559A pdb=" N ALA D 722 " --> pdb=" O LYS D 718 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASN D 723 " --> pdb=" O LYS D 719 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASP D 724 " --> pdb=" O LEU D 720 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN D 725 " --> pdb=" O SER D 721 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU D 727 " --> pdb=" O ASN D 723 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA D 728 " --> pdb=" O ASP D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 757 removed outlier: 4.164A pdb=" N ALA D 757 " --> pdb=" O CYS D 753 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 34 removed outlier: 4.262A pdb=" N GLU E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 40 removed outlier: 3.665A pdb=" N TRP E 40 " --> pdb=" O TRP E 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 37 through 40' Processing helix chain 'E' and resid 41 through 52 removed outlier: 3.911A pdb=" N ASP E 52 " --> pdb=" O PHE E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 59 removed outlier: 3.636A pdb=" N GLU E 57 " --> pdb=" O PRO E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 71 through 81 Processing helix chain 'E' and resid 82 through 100 Processing helix chain 'E' and resid 128 through 144 Processing helix chain 'E' and resid 234 through 239 removed outlier: 3.758A pdb=" N THR E 238 " --> pdb=" O ARG E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 268 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 296 removed outlier: 4.005A 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: 3.806A pdb=" N LYS E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 343 removed outlier: 4.482A pdb=" N GLN E 340 " --> pdb=" O GLY E 336 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG E 341 " --> pdb=" O GLY E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 352 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 435 through 439 removed outlier: 4.287A pdb=" N GLN E 439 " --> pdb=" O MET E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 446 removed outlier: 4.013A 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 removed outlier: 3.707A pdb=" N ASN E 482 " --> pdb=" O THR E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 487 No H-bonds generated for 'chain 'E' and resid 485 through 487' Processing helix chain 'E' and resid 488 through 494 Processing helix chain 'E' and resid 510 through 520 removed outlier: 6.393A pdb=" N ALA E 515 " --> pdb=" O TYR E 512 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS E 516 " --> pdb=" O LYS E 513 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU E 517 " --> pdb=" O ARG E 514 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU E 518 " --> pdb=" O ALA E 515 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR E 520 " --> pdb=" O LEU E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 530 removed outlier: 3.578A pdb=" N LEU E 525 " --> pdb=" O ASP E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 563 removed outlier: 3.920A pdb=" N GLN E 552 " --> pdb=" O ASP E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 589 removed outlier: 3.975A pdb=" N SER E 587 " --> pdb=" O ARG E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 613 removed outlier: 3.700A pdb=" N MET E 612 " --> pdb=" O GLU E 608 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN E 613 " --> pdb=" O LLP E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 624 through 629 Processing helix chain 'E' and resid 645 through 664 Processing helix chain 'E' and resid 664 through 670 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 removed outlier: 3.526A pdb=" N GLN E 701 " --> pdb=" O THR E 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 720 Processing helix chain 'E' and resid 721 through 741 removed outlier: 4.271A pdb=" N ALA E 726 " --> pdb=" O ALA E 722 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU E 727 " --> pdb=" O ASN E 723 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA E 728 " --> pdb=" O ASP E 724 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS E 729 " --> pdb=" O ASN E 725 " (cutoff:3.500A) Processing helix chain 'E' and resid 742 through 745 removed outlier: 3.615A pdb=" N ILE E 745 " --> pdb=" O TRP E 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 742 through 745' Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 removed outlier: 3.540A pdb=" N GLY B 824 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 186 Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 186 removed outlier: 7.367A pdb=" N MET A 148 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N TYR A 221 " --> pdb=" O MET A 148 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA A 150 " --> pdb=" O TYR A 221 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU A 223 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY A 152 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 376 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL A 377 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 164 Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA6, first strand: chain 'A' and resid 571 through 574 removed outlier: 6.321A pdb=" N LEU A 501 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N PHE A 539 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 503 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N SER A 541 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE A 505 " --> pdb=" O SER A 541 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N CYS A 506 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N TRP A 592 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL A 620 " --> pdb=" O TRP A 592 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASN A 594 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASN A 617 " --> pdb=" O TRP A 635 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU A 637 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER A 619 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 746 through 750 removed outlier: 3.822A pdb=" N HIS A 746 " --> pdb=" O ASP A 771 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 769 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS A 750 " --> pdb=" O GLN A 767 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLN A 767 " --> pdb=" O LYS A 750 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 766 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR A 813 " --> pdb=" O VAL A 805 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 798 through 801 Processing sheet with id=AA9, first strand: chain 'A' and resid 824 through 826 Processing sheet with id=AB1, first strand: chain 'B' and resid 109 through 110 removed outlier: 7.497A pdb=" N MET B 148 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N TYR B 221 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 150 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N LEU B 223 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY B 152 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP B 224 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 209 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 208 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 109 through 110 removed outlier: 7.497A pdb=" N MET B 148 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N TYR B 221 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 150 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N LEU B 223 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY B 152 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 163 through 164 Processing sheet with id=AB4, first strand: chain 'B' and resid 274 through 277 removed outlier: 3.733A pdb=" N GLU B 376 " --> pdb=" O SER B 311 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AB6, first strand: chain 'B' and resid 571 through 573 removed outlier: 8.503A pdb=" N ILE B 572 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE B 538 " --> pdb=" O ILE B 572 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU B 501 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N PHE B 539 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE B 503 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N SER B 541 " --> pdb=" O ILE B 503 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE B 505 " --> pdb=" O SER B 541 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N CYS B 506 " --> pdb=" O MET B 593 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASN B 617 " --> pdb=" O TRP B 635 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU B 637 " --> pdb=" O ASN B 617 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N SER B 619 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 746 through 750 removed outlier: 4.040A pdb=" N HIS B 746 " --> pdb=" O ASP B 771 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP B 771 " --> pdb=" O HIS B 746 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL B 769 " --> pdb=" O VAL B 748 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 794 through 801 removed outlier: 6.920A pdb=" N LYS B 794 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLN B 789 " --> pdb=" O LYS B 794 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL B 796 " --> pdb=" O LYS B 787 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS B 787 " --> pdb=" O VAL B 796 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL B 830 " --> pdb=" O LEU B 851 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AC1, first strand: chain 'C' and resid 14 through 15 removed outlier: 3.550A pdb=" N LYS D 827 " --> pdb=" O LEU D 786 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS D 787 " --> pdb=" O VAL D 796 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL D 796 " --> pdb=" O LYS D 787 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLN D 789 " --> pdb=" O LYS D 794 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS D 794 " --> pdb=" O GLN D 789 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.641A pdb=" N VAL D 830 " --> pdb=" O LEU D 851 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 185 through 186 Processing sheet with id=AC4, first strand: chain 'C' and resid 185 through 186 removed outlier: 4.425A pdb=" N LYS C 219 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 110 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL C 151 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TYR C 112 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N PHE C 153 " --> pdb=" O TYR C 112 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AC6, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AC7, first strand: chain 'C' and resid 378 through 379 Processing sheet with id=AC8, first strand: chain 'C' and resid 571 through 574 Processing sheet with id=AC9, first strand: chain 'C' and resid 619 through 620 removed outlier: 7.202A pdb=" N SER C 619 " --> pdb=" O LEU C 637 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 746 through 747 removed outlier: 3.736A pdb=" N HIS C 746 " --> pdb=" O ASP C 771 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 796 through 798 removed outlier: 6.968A pdb=" N VAL C 785 " --> pdb=" O TYR C 797 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 784 " --> pdb=" O GLY C 829 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY C 829 " --> pdb=" O VAL C 784 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 757 through 759 removed outlier: 4.236A pdb=" N ALA E 758 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N SER E 825 " --> pdb=" O GLU E 788 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU E 788 " --> pdb=" O SER E 825 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LYS E 787 " --> pdb=" O VAL E 796 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL E 796 " --> pdb=" O LYS E 787 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLN E 789 " --> pdb=" O LYS E 794 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LYS E 794 " --> pdb=" O GLN E 789 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 757 through 759 removed outlier: 4.236A pdb=" N ALA E 758 " --> pdb=" O THR D 17 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 185 through 186 Processing sheet with id=AD6, first strand: chain 'D' and resid 185 through 186 removed outlier: 3.530A pdb=" N LEU D 222 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N MET D 148 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N TYR D 221 " --> pdb=" O MET D 148 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA D 150 " --> pdb=" O TYR D 221 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU D 223 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY D 152 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA D 111 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASN D 277 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N PHE D 113 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU D 376 " --> pdb=" O SER D 311 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL D 377 " --> pdb=" O GLY D 407 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 162 through 164 Processing sheet with id=AD8, first strand: chain 'D' and resid 325 through 326 Processing sheet with id=AD9, first strand: chain 'D' and resid 571 through 573 removed outlier: 3.554A pdb=" N SER D 541 " --> pdb=" O PHE D 505 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET D 502 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N MET D 593 " --> pdb=" O MET D 502 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY D 504 " --> pdb=" O MET D 593 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASN D 617 " --> pdb=" O TRP D 635 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU D 637 " --> pdb=" O ASN D 617 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N SER D 619 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 746 through 751 removed outlier: 6.284A pdb=" N VAL D 747 " --> pdb=" O ASP D 771 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASP D 771 " --> pdb=" O VAL D 747 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER D 749 " --> pdb=" O VAL D 769 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 818 " --> pdb=" O ILE D 764 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL D 766 " --> pdb=" O ALA D 816 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY D 806 " --> pdb=" O THR D 813 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU D 815 " --> pdb=" O MET D 804 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N MET D 804 " --> pdb=" O GLU D 815 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 185 through 186 Processing sheet with id=AE3, first strand: chain 'E' and resid 185 through 186 removed outlier: 7.191A 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: 6.549A pdb=" N ALA E 150 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU E 223 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY E 152 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL E 110 " --> pdb=" O CYS E 149 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL E 151 " --> pdb=" O VAL E 110 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR E 112 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N PHE E 153 " --> pdb=" O TYR E 112 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR E 274 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N THR E 314 " --> pdb=" O TYR E 274 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N CYS E 276 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N SER E 311 " --> pdb=" O GLU E 376 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N ASN E 378 " --> pdb=" O SER E 311 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR E 313 " --> pdb=" O ASN E 378 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL E 377 " --> pdb=" O GLY E 407 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 161 through 164 Processing sheet with id=AE5, first strand: chain 'E' and resid 325 through 326 Processing sheet with id=AE6, first strand: chain 'E' and resid 571 through 574 removed outlier: 5.197A pdb=" N CYS E 506 " --> pdb=" O MET E 593 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TRP E 592 " --> pdb=" O LEU E 618 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL E 620 " --> pdb=" O TRP E 592 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASN E 594 " --> pdb=" O VAL E 620 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN E 617 " --> pdb=" O TRP E 635 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LEU E 637 " --> pdb=" O ASN E 617 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N SER E 619 " --> pdb=" O LEU E 637 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 746 through 747 removed outlier: 3.641A pdb=" N HIS E 746 " --> pdb=" O ASP E 771 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASN E 811 " --> pdb=" O HIS E 807 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N HIS E 807 " --> pdb=" O ASN E 811 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR E 813 " --> pdb=" O VAL E 805 " (cutoff:3.500A) 1508 hydrogen bonds defined for protein. 4185 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: 7.34 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5874 1.31 - 1.44: 10087 1.44 - 1.57: 19566 1.57 - 1.70: 12 1.70 - 1.83: 325 Bond restraints: 35864 Sorted by residual: bond pdb=" OP4 LLP D 609 " pdb=" P LLP D 609 " ideal model delta sigma weight residual 1.726 1.605 0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" OP4 LLP E 609 " pdb=" P LLP E 609 " ideal model delta sigma weight residual 1.726 1.611 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" OP4 LLP B 609 " pdb=" P LLP B 609 " ideal model delta sigma weight residual 1.726 1.612 0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" OP4 LLP A 609 " pdb=" P LLP A 609 " ideal model delta sigma weight residual 1.726 1.612 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C4 AMP D 901 " pdb=" C5 AMP D 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.06e+01 ... (remaining 35859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 47756 2.99 - 5.98: 713 5.98 - 8.97: 84 8.97 - 11.96: 28 11.96 - 14.95: 4 Bond angle restraints: 48585 Sorted by residual: angle pdb=" N ARG D 583 " pdb=" CA ARG D 583 " pdb=" C ARG D 583 " ideal model delta sigma weight residual 113.72 100.46 13.26 1.30e+00 5.92e-01 1.04e+02 angle pdb=" N ASN C 372 " pdb=" CA ASN C 372 " pdb=" C ASN C 372 " ideal model delta sigma weight residual 113.02 100.86 12.16 1.20e+00 6.94e-01 1.03e+02 angle pdb=" N LEU B 581 " pdb=" CA LEU B 581 " pdb=" C LEU B 581 " ideal model delta sigma weight residual 111.07 101.61 9.46 1.07e+00 8.73e-01 7.81e+01 angle pdb=" C ASN C 372 " pdb=" CA ASN C 372 " pdb=" CB ASN C 372 " ideal model delta sigma weight residual 110.37 125.32 -14.95 1.78e+00 3.16e-01 7.05e+01 angle pdb=" N ASP A 30 " pdb=" CA ASP A 30 " pdb=" C ASP A 30 " ideal model delta sigma weight residual 114.75 106.59 8.16 1.26e+00 6.30e-01 4.19e+01 ... (remaining 48580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 20023 34.93 - 69.87: 1068 69.87 - 104.80: 68 104.80 - 139.73: 6 139.73 - 174.67: 8 Dihedral angle restraints: 21173 sinusoidal: 8718 harmonic: 12455 Sorted by residual: dihedral pdb=" CA ARG C 598 " pdb=" C ARG C 598 " pdb=" N PRO C 599 " pdb=" CA PRO C 599 " ideal model delta harmonic sigma weight residual -180.00 -65.63 -114.37 0 5.00e+00 4.00e-02 5.23e+02 dihedral pdb=" C2' AMP E 901 " pdb=" C1' AMP E 901 " pdb=" N9 AMP E 901 " pdb=" C4 AMP E 901 " ideal model delta sinusoidal sigma weight residual 91.55 -93.78 -174.67 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C2' AMP E 902 " pdb=" C1' AMP E 902 " pdb=" N9 AMP E 902 " pdb=" C4 AMP E 902 " ideal model delta sinusoidal sigma weight residual 91.55 -103.07 -165.38 1 2.00e+01 2.50e-03 4.72e+01 ... (remaining 21170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 4785 0.109 - 0.217: 225 0.217 - 0.326: 10 0.326 - 0.434: 1 0.434 - 0.543: 1 Chirality restraints: 5022 Sorted by residual: chirality pdb=" CA CYS C 374 " pdb=" N CYS C 374 " pdb=" C CYS C 374 " pdb=" CB CYS C 374 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" CA ASN C 372 " pdb=" N ASN C 372 " pdb=" C ASN C 372 " pdb=" CB ASN C 372 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA VAL D 319 " pdb=" N VAL D 319 " pdb=" C VAL D 319 " pdb=" CB VAL D 319 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 5019 not shown) Planarity restraints: 6251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP E 609 " -0.082 2.00e-02 2.50e+03 8.49e-02 7.20e+01 pdb=" NZ LLP E 609 " 0.072 2.00e-02 2.50e+03 pdb=" C4 LLP E 609 " -0.087 2.00e-02 2.50e+03 pdb=" C4' LLP E 609 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP A 609 " 0.046 2.00e-02 2.50e+03 4.74e-02 2.25e+01 pdb=" NZ LLP A 609 " -0.041 2.00e-02 2.50e+03 pdb=" C4 LLP A 609 " 0.048 2.00e-02 2.50e+03 pdb=" C4' LLP A 609 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 599 " 0.022 2.00e-02 2.50e+03 4.41e-02 1.94e+01 pdb=" C PRO D 599 " -0.076 2.00e-02 2.50e+03 pdb=" O PRO D 599 " 0.029 2.00e-02 2.50e+03 pdb=" N LEU D 600 " 0.025 2.00e-02 2.50e+03 ... (remaining 6248 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1255 2.70 - 3.25: 33977 3.25 - 3.80: 57175 3.80 - 4.35: 76103 4.35 - 4.90: 128101 Nonbonded interactions: 296611 Sorted by model distance: nonbonded pdb=" O THR A 202 " pdb=" ND2 ASN A 203 " model vdw 2.146 3.120 nonbonded pdb=" O LEU B 518 " pdb=" OH TYR B 658 " model vdw 2.196 3.040 nonbonded pdb=" N GLU C 328 " pdb=" OE1 GLU C 328 " model vdw 2.199 3.120 nonbonded pdb=" O ILE C 344 " pdb=" N TRP C 346 " model vdw 2.202 3.120 nonbonded pdb=" OE1 GLN A 212 " pdb=" ND2 ASN A 214 " model vdw 2.203 3.120 ... (remaining 296606 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.290 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.070 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 : 0.008 0.121 35864 Z= 0.412 Angle : 0.943 14.949 48585 Z= 0.559 Chirality : 0.054 0.543 5022 Planarity : 0.005 0.085 6251 Dihedral : 19.592 174.668 13223 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.54 % Favored : 93.29 % Rotamer: Outliers : 4.86 % Allowed : 28.28 % Favored : 66.87 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -1.46 (0.12), residues: 4235 helix: -0.04 (0.12), residues: 1694 sheet: -0.91 (0.21), residues: 640 loop : -1.83 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 741 TYR 0.029 0.002 TYR E 512 PHE 0.027 0.002 PHE C 812 TRP 0.027 0.002 TRP D 40 HIS 0.010 0.001 HIS D 316 Details of bonding type rmsd covalent geometry : bond 0.00816 (35864) covalent geometry : angle 0.94253 (48585) hydrogen bonds : bond 0.17947 ( 1489) hydrogen bonds : angle 7.30386 ( 4185) *********************** 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 728 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 549 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7027 (tptp) cc_final: 0.6609 (tppt) REVERT: A 232 GLU cc_start: 0.8552 (tp30) cc_final: 0.7840 (pm20) REVERT: A 340 GLN cc_start: 0.8231 (mt0) cc_final: 0.7736 (mm-40) REVERT: A 527 LYS cc_start: 0.8790 (mtpp) cc_final: 0.8530 (mtmt) REVERT: A 554 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8667 (tt) REVERT: A 674 LYS cc_start: 0.8730 (ttmm) cc_final: 0.8347 (pmtt) REVERT: A 756 MET cc_start: 0.8054 (tpp) cc_final: 0.7551 (ptt) REVERT: A 763 LYS cc_start: 0.8337 (mptt) cc_final: 0.7807 (mtpp) REVERT: A 792 ASP cc_start: 0.7710 (m-30) cc_final: 0.7397 (t0) REVERT: A 837 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7799 (t0) REVERT: B 143 ASP cc_start: 0.8308 (m-30) cc_final: 0.8097 (m-30) REVERT: B 149 CYS cc_start: 0.8673 (m) cc_final: 0.8101 (p) REVERT: B 310 SER cc_start: 0.8361 (m) cc_final: 0.7989 (p) REVERT: B 344 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7310 (pt) REVERT: B 350 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7226 (tp) REVERT: B 433 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8024 (tppt) REVERT: B 523 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7792 (pt0) REVERT: B 545 HIS cc_start: 0.7552 (t-90) cc_final: 0.7265 (t70) REVERT: B 608 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8402 (mt-10) REVERT: B 674 LYS cc_start: 0.8039 (mmtm) cc_final: 0.7400 (pmmt) REVERT: B 707 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8217 (t70) REVERT: C 24 LYS cc_start: 0.6885 (mmpt) cc_final: 0.6673 (mmtt) REVERT: C 116 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.8646 (pt0) REVERT: C 196 VAL cc_start: 0.8635 (m) cc_final: 0.8392 (t) REVERT: C 229 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7671 (mpt) REVERT: C 341 ARG cc_start: 0.7091 (mtp180) cc_final: 0.6863 (tpt-90) REVERT: C 516 HIS cc_start: 0.7715 (OUTLIER) cc_final: 0.7319 (m-70) REVERT: C 639 GLU cc_start: 0.4492 (OUTLIER) cc_final: 0.3915 (tm-30) REVERT: C 641 ARG cc_start: 0.4442 (OUTLIER) cc_final: 0.4061 (ptp-170) REVERT: C 735 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6099 (tppp) REVERT: C 765 LYS cc_start: 0.6220 (tmtt) cc_final: 0.5852 (tmtt) REVERT: C 775 LEU cc_start: 0.6800 (mp) cc_final: 0.6462 (pt) REVERT: C 803 LYS cc_start: 0.6945 (tppp) cc_final: 0.6188 (ptpt) REVERT: C 815 GLU cc_start: 0.6515 (tt0) cc_final: 0.6216 (tm-30) REVERT: D 54 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: D 166 MET cc_start: 0.7854 (mtp) cc_final: 0.7449 (pmm) REVERT: D 378 ASN cc_start: 0.8529 (p0) cc_final: 0.8167 (p0) REVERT: D 390 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7748 (mm-40) REVERT: D 393 SER cc_start: 0.7657 (OUTLIER) cc_final: 0.7244 (p) REVERT: D 523 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8278 (mp0) REVERT: D 612 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7900 (mmt) REVERT: D 724 ASP cc_start: 0.8183 (t0) cc_final: 0.7849 (t70) REVERT: E 7 TYR cc_start: 0.7011 (t80) cc_final: 0.6706 (t80) REVERT: E 12 GLN cc_start: 0.6730 (mp10) cc_final: 0.6453 (mp10) REVERT: E 19 LYS cc_start: 0.7227 (mttm) cc_final: 0.6553 (mmmt) REVERT: E 161 LYS cc_start: 0.8126 (tttm) cc_final: 0.7921 (tptp) REVERT: E 378 ASN cc_start: 0.8583 (p0) cc_final: 0.8172 (p0) REVERT: E 394 ASN cc_start: 0.8449 (t0) cc_final: 0.8024 (m110) REVERT: E 455 GLU cc_start: 0.7845 (tt0) cc_final: 0.7362 (tt0) REVERT: E 508 ARG cc_start: 0.8138 (ttp-170) cc_final: 0.7703 (ttm170) REVERT: E 756 MET cc_start: 0.5563 (pmm) cc_final: 0.5124 (ttp) outliers start: 179 outliers final: 64 residues processed: 689 average time/residue: 0.6451 time to fit residues: 536.3873 Evaluate side-chains 473 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 391 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 852 ASN Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 641 ARG Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 766 VAL Chi-restraints excluded: chain C residue 814 PHE Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 825 SER Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 606 SER Chi-restraints excluded: chain D residue 612 MET Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 725 ASN Chi-restraints excluded: chain E residue 743 ASP Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 760 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.0970 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 0.8980 chunk 424 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 overall best weight: 3.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 178 ASN A 203 ASN A 378 ASN B 9 ASN ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 230 ASN B 378 ASN B 613 ASN B 746 HIS ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 ASN C 646 GLN C 725 ASN C 836 ASN C 843 GLN D 41 ASN D 248 ASN D 252 GLN D 356 ASN D 394 ASN D 404 ASN D 545 HIS D 649 GLN D 725 ASN D 762 GLN E 9 ASN E 169 GLN E 178 ASN E 301 ASN E 499 ASN E 534 HIS E 552 GLN E 617 ASN E 644 GLN E 649 GLN E 673 ASN E 723 ASN E 843 GLN ** E 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.149320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111123 restraints weight = 47445.656| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.14 r_work: 0.3168 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 35864 Z= 0.189 Angle : 0.651 10.336 48585 Z= 0.328 Chirality : 0.044 0.162 5022 Planarity : 0.005 0.067 6251 Dihedral : 10.564 165.786 4938 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.94 % Favored : 94.95 % Rotamer: Outliers : 6.87 % Allowed : 24.88 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -1.00 (0.13), residues: 4235 helix: 0.33 (0.12), residues: 1736 sheet: -0.65 (0.21), residues: 650 loop : -1.60 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 598 TYR 0.023 0.002 TYR A 696 PHE 0.020 0.002 PHE A 160 TRP 0.022 0.002 TRP C 346 HIS 0.005 0.001 HIS C 405 Details of bonding type rmsd covalent geometry : bond 0.00442 (35864) covalent geometry : angle 0.65065 (48585) hydrogen bonds : bond 0.04498 ( 1489) hydrogen bonds : angle 5.32534 ( 4185) *********************** 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 697 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 253 poor density : 444 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7834 (mmmt) REVERT: A 161 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8293 (ttmp) REVERT: A 232 GLU cc_start: 0.8520 (tp30) cc_final: 0.7780 (pm20) REVERT: A 295 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: A 340 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7794 (mm-40) REVERT: A 527 LYS cc_start: 0.8704 (mtpp) cc_final: 0.8459 (mtmt) REVERT: A 554 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8626 (tt) REVERT: A 583 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8365 (mtp180) REVERT: A 674 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8346 (pmtt) REVERT: A 727 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7186 (tt) REVERT: A 754 MET cc_start: 0.7951 (mtm) cc_final: 0.7561 (ttp) REVERT: A 756 MET cc_start: 0.8046 (tpp) cc_final: 0.7555 (ptt) REVERT: A 763 LYS cc_start: 0.8356 (mptt) cc_final: 0.7834 (mtpp) REVERT: A 792 ASP cc_start: 0.7498 (m-30) cc_final: 0.7181 (t0) REVERT: A 815 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: A 819 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6362 (tm-30) REVERT: A 837 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7700 (t0) REVERT: B 143 ASP cc_start: 0.8302 (m-30) cc_final: 0.8093 (m-30) REVERT: B 149 CYS cc_start: 0.8448 (m) cc_final: 0.7783 (p) REVERT: B 171 ILE cc_start: 0.8124 (mt) cc_final: 0.7923 (mm) REVERT: B 230 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.7264 (t0) REVERT: B 239 TYR cc_start: 0.7916 (m-10) cc_final: 0.7639 (m-10) REVERT: B 245 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7181 (OUTLIER) REVERT: B 266 LYS cc_start: 0.7766 (mtpt) cc_final: 0.7562 (ptmm) REVERT: B 310 SER cc_start: 0.8167 (OUTLIER) cc_final: 0.7771 (p) REVERT: B 334 TYR cc_start: 0.6740 (m-80) cc_final: 0.6319 (m-80) REVERT: B 344 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7403 (pt) REVERT: B 350 ILE cc_start: 0.7395 (OUTLIER) cc_final: 0.7167 (tp) REVERT: B 433 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8016 (tppt) REVERT: B 545 HIS cc_start: 0.7496 (t-90) cc_final: 0.7169 (t70) REVERT: B 608 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8650 (mt-10) REVERT: B 622 ASP cc_start: 0.7918 (t70) cc_final: 0.7413 (t0) REVERT: B 644 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8414 (mm-40) REVERT: B 668 MET cc_start: 0.9430 (ttm) cc_final: 0.9189 (ttm) REVERT: B 674 LYS cc_start: 0.8065 (mmtm) cc_final: 0.7413 (pmmt) REVERT: B 719 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7513 (mttp) REVERT: B 754 MET cc_start: 0.6716 (ttt) cc_final: 0.6354 (ttt) REVERT: B 765 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.6373 (mptt) REVERT: B 852 ASN cc_start: 0.7170 (OUTLIER) cc_final: 0.5992 (p0) REVERT: C 116 GLU cc_start: 0.9438 (OUTLIER) cc_final: 0.8820 (mt-10) REVERT: C 196 VAL cc_start: 0.8568 (m) cc_final: 0.8360 (t) REVERT: C 219 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8250 (mptt) REVERT: C 241 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8704 (tt) REVERT: C 249 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6565 (tpt-90) REVERT: C 346 TRP cc_start: 0.5438 (t-100) cc_final: 0.5133 (t-100) REVERT: C 350 ILE cc_start: 0.5462 (OUTLIER) cc_final: 0.5166 (mp) REVERT: C 359 ASP cc_start: 0.7173 (m-30) cc_final: 0.6847 (t0) REVERT: C 390 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6322 (mt0) REVERT: C 639 GLU cc_start: 0.4589 (OUTLIER) cc_final: 0.3824 (tm-30) REVERT: C 641 ARG cc_start: 0.4471 (OUTLIER) cc_final: 0.3729 (ptp90) REVERT: C 735 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6408 (mptp) REVERT: C 745 ILE cc_start: 0.5668 (OUTLIER) cc_final: 0.4870 (pp) REVERT: C 765 LYS cc_start: 0.6367 (tmtt) cc_final: 0.6002 (tmtt) REVERT: C 803 LYS cc_start: 0.6929 (tppp) cc_final: 0.6213 (ptpt) REVERT: C 804 MET cc_start: 0.4314 (OUTLIER) cc_final: 0.3259 (tpt) REVERT: C 815 GLU cc_start: 0.6484 (tt0) cc_final: 0.6144 (tm-30) REVERT: C 832 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6446 (mmm) REVERT: D 54 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6869 (m-30) REVERT: D 58 LYS cc_start: 0.7102 (tptp) cc_final: 0.6872 (tttt) REVERT: D 166 MET cc_start: 0.7837 (mtp) cc_final: 0.7166 (pmt) REVERT: D 246 TRP cc_start: 0.6752 (m100) cc_final: 0.6426 (t-100) REVERT: D 277 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.8621 (m110) REVERT: D 302 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6901 (mt0) REVERT: D 390 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7869 (mm-40) REVERT: D 443 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: D 517 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8603 (mp) REVERT: D 545 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.6989 (m-70) REVERT: D 556 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7430 (ttmt) REVERT: D 590 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8301 (m-30) REVERT: D 695 HIS cc_start: 0.8678 (m-70) cc_final: 0.8438 (m170) REVERT: D 724 ASP cc_start: 0.8249 (t0) cc_final: 0.7760 (t70) REVERT: D 743 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7426 (m-30) REVERT: D 812 PHE cc_start: 0.7393 (m-80) cc_final: 0.7084 (m-80) REVERT: D 815 GLU cc_start: 0.6840 (tt0) cc_final: 0.6505 (tp30) REVERT: D 832 MET cc_start: 0.6937 (ttp) cc_final: 0.6671 (ttp) REVERT: E 12 GLN cc_start: 0.7817 (mp10) cc_final: 0.7449 (mp10) REVERT: E 15 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7736 (mp0) REVERT: E 19 LYS cc_start: 0.8096 (mttm) cc_final: 0.7694 (mttt) REVERT: E 27 LYS cc_start: 0.8153 (tppt) cc_final: 0.7579 (tptm) REVERT: E 94 MET cc_start: 0.7588 (ttm) cc_final: 0.7277 (ttm) REVERT: E 241 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8467 (tt) REVERT: E 246 TRP cc_start: 0.8348 (m100) cc_final: 0.8042 (m100) REVERT: E 324 ASP cc_start: 0.7181 (m-30) cc_final: 0.6909 (m-30) REVERT: E 359 ASP cc_start: 0.7010 (t0) cc_final: 0.6774 (t0) REVERT: E 363 ARG cc_start: 0.6407 (mpp80) cc_final: 0.6057 (mtp85) REVERT: E 392 PHE cc_start: 0.8786 (m-10) cc_final: 0.8303 (m-10) REVERT: E 394 ASN cc_start: 0.8823 (t0) cc_final: 0.8044 (m110) REVERT: E 446 HIS cc_start: 0.8786 (OUTLIER) cc_final: 0.8562 (m90) REVERT: E 508 ARG cc_start: 0.8623 (ttp-170) cc_final: 0.7981 (ttm-80) REVERT: E 521 ASP cc_start: 0.8074 (t0) cc_final: 0.7764 (t70) REVERT: E 554 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8296 (tt) REVERT: E 724 ASP cc_start: 0.7471 (t0) cc_final: 0.7172 (t70) REVERT: E 756 MET cc_start: 0.5922 (pmm) cc_final: 0.4862 (ttp) REVERT: E 802 PHE cc_start: 0.7732 (m-10) cc_final: 0.7374 (m-10) REVERT: E 827 LYS cc_start: 0.7181 (ttmm) cc_final: 0.6739 (ttmt) outliers start: 253 outliers final: 79 residues processed: 642 average time/residue: 0.6785 time to fit residues: 524.4146 Evaluate side-chains 488 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 366 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 815 GLU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 246 TRP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 719 LYS Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain B residue 852 ASN Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 390 GLN Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 641 ARG Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 745 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 766 VAL Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 804 MET Chi-restraints excluded: chain C residue 814 PHE Chi-restraints excluded: chain C residue 825 SER Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 743 ASP Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 446 HIS Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 750 LYS Chi-restraints excluded: chain E residue 784 VAL Chi-restraints excluded: chain E residue 805 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 339 optimal weight: 0.0970 chunk 88 optimal weight: 10.0000 chunk 373 optimal weight: 0.9980 chunk 220 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 221 optimal weight: 10.0000 chunk 389 optimal weight: 3.9990 chunk 402 optimal weight: 0.7980 chunk 235 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 overall best weight: 1.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN B 227 ASN B 378 ASN B 441 ASN B 613 ASN D 378 ASN D 404 ASN D 545 HIS D 649 GLN ** D 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS E 617 ASN E 644 GLN ** E 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.150451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112561 restraints weight = 47204.250| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.23 r_work: 0.3193 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35864 Z= 0.117 Angle : 0.573 13.331 48585 Z= 0.283 Chirality : 0.042 0.148 5022 Planarity : 0.004 0.059 6251 Dihedral : 9.515 166.099 4875 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.34 % Favored : 95.63 % Rotamer: Outliers : 5.24 % Allowed : 26.70 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -0.66 (0.13), residues: 4235 helix: 0.68 (0.13), residues: 1729 sheet: -0.44 (0.21), residues: 627 loop : -1.48 (0.13), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 598 TYR 0.021 0.001 TYR D 696 PHE 0.019 0.001 PHE E 160 TRP 0.013 0.001 TRP D 40 HIS 0.023 0.001 HIS D 545 Details of bonding type rmsd covalent geometry : bond 0.00262 (35864) covalent geometry : angle 0.57322 (48585) hydrogen bonds : bond 0.03796 ( 1489) hydrogen bonds : angle 4.97243 ( 4185) *********************** 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 608 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 415 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7775 (mmmt) REVERT: A 161 LYS cc_start: 0.8529 (ttpp) cc_final: 0.8279 (ttmp) REVERT: A 228 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7492 (p0) REVERT: A 232 GLU cc_start: 0.8511 (tp30) cc_final: 0.7715 (pm20) REVERT: A 235 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7542 (ttt180) REVERT: A 340 GLN cc_start: 0.8313 (mt0) cc_final: 0.7829 (mm-40) REVERT: A 527 LYS cc_start: 0.8674 (mtpp) cc_final: 0.8369 (mtmt) REVERT: A 554 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8677 (tt) REVERT: A 583 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8412 (mtp180) REVERT: A 674 LYS cc_start: 0.8684 (ttmm) cc_final: 0.8358 (pmtt) REVERT: A 754 MET cc_start: 0.7739 (mtm) cc_final: 0.7443 (ttp) REVERT: A 756 MET cc_start: 0.7989 (tpp) cc_final: 0.7497 (ptt) REVERT: A 763 LYS cc_start: 0.8366 (mptt) cc_final: 0.7777 (mtpp) REVERT: A 792 ASP cc_start: 0.7522 (m-30) cc_final: 0.7156 (t0) REVERT: A 807 HIS cc_start: 0.6638 (OUTLIER) cc_final: 0.6422 (t-170) REVERT: A 837 ASP cc_start: 0.8140 (m-30) cc_final: 0.7718 (t0) REVERT: A 849 LYS cc_start: 0.8019 (ttmm) cc_final: 0.7773 (mttt) REVERT: B 149 CYS cc_start: 0.8418 (m) cc_final: 0.7702 (p) REVERT: B 239 TYR cc_start: 0.7908 (m-10) cc_final: 0.7555 (m-10) REVERT: B 245 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7031 (OUTLIER) REVERT: B 310 SER cc_start: 0.8158 (m) cc_final: 0.7768 (p) REVERT: B 344 ILE cc_start: 0.7704 (tp) cc_final: 0.7383 (pt) REVERT: B 350 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.7027 (tp) REVERT: B 352 MET cc_start: 0.7504 (ttp) cc_final: 0.7234 (ttm) REVERT: B 433 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8076 (tppt) REVERT: B 545 HIS cc_start: 0.7460 (t-90) cc_final: 0.7165 (t70) REVERT: B 552 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.6137 (mm-40) REVERT: B 561 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8122 (mp) REVERT: B 608 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8639 (mt-10) REVERT: B 622 ASP cc_start: 0.7749 (t70) cc_final: 0.7230 (t0) REVERT: B 668 MET cc_start: 0.9407 (ttm) cc_final: 0.9153 (ttm) REVERT: B 707 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8073 (t0) REVERT: B 754 MET cc_start: 0.6656 (ttt) cc_final: 0.6318 (ttt) REVERT: C 14 LYS cc_start: 0.7571 (mptt) cc_final: 0.6789 (mtpm) REVERT: C 116 GLU cc_start: 0.9422 (OUTLIER) cc_final: 0.8867 (pt0) REVERT: C 229 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7497 (mpt) REVERT: C 233 PHE cc_start: 0.7700 (m-10) cc_final: 0.7215 (m-80) REVERT: C 241 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8734 (tt) REVERT: C 359 ASP cc_start: 0.7096 (m-30) cc_final: 0.6793 (t0) REVERT: C 612 MET cc_start: 0.7930 (mpt) cc_final: 0.7627 (mmp) REVERT: C 639 GLU cc_start: 0.4710 (OUTLIER) cc_final: 0.4024 (tm-30) REVERT: C 735 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6383 (mptp) REVERT: C 745 ILE cc_start: 0.5606 (OUTLIER) cc_final: 0.4890 (pp) REVERT: C 754 MET cc_start: 0.3340 (OUTLIER) cc_final: 0.1982 (tmm) REVERT: C 765 LYS cc_start: 0.6307 (tmtt) cc_final: 0.5908 (tmtt) REVERT: C 803 LYS cc_start: 0.6955 (tppp) cc_final: 0.6086 (mppt) REVERT: C 804 MET cc_start: 0.4497 (OUTLIER) cc_final: 0.3314 (tpt) REVERT: C 815 GLU cc_start: 0.6451 (tt0) cc_final: 0.6200 (tm-30) REVERT: C 817 GLU cc_start: 0.8193 (pt0) cc_final: 0.7615 (tp30) REVERT: C 832 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.6415 (mmm) REVERT: D 58 LYS cc_start: 0.6973 (tptp) cc_final: 0.6726 (tttm) REVERT: D 157 TYR cc_start: 0.7461 (m-80) cc_final: 0.7109 (m-80) REVERT: D 166 MET cc_start: 0.7847 (mtp) cc_final: 0.7149 (pmt) REVERT: D 239 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.7038 (m-10) REVERT: D 247 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7636 (mm-30) REVERT: D 306 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7818 (mm) REVERT: D 390 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7913 (mm-40) REVERT: D 430 TYR cc_start: 0.8138 (m-80) cc_final: 0.7816 (m-80) REVERT: D 438 ASP cc_start: 0.8047 (t0) cc_final: 0.7760 (t0) REVERT: D 473 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7925 (tt0) REVERT: D 545 HIS cc_start: 0.7415 (t-90) cc_final: 0.6980 (m-70) REVERT: D 590 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8233 (m-30) REVERT: D 695 HIS cc_start: 0.8678 (m-70) cc_final: 0.8411 (m170) REVERT: D 724 ASP cc_start: 0.8317 (t0) cc_final: 0.7773 (t70) REVERT: D 727 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7382 (tm) REVERT: D 743 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: D 815 GLU cc_start: 0.6725 (tt0) cc_final: 0.6512 (tp30) REVERT: E 12 GLN cc_start: 0.7860 (mp10) cc_final: 0.7561 (mp10) REVERT: E 241 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8418 (tt) REVERT: E 246 TRP cc_start: 0.8291 (m100) cc_final: 0.7986 (m100) REVERT: E 295 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6969 (tm-30) REVERT: E 508 ARG cc_start: 0.8646 (ttp-170) cc_final: 0.7971 (ttm170) REVERT: E 720 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8131 (tt) REVERT: E 724 ASP cc_start: 0.7511 (t0) cc_final: 0.7227 (t70) REVERT: E 756 MET cc_start: 0.5931 (pmm) cc_final: 0.4930 (ttp) REVERT: E 802 PHE cc_start: 0.7823 (m-10) cc_final: 0.7590 (m-10) REVERT: E 827 LYS cc_start: 0.7029 (ttmm) cc_final: 0.6651 (ttmt) outliers start: 193 outliers final: 70 residues processed: 556 average time/residue: 0.6355 time to fit residues: 427.6249 Evaluate side-chains 461 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 363 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 451 VAL 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 566 GLU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 552 GLN Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 455 GLU Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 745 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 766 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 804 MET Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 814 PHE Chi-restraints excluded: chain C residue 825 SER Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 743 ASP Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 605 THR 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 784 VAL Chi-restraints excluded: chain E residue 805 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 331 optimal weight: 20.0000 chunk 162 optimal weight: 30.0000 chunk 283 optimal weight: 9.9990 chunk 357 optimal weight: 9.9990 chunk 105 optimal weight: 30.0000 chunk 126 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 251 optimal weight: 20.0000 chunk 218 optimal weight: 1.9990 chunk 396 optimal weight: 6.9990 chunk 312 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN A 214 ASN ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN B 378 ASN D 277 ASN D 378 ASN D 649 GLN ** D 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN E 446 HIS ** E 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.141939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.102603 restraints weight = 47157.723| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.13 r_work: 0.3052 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 35864 Z= 0.300 Angle : 0.714 12.964 48585 Z= 0.357 Chirality : 0.047 0.160 5022 Planarity : 0.005 0.065 6251 Dihedral : 9.468 162.117 4858 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.74 % Favored : 94.24 % Rotamer: Outliers : 7.19 % Allowed : 25.29 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -1.03 (0.12), residues: 4235 helix: 0.22 (0.12), residues: 1761 sheet: -0.50 (0.21), residues: 631 loop : -1.61 (0.13), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 741 TYR 0.031 0.002 TYR D 696 PHE 0.028 0.002 PHE E 509 TRP 0.029 0.002 TRP C 346 HIS 0.007 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00718 (35864) covalent geometry : angle 0.71351 (48585) hydrogen bonds : bond 0.05033 ( 1489) hydrogen bonds : angle 5.24418 ( 4185) *********************** 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 619 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 265 poor density : 354 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7743 (mtt90) REVERT: A 74 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7265 (mmp-170) REVERT: A 106 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7737 (mmmt) REVERT: A 232 GLU cc_start: 0.8569 (tp30) cc_final: 0.7752 (pm20) REVERT: A 235 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7467 (ttt180) REVERT: A 340 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7779 (mm-40) REVERT: A 527 LYS cc_start: 0.8783 (mtpp) cc_final: 0.8477 (mtmt) REVERT: A 554 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8674 (tt) REVERT: A 564 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7031 (mtp180) REVERT: A 583 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8410 (mtp180) REVERT: A 674 LYS cc_start: 0.8752 (ttmm) cc_final: 0.8368 (pmtt) REVERT: A 756 MET cc_start: 0.8152 (tpp) cc_final: 0.7578 (ptt) REVERT: A 759 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: A 763 LYS cc_start: 0.8321 (mptt) cc_final: 0.7906 (mmmt) REVERT: A 792 ASP cc_start: 0.7652 (m-30) cc_final: 0.7163 (t0) REVERT: A 807 HIS cc_start: 0.6693 (OUTLIER) cc_final: 0.6393 (t-170) REVERT: A 837 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7759 (t0) REVERT: B 149 CYS cc_start: 0.8627 (m) cc_final: 0.7941 (p) REVERT: B 209 TYR cc_start: 0.7530 (m-10) cc_final: 0.7123 (m-10) REVERT: B 239 TYR cc_start: 0.7854 (m-10) cc_final: 0.7486 (m-10) REVERT: B 245 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7119 (p0) REVERT: B 295 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.5620 (mp0) REVERT: B 310 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.7985 (p) REVERT: B 344 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7462 (pt) REVERT: B 433 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8050 (tppt) REVERT: B 521 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7804 (t70) REVERT: B 523 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7704 (pt0) REVERT: B 545 HIS cc_start: 0.7402 (t-90) cc_final: 0.7006 (t70) REVERT: B 561 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8222 (mp) REVERT: B 608 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8489 (mt-10) REVERT: B 707 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8102 (t0) REVERT: B 765 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.6995 (mptt) REVERT: B 781 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7886 (tp) REVERT: C 14 LYS cc_start: 0.7492 (mptt) cc_final: 0.6744 (mtpm) REVERT: C 116 GLU cc_start: 0.9412 (OUTLIER) cc_final: 0.8532 (pt0) REVERT: C 222 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8338 (mt) REVERT: C 233 PHE cc_start: 0.7796 (m-10) cc_final: 0.7317 (m-80) REVERT: C 363 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7343 (mpp80) REVERT: C 366 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7429 (tt) REVERT: C 390 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.6591 (mt0) REVERT: C 516 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.7371 (m-70) REVERT: C 612 MET cc_start: 0.7961 (mpt) cc_final: 0.7649 (mmp) REVERT: C 639 GLU cc_start: 0.4589 (OUTLIER) cc_final: 0.3995 (tm-30) REVERT: C 643 TYR cc_start: 0.5647 (OUTLIER) cc_final: 0.5011 (m-80) REVERT: C 740 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7077 (tp30) REVERT: C 765 LYS cc_start: 0.6058 (tmtt) cc_final: 0.5727 (tmtt) REVERT: C 803 LYS cc_start: 0.7071 (tppp) cc_final: 0.6349 (ptpp) REVERT: C 804 MET cc_start: 0.4965 (OUTLIER) cc_final: 0.3837 (tpt) REVERT: C 815 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6207 (tm-30) REVERT: C 817 GLU cc_start: 0.8111 (pt0) cc_final: 0.7564 (tp30) REVERT: D 36 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8703 (mmt) REVERT: D 54 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.6978 (m-30) REVERT: D 157 TYR cc_start: 0.8013 (m-80) cc_final: 0.7561 (m-80) REVERT: D 166 MET cc_start: 0.8041 (mtp) cc_final: 0.7309 (pmt) REVERT: D 393 SER cc_start: 0.8584 (t) cc_final: 0.8279 (p) REVERT: D 430 TYR cc_start: 0.8167 (m-80) cc_final: 0.7919 (m-80) REVERT: D 433 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8077 (tptt) REVERT: D 473 GLU cc_start: 0.8284 (tm-30) cc_final: 0.8056 (tt0) REVERT: D 477 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7097 (mm110) REVERT: D 494 GLU cc_start: 0.8375 (tp30) cc_final: 0.8126 (tp30) REVERT: D 545 HIS cc_start: 0.7707 (t-90) cc_final: 0.6961 (m-70) REVERT: D 590 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.7993 (m-30) REVERT: D 724 ASP cc_start: 0.8204 (t0) cc_final: 0.7704 (t70) REVERT: D 727 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7360 (tm) REVERT: E 12 GLN cc_start: 0.8077 (mp10) cc_final: 0.7859 (mp10) REVERT: E 15 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7809 (mp0) REVERT: E 19 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7628 (mttt) REVERT: E 27 LYS cc_start: 0.8174 (tppt) cc_final: 0.7708 (tptm) REVERT: E 204 TYR cc_start: 0.7441 (p90) cc_final: 0.7156 (p90) REVERT: E 241 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8658 (tt) REVERT: E 246 TRP cc_start: 0.8213 (m100) cc_final: 0.7920 (m100) REVERT: E 253 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.6818 (mm-30) REVERT: E 333 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7390 (ttpp) REVERT: E 473 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7923 (pt0) REVERT: E 508 ARG cc_start: 0.8761 (ttp-170) cc_final: 0.8097 (ttm-80) REVERT: E 579 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8362 (mtm) REVERT: E 719 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7648 (ptpp) REVERT: E 724 ASP cc_start: 0.7557 (t0) cc_final: 0.7236 (t70) REVERT: E 754 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.7031 (pmm) REVERT: E 756 MET cc_start: 0.6148 (pmm) cc_final: 0.5092 (ttp) REVERT: E 765 LYS cc_start: 0.8385 (ttmm) cc_final: 0.8180 (ttmm) outliers start: 265 outliers final: 107 residues processed: 565 average time/residue: 0.6591 time to fit residues: 449.6355 Evaluate side-chains 473 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 321 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 641 ARG Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 246 TRP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 390 GLN Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 455 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 766 VAL Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 804 MET Chi-restraints excluded: chain C residue 814 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 825 SER Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 333 LYS 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 477 GLN Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 719 LYS Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 784 VAL Chi-restraints excluded: chain E residue 805 VAL Chi-restraints excluded: chain E residue 830 VAL Chi-restraints excluded: chain E residue 849 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 122 optimal weight: 5.9990 chunk 317 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 391 optimal weight: 2.9990 chunk 418 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 380 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 378 ASN D 277 ASN D 649 GLN D 725 ASN E 277 ASN E 360 HIS E 394 ASN ** E 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.145780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106424 restraints weight = 46858.404| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.23 r_work: 0.3117 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35864 Z= 0.131 Angle : 0.577 13.554 48585 Z= 0.283 Chirality : 0.042 0.172 5022 Planarity : 0.004 0.051 6251 Dihedral : 8.992 162.834 4858 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.72 % Allowed : 27.79 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -0.68 (0.13), residues: 4235 helix: 0.59 (0.12), residues: 1752 sheet: -0.36 (0.20), residues: 641 loop : -1.49 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 598 TYR 0.020 0.001 TYR D 696 PHE 0.021 0.001 PHE E 160 TRP 0.015 0.001 TRP D 40 HIS 0.003 0.001 HIS E 807 Details of bonding type rmsd covalent geometry : bond 0.00304 (35864) covalent geometry : angle 0.57701 (48585) hydrogen bonds : bond 0.03747 ( 1489) hydrogen bonds : angle 4.87502 ( 4185) *********************** 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 543 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 369 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7705 (mmmt) REVERT: A 161 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8265 (ttmp) REVERT: A 228 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7538 (p0) REVERT: A 232 GLU cc_start: 0.8554 (tp30) cc_final: 0.7758 (pm20) REVERT: A 233 PHE cc_start: 0.8461 (m-10) cc_final: 0.8218 (m-10) REVERT: A 235 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7443 (ttt180) REVERT: A 334 TYR cc_start: 0.7858 (m-80) cc_final: 0.7597 (m-80) REVERT: A 340 GLN cc_start: 0.8285 (mt0) cc_final: 0.7844 (mm-40) REVERT: A 527 LYS cc_start: 0.8720 (mtpp) cc_final: 0.8392 (mtmt) REVERT: A 583 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8384 (mtp180) REVERT: A 674 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8355 (pmtt) REVERT: A 756 MET cc_start: 0.8172 (tpp) cc_final: 0.7566 (ptt) REVERT: A 763 LYS cc_start: 0.8330 (mptt) cc_final: 0.7823 (mttp) REVERT: A 792 ASP cc_start: 0.7537 (m-30) cc_final: 0.7136 (t70) REVERT: A 807 HIS cc_start: 0.6570 (OUTLIER) cc_final: 0.6307 (t-170) REVERT: A 837 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7737 (t0) REVERT: B 149 CYS cc_start: 0.8423 (m) cc_final: 0.7647 (p) REVERT: B 166 MET cc_start: 0.6825 (ttp) cc_final: 0.6604 (tpt) REVERT: B 193 ASN cc_start: 0.7434 (t0) cc_final: 0.7172 (m-40) REVERT: B 230 ASN cc_start: 0.7373 (OUTLIER) cc_final: 0.7167 (t0) REVERT: B 239 TYR cc_start: 0.7891 (m-10) cc_final: 0.7479 (m-80) REVERT: B 245 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7060 (p0) REVERT: B 310 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.7786 (p) REVERT: B 344 ILE cc_start: 0.7643 (tp) cc_final: 0.7387 (pt) REVERT: B 433 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8092 (tppt) REVERT: B 523 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7612 (pt0) REVERT: B 545 HIS cc_start: 0.7383 (t-90) cc_final: 0.7045 (t70) REVERT: B 552 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6265 (mm-40) REVERT: B 561 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8149 (mp) REVERT: B 608 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8339 (pt0) REVERT: B 622 ASP cc_start: 0.7890 (t0) cc_final: 0.7680 (t70) REVERT: B 749 SER cc_start: 0.7063 (OUTLIER) cc_final: 0.6843 (p) REVERT: C 14 LYS cc_start: 0.7434 (mptt) cc_final: 0.6727 (mtpm) REVERT: C 83 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8035 (mp0) REVERT: C 116 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.8425 (pt0) REVERT: C 233 PHE cc_start: 0.7813 (m-10) cc_final: 0.7342 (m-80) REVERT: C 298 LEU cc_start: 0.6726 (mt) cc_final: 0.6484 (tp) REVERT: C 612 MET cc_start: 0.7887 (mpt) cc_final: 0.7563 (mmp) REVERT: C 639 GLU cc_start: 0.4480 (OUTLIER) cc_final: 0.4051 (tm-30) REVERT: C 735 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6365 (tppp) REVERT: C 765 LYS cc_start: 0.6090 (tmtt) cc_final: 0.5725 (tmtt) REVERT: C 775 LEU cc_start: 0.7301 (mm) cc_final: 0.6964 (mp) REVERT: C 803 LYS cc_start: 0.7071 (tppp) cc_final: 0.6185 (mppt) REVERT: C 804 MET cc_start: 0.4887 (OUTLIER) cc_final: 0.3952 (tpt) REVERT: C 815 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6190 (tm-30) REVERT: C 817 GLU cc_start: 0.8072 (pt0) cc_final: 0.7554 (tp30) REVERT: C 832 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6753 (mmm) REVERT: D 30 ASP cc_start: 0.7596 (t70) cc_final: 0.7254 (t0) REVERT: D 36 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8557 (mmt) REVERT: D 51 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.5875 (mp) REVERT: D 157 TYR cc_start: 0.7955 (m-80) cc_final: 0.7543 (m-80) REVERT: D 166 MET cc_start: 0.8009 (mtp) cc_final: 0.7291 (pmt) REVERT: D 205 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6453 (tp40) REVERT: D 239 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.7473 (m-10) REVERT: D 247 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8024 (mm-30) REVERT: D 335 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7536 (mmm) REVERT: D 393 SER cc_start: 0.8509 (t) cc_final: 0.8213 (p) REVERT: D 430 TYR cc_start: 0.8172 (m-80) cc_final: 0.7925 (m-80) REVERT: D 433 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8025 (tptt) REVERT: D 477 GLN cc_start: 0.7842 (tm-30) cc_final: 0.6936 (mm110) REVERT: D 494 GLU cc_start: 0.8359 (tp30) cc_final: 0.8121 (tp30) REVERT: D 545 HIS cc_start: 0.7643 (t-90) cc_final: 0.6908 (m-70) REVERT: D 590 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8065 (m-30) REVERT: D 724 ASP cc_start: 0.8208 (t0) cc_final: 0.7661 (t70) REVERT: D 727 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7393 (tm) REVERT: D 830 VAL cc_start: 0.7267 (OUTLIER) cc_final: 0.6941 (p) REVERT: E 12 GLN cc_start: 0.8045 (mp10) cc_final: 0.7779 (mp10) REVERT: E 19 LYS cc_start: 0.8173 (mptp) cc_final: 0.7655 (mttt) REVERT: E 27 LYS cc_start: 0.8142 (tppt) cc_final: 0.7727 (tptp) REVERT: E 74 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7613 (tpt-90) REVERT: E 76 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.6134 (mm-30) REVERT: E 204 TYR cc_start: 0.7299 (p90) cc_final: 0.6985 (p90) REVERT: E 241 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8558 (tt) REVERT: E 246 TRP cc_start: 0.8144 (m100) cc_final: 0.7853 (m100) REVERT: E 508 ARG cc_start: 0.8723 (ttp-170) cc_final: 0.8029 (ttm170) REVERT: E 724 ASP cc_start: 0.7564 (t0) cc_final: 0.7158 (t70) REVERT: E 754 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.7036 (pmm) REVERT: E 756 MET cc_start: 0.6265 (pmm) cc_final: 0.5114 (ttp) REVERT: E 827 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6777 (mtmt) outliers start: 174 outliers final: 68 residues processed: 506 average time/residue: 0.6766 time to fit residues: 410.8251 Evaluate side-chains 435 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 334 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 246 TRP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 552 GLN Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 455 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 766 VAL Chi-restraints excluded: chain C residue 804 MET Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 814 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 825 SER Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 784 VAL Chi-restraints excluded: chain E residue 827 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 64 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 305 optimal weight: 10.0000 chunk 274 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 314 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 281 optimal weight: 9.9990 chunk 263 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 HIS D 277 ASN D 649 GLN E 360 HIS E 394 ASN ** E 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.141540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.100785 restraints weight = 47175.967| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.32 r_work: 0.3052 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 35864 Z= 0.294 Angle : 0.686 13.454 48585 Z= 0.340 Chirality : 0.047 0.158 5022 Planarity : 0.005 0.055 6251 Dihedral : 9.078 158.709 4852 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 6.30 % Allowed : 26.46 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -0.89 (0.12), residues: 4235 helix: 0.39 (0.12), residues: 1738 sheet: -0.37 (0.21), residues: 627 loop : -1.60 (0.13), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 741 TYR 0.032 0.002 TYR D 696 PHE 0.026 0.002 PHE A 160 TRP 0.018 0.002 TRP B 40 HIS 0.005 0.001 HIS C 446 Details of bonding type rmsd covalent geometry : bond 0.00706 (35864) covalent geometry : angle 0.68637 (48585) hydrogen bonds : bond 0.04785 ( 1489) hydrogen bonds : angle 5.11100 ( 4185) *********************** 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 571 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 339 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7765 (mmmt) REVERT: A 228 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7666 (p0) REVERT: A 232 GLU cc_start: 0.8612 (tp30) cc_final: 0.7870 (pm20) REVERT: A 233 PHE cc_start: 0.8495 (m-10) cc_final: 0.8265 (m-10) REVERT: A 235 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7736 (mtp180) REVERT: A 340 GLN cc_start: 0.8358 (mt0) cc_final: 0.7880 (mm-40) REVERT: A 424 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8211 (mmm160) REVERT: A 465 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8631 (mttm) REVERT: A 527 LYS cc_start: 0.8829 (mtpp) cc_final: 0.8567 (mtmt) REVERT: A 554 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8684 (tt) REVERT: A 564 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7270 (mtp180) REVERT: A 583 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8549 (mtp180) REVERT: A 608 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.8724 (mt-10) REVERT: A 674 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8379 (pmtt) REVERT: A 754 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7755 (ttp) REVERT: A 756 MET cc_start: 0.8180 (tpp) cc_final: 0.7672 (ptt) REVERT: A 763 LYS cc_start: 0.8346 (mptt) cc_final: 0.7907 (mmmt) REVERT: A 792 ASP cc_start: 0.7638 (m-30) cc_final: 0.7284 (t70) REVERT: A 807 HIS cc_start: 0.6728 (OUTLIER) cc_final: 0.6453 (t-170) REVERT: A 837 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7814 (t0) REVERT: B 149 CYS cc_start: 0.8601 (m) cc_final: 0.8017 (p) REVERT: B 193 ASN cc_start: 0.7477 (t0) cc_final: 0.7236 (m-40) REVERT: B 230 ASN cc_start: 0.7993 (OUTLIER) cc_final: 0.7334 (t0) REVERT: B 310 SER cc_start: 0.8507 (m) cc_final: 0.8118 (p) REVERT: B 433 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8189 (tppt) REVERT: B 521 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7580 (t0) REVERT: B 523 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7834 (pt0) REVERT: B 545 HIS cc_start: 0.7476 (t-90) cc_final: 0.7084 (t70) REVERT: B 561 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8416 (mp) REVERT: B 608 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8515 (pt0) REVERT: B 612 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8481 (mmm) REVERT: B 707 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8164 (t0) REVERT: B 754 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6265 (ttt) REVERT: B 765 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7303 (mptt) REVERT: C 14 LYS cc_start: 0.7825 (mptt) cc_final: 0.7100 (mtpm) REVERT: C 82 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7610 (ptmm) REVERT: C 116 GLU cc_start: 0.9432 (OUTLIER) cc_final: 0.8597 (pt0) REVERT: C 222 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8457 (mt) REVERT: C 233 PHE cc_start: 0.7830 (m-10) cc_final: 0.7379 (m-80) REVERT: C 249 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.6455 (tpt-90) REVERT: C 390 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.6703 (mt0) REVERT: C 488 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7799 (mtp180) REVERT: C 612 MET cc_start: 0.7985 (mpt) cc_final: 0.7690 (mmp) REVERT: C 639 GLU cc_start: 0.4437 (OUTLIER) cc_final: 0.4063 (tm-30) REVERT: C 765 LYS cc_start: 0.6071 (tmtt) cc_final: 0.5691 (tmtt) REVERT: C 803 LYS cc_start: 0.7247 (tppp) cc_final: 0.6475 (ptpp) REVERT: C 804 MET cc_start: 0.5040 (OUTLIER) cc_final: 0.4179 (tpt) REVERT: C 815 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.6019 (tm-30) REVERT: C 817 GLU cc_start: 0.8017 (pt0) cc_final: 0.7606 (tp30) REVERT: D 15 GLU cc_start: 0.8234 (tt0) cc_final: 0.7926 (mp0) REVERT: D 51 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6075 (mp) REVERT: D 54 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7047 (m-30) REVERT: D 166 MET cc_start: 0.8113 (mtp) cc_final: 0.7406 (pmt) REVERT: D 228 ASP cc_start: 0.7052 (p0) cc_final: 0.6815 (p0) REVERT: D 247 GLU cc_start: 0.8225 (mm-30) cc_final: 0.8007 (mm-30) REVERT: D 294 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.4658 (mp0) REVERT: D 335 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7830 (mmm) REVERT: D 393 SER cc_start: 0.8619 (t) cc_final: 0.8339 (p) REVERT: D 433 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8112 (tptt) REVERT: D 477 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7350 (mm110) REVERT: D 494 GLU cc_start: 0.8387 (tp30) cc_final: 0.8117 (tp30) REVERT: D 545 HIS cc_start: 0.7880 (t-90) cc_final: 0.7097 (m-70) REVERT: D 590 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8366 (m-30) REVERT: D 724 ASP cc_start: 0.8320 (t0) cc_final: 0.7855 (t70) REVERT: D 727 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7537 (tm) REVERT: E 19 LYS cc_start: 0.8271 (mptp) cc_final: 0.7742 (mttt) REVERT: E 27 LYS cc_start: 0.8119 (tppt) cc_final: 0.7770 (tptp) REVERT: E 74 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7408 (mmm160) REVERT: E 76 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6391 (mm-30) REVERT: E 241 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8818 (tt) REVERT: E 272 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8523 (mt-10) REVERT: E 333 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7360 (ttpp) REVERT: E 356 ASN cc_start: 0.7444 (t0) cc_final: 0.6868 (p0) REVERT: E 508 ARG cc_start: 0.8814 (ttp-170) cc_final: 0.8188 (ttm170) REVERT: E 511 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.7886 (m) REVERT: E 608 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8658 (mt-10) REVERT: E 719 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7633 (ptpp) REVERT: E 724 ASP cc_start: 0.7672 (t0) cc_final: 0.7349 (t70) REVERT: E 750 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7084 (ttpt) REVERT: E 754 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.7177 (pmm) REVERT: E 756 MET cc_start: 0.6555 (pmm) cc_final: 0.5420 (ttp) REVERT: E 827 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.7093 (mtmt) outliers start: 232 outliers final: 107 residues processed: 528 average time/residue: 0.6999 time to fit residues: 441.5303 Evaluate side-chains 469 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 316 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 246 TRP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain C residue 89 LYS 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 166 MET Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 390 GLN Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 455 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 766 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 804 MET Chi-restraints excluded: chain C residue 814 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 825 SER Chi-restraints excluded: chain C residue 838 LYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 333 LYS 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 554 LEU Chi-restraints excluded: chain E residue 579 MET 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 747 VAL Chi-restraints excluded: chain E residue 750 LYS Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 767 GLN Chi-restraints excluded: chain E residue 784 VAL Chi-restraints excluded: chain E residue 805 VAL Chi-restraints excluded: chain E residue 827 LYS Chi-restraints excluded: chain E residue 830 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 321 optimal weight: 4.9990 chunk 229 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 158 optimal weight: 20.0000 chunk 160 optimal weight: 3.9990 chunk 287 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 227 optimal weight: 5.9990 chunk 366 optimal weight: 2.9990 chunk 354 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN D 277 ASN D 649 GLN E 394 ASN ** E 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.143984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104125 restraints weight = 46838.584| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.22 r_work: 0.3091 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35864 Z= 0.151 Angle : 0.600 13.518 48585 Z= 0.292 Chirality : 0.043 0.159 5022 Planarity : 0.004 0.051 6251 Dihedral : 8.787 159.230 4852 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.07 % Allowed : 27.82 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -0.68 (0.13), residues: 4235 helix: 0.61 (0.12), residues: 1751 sheet: -0.27 (0.21), residues: 637 loop : -1.55 (0.13), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 741 TYR 0.025 0.001 TYR C 768 PHE 0.022 0.001 PHE E 160 TRP 0.015 0.001 TRP D 40 HIS 0.003 0.001 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00357 (35864) covalent geometry : angle 0.60026 (48585) hydrogen bonds : bond 0.03868 ( 1489) hydrogen bonds : angle 4.88125 ( 4185) *********************** 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 539 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 352 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8012 (mmtt) cc_final: 0.7679 (mmmt) REVERT: A 161 LYS cc_start: 0.8603 (ttpp) cc_final: 0.8287 (ttmp) REVERT: A 175 ASP cc_start: 0.8344 (t0) cc_final: 0.8054 (t0) REVERT: A 228 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7571 (p0) REVERT: A 232 GLU cc_start: 0.8548 (tp30) cc_final: 0.7749 (pm20) REVERT: A 233 PHE cc_start: 0.8498 (m-10) cc_final: 0.8247 (m-10) REVERT: A 235 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7454 (ttt180) REVERT: A 340 GLN cc_start: 0.8303 (mt0) cc_final: 0.7869 (mm-40) REVERT: A 527 LYS cc_start: 0.8727 (mtpp) cc_final: 0.8402 (mtmt) REVERT: A 554 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8576 (tt) REVERT: A 583 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8407 (mtp180) REVERT: A 674 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8378 (pmtt) REVERT: A 754 MET cc_start: 0.7974 (mtm) cc_final: 0.7634 (ttp) REVERT: A 756 MET cc_start: 0.8223 (tpp) cc_final: 0.7667 (ptt) REVERT: A 763 LYS cc_start: 0.8334 (mptt) cc_final: 0.7851 (mmmt) REVERT: A 792 ASP cc_start: 0.7582 (m-30) cc_final: 0.7153 (t70) REVERT: A 807 HIS cc_start: 0.6615 (OUTLIER) cc_final: 0.6339 (t-170) REVERT: A 837 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7756 (t0) REVERT: B 4 LYS cc_start: 0.6430 (OUTLIER) cc_final: 0.5922 (tptm) REVERT: B 36 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8045 (tpt) REVERT: B 149 CYS cc_start: 0.8443 (m) cc_final: 0.7674 (p) REVERT: B 265 LYS cc_start: 0.7642 (ptmt) cc_final: 0.7065 (mptt) REVERT: B 292 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.6931 (m-80) REVERT: B 310 SER cc_start: 0.8265 (OUTLIER) cc_final: 0.7836 (p) REVERT: B 433 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8133 (tppt) REVERT: B 521 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7551 (t70) REVERT: B 523 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7637 (pt0) REVERT: B 545 HIS cc_start: 0.7360 (t-90) cc_final: 0.6973 (t70) REVERT: B 561 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8244 (mp) REVERT: B 608 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8478 (pt0) REVERT: B 612 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8282 (mmm) REVERT: B 749 SER cc_start: 0.7138 (OUTLIER) cc_final: 0.6866 (p) REVERT: B 765 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7112 (mptt) REVERT: C 1 MET cc_start: 0.5643 (ptt) cc_final: 0.4848 (tmm) REVERT: C 14 LYS cc_start: 0.7479 (mptt) cc_final: 0.6789 (mtpm) REVERT: C 82 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7664 (ptmm) REVERT: C 116 GLU cc_start: 0.9354 (OUTLIER) cc_final: 0.8568 (pt0) REVERT: C 222 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8208 (mt) REVERT: C 233 PHE cc_start: 0.7867 (m-10) cc_final: 0.7392 (m-80) REVERT: C 298 LEU cc_start: 0.6758 (mt) cc_final: 0.6518 (tp) REVERT: C 612 MET cc_start: 0.7891 (mpt) cc_final: 0.7564 (mmp) REVERT: C 639 GLU cc_start: 0.4425 (OUTLIER) cc_final: 0.4152 (tm-30) REVERT: C 765 LYS cc_start: 0.6041 (tmtt) cc_final: 0.5649 (tmtt) REVERT: C 803 LYS cc_start: 0.7150 (tppp) cc_final: 0.6269 (mppt) REVERT: C 804 MET cc_start: 0.5158 (OUTLIER) cc_final: 0.4271 (tpt) REVERT: C 815 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.6114 (tm-30) REVERT: C 817 GLU cc_start: 0.8083 (pt0) cc_final: 0.7577 (tp30) REVERT: C 832 MET cc_start: 0.7062 (mmm) cc_final: 0.6683 (mmm) REVERT: D 15 GLU cc_start: 0.8163 (tt0) cc_final: 0.7797 (mp0) REVERT: D 51 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6012 (mp) REVERT: D 157 TYR cc_start: 0.8021 (m-80) cc_final: 0.7521 (m-80) REVERT: D 166 MET cc_start: 0.8060 (mtp) cc_final: 0.7326 (pmt) REVERT: D 294 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.4388 (mp0) REVERT: D 393 SER cc_start: 0.8507 (t) cc_final: 0.8233 (p) REVERT: D 433 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8057 (tptt) REVERT: D 477 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7171 (mm110) REVERT: D 494 GLU cc_start: 0.8360 (tp30) cc_final: 0.8090 (tp30) REVERT: D 545 HIS cc_start: 0.7663 (t-90) cc_final: 0.6893 (m-70) REVERT: D 590 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: D 724 ASP cc_start: 0.8211 (t0) cc_final: 0.7718 (t70) REVERT: D 727 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7408 (tm) REVERT: E 19 LYS cc_start: 0.8112 (mptp) cc_final: 0.7597 (mttt) REVERT: E 27 LYS cc_start: 0.8136 (tppt) cc_final: 0.7714 (tptp) REVERT: E 74 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7716 (tmt170) REVERT: E 76 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.5874 (mm-30) REVERT: E 106 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8019 (pttt) REVERT: E 204 TYR cc_start: 0.7220 (p90) cc_final: 0.7012 (p90) REVERT: E 241 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8665 (tt) REVERT: E 356 ASN cc_start: 0.7334 (t0) cc_final: 0.6746 (p0) REVERT: E 508 ARG cc_start: 0.8716 (ttp-170) cc_final: 0.7960 (ttm170) REVERT: E 511 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7904 (p) REVERT: E 719 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7514 (ptpp) REVERT: E 724 ASP cc_start: 0.7620 (t0) cc_final: 0.7271 (t70) REVERT: E 733 LEU cc_start: 0.7206 (pp) cc_final: 0.6932 (mt) REVERT: E 754 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.7023 (pmm) REVERT: E 756 MET cc_start: 0.6437 (pmm) cc_final: 0.5359 (tpp) REVERT: E 827 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6781 (mtmt) outliers start: 187 outliers final: 91 residues processed: 505 average time/residue: 0.6853 time to fit residues: 415.2746 Evaluate side-chains 455 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 329 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 455 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 766 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 804 MET Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 814 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 825 SER Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 241 LEU 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 579 MET Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 719 LYS Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 784 VAL Chi-restraints excluded: chain E residue 827 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 283 optimal weight: 10.0000 chunk 162 optimal weight: 30.0000 chunk 22 optimal weight: 6.9990 chunk 366 optimal weight: 0.9980 chunk 360 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 394 optimal weight: 0.4980 chunk 132 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN D 277 ASN D 649 GLN E 360 HIS E 394 ASN ** E 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103607 restraints weight = 46847.449| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.24 r_work: 0.3078 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35864 Z= 0.177 Angle : 0.618 14.365 48585 Z= 0.300 Chirality : 0.043 0.152 5022 Planarity : 0.004 0.053 6251 Dihedral : 8.642 156.941 4850 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.02 % Allowed : 28.06 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -0.65 (0.13), residues: 4235 helix: 0.60 (0.12), residues: 1765 sheet: -0.22 (0.21), residues: 629 loop : -1.52 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 741 TYR 0.026 0.001 TYR D 696 PHE 0.023 0.002 PHE E 160 TRP 0.016 0.001 TRP D 40 HIS 0.004 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00423 (35864) covalent geometry : angle 0.61752 (48585) hydrogen bonds : bond 0.03995 ( 1489) hydrogen bonds : angle 4.85994 ( 4185) *********************** 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 530 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 345 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7131 (tptp) cc_final: 0.6680 (tppt) REVERT: A 106 LYS cc_start: 0.7986 (mmtt) cc_final: 0.7664 (mmmt) REVERT: A 161 LYS cc_start: 0.8606 (ttpp) cc_final: 0.8300 (ttmp) REVERT: A 175 ASP cc_start: 0.8319 (t0) cc_final: 0.8041 (t0) REVERT: A 228 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7591 (p0) REVERT: A 232 GLU cc_start: 0.8513 (tp30) cc_final: 0.7715 (pm20) REVERT: A 233 PHE cc_start: 0.8477 (m-10) cc_final: 0.8258 (m-10) REVERT: A 235 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7455 (ttt180) REVERT: A 239 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.8295 (m-10) REVERT: A 340 GLN cc_start: 0.8286 (mt0) cc_final: 0.7864 (mm-40) REVERT: A 527 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8399 (mtmt) REVERT: A 554 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8604 (tt) REVERT: A 564 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7455 (mtp180) REVERT: A 583 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8421 (mtp180) REVERT: A 674 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8375 (pmtt) REVERT: A 754 MET cc_start: 0.7958 (mtm) cc_final: 0.7599 (ttp) REVERT: A 756 MET cc_start: 0.8172 (tpp) cc_final: 0.7641 (ptt) REVERT: A 763 LYS cc_start: 0.8360 (mptt) cc_final: 0.7869 (mmmt) REVERT: A 792 ASP cc_start: 0.7584 (m-30) cc_final: 0.7139 (t70) REVERT: A 807 HIS cc_start: 0.6654 (OUTLIER) cc_final: 0.6384 (t-170) REVERT: A 837 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7756 (t0) REVERT: B 4 LYS cc_start: 0.6489 (OUTLIER) cc_final: 0.5789 (tptm) REVERT: B 12 GLN cc_start: 0.4207 (OUTLIER) cc_final: 0.3930 (pm20) REVERT: B 24 LYS cc_start: 0.8523 (mmmm) cc_final: 0.8116 (tttm) REVERT: B 36 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8089 (tpt) REVERT: B 149 CYS cc_start: 0.8418 (m) cc_final: 0.7690 (p) REVERT: B 193 ASN cc_start: 0.7464 (t0) cc_final: 0.7218 (m-40) REVERT: B 209 TYR cc_start: 0.7512 (m-10) cc_final: 0.6974 (m-10) REVERT: B 245 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7114 (p0) REVERT: B 292 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.6949 (m-80) REVERT: B 310 SER cc_start: 0.8336 (OUTLIER) cc_final: 0.7894 (p) REVERT: B 433 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8171 (tppt) REVERT: B 523 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7676 (pt0) REVERT: B 545 HIS cc_start: 0.7357 (t-90) cc_final: 0.6959 (t70) REVERT: B 561 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8228 (mp) REVERT: B 608 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8420 (pt0) REVERT: B 612 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8356 (mmm) REVERT: B 765 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7208 (mptt) REVERT: B 781 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7721 (tp) REVERT: C 1 MET cc_start: 0.5608 (ptt) cc_final: 0.4750 (tmm) REVERT: C 14 LYS cc_start: 0.7491 (mptt) cc_final: 0.6809 (mtpm) REVERT: C 82 LYS cc_start: 0.7959 (mmmt) cc_final: 0.7693 (ptmm) REVERT: C 116 GLU cc_start: 0.9376 (OUTLIER) cc_final: 0.8546 (pt0) REVERT: C 222 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8226 (mt) REVERT: C 233 PHE cc_start: 0.7869 (m-10) cc_final: 0.7407 (m-80) REVERT: C 298 LEU cc_start: 0.6778 (mt) cc_final: 0.6505 (tp) REVERT: C 390 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.6281 (mt0) REVERT: C 612 MET cc_start: 0.7891 (mpt) cc_final: 0.7563 (mmp) REVERT: C 639 GLU cc_start: 0.4345 (OUTLIER) cc_final: 0.4100 (tm-30) REVERT: C 735 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6298 (tppp) REVERT: C 765 LYS cc_start: 0.6003 (tmtt) cc_final: 0.5549 (tmtt) REVERT: C 775 LEU cc_start: 0.7217 (mm) cc_final: 0.6864 (mp) REVERT: C 803 LYS cc_start: 0.7182 (tppp) cc_final: 0.6372 (ptpp) REVERT: C 804 MET cc_start: 0.5173 (OUTLIER) cc_final: 0.4285 (tpt) REVERT: C 815 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.6049 (tm-30) REVERT: C 817 GLU cc_start: 0.8083 (pt0) cc_final: 0.7599 (tp30) REVERT: D 3 ILE cc_start: 0.5260 (OUTLIER) cc_final: 0.5019 (tt) REVERT: D 15 GLU cc_start: 0.8135 (tt0) cc_final: 0.7829 (mp0) REVERT: D 51 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6192 (mp) REVERT: D 157 TYR cc_start: 0.8045 (m-80) cc_final: 0.7508 (m-80) REVERT: D 166 MET cc_start: 0.8099 (mtp) cc_final: 0.7349 (pmt) REVERT: D 294 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.4304 (mp0) REVERT: D 393 SER cc_start: 0.8507 (t) cc_final: 0.8243 (p) REVERT: D 430 TYR cc_start: 0.7877 (m-80) cc_final: 0.7652 (m-80) REVERT: D 433 LYS cc_start: 0.8494 (mmtt) cc_final: 0.7997 (tptt) REVERT: D 477 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7189 (mm110) REVERT: D 494 GLU cc_start: 0.8360 (tp30) cc_final: 0.8117 (tp30) REVERT: D 545 HIS cc_start: 0.7653 (t-90) cc_final: 0.6852 (m-70) REVERT: D 590 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: D 724 ASP cc_start: 0.8194 (t0) cc_final: 0.7713 (t70) REVERT: D 727 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7393 (tm) REVERT: D 813 THR cc_start: 0.7300 (OUTLIER) cc_final: 0.7056 (p) REVERT: E 19 LYS cc_start: 0.8059 (mptp) cc_final: 0.7564 (mttt) REVERT: E 27 LYS cc_start: 0.8109 (tppt) cc_final: 0.7711 (tptp) REVERT: E 74 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7694 (tmt170) REVERT: E 76 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5895 (mm-30) REVERT: E 106 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8035 (pttt) REVERT: E 241 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8673 (tt) REVERT: E 356 ASN cc_start: 0.7370 (t0) cc_final: 0.6870 (p0) REVERT: E 508 ARG cc_start: 0.8707 (ttp-170) cc_final: 0.8068 (ttm110) REVERT: E 511 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7911 (p) REVERT: E 719 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7578 (ptpp) REVERT: E 724 ASP cc_start: 0.7691 (t0) cc_final: 0.7348 (t70) REVERT: E 733 LEU cc_start: 0.7183 (pp) cc_final: 0.6886 (mt) REVERT: E 741 ARG cc_start: 0.6539 (ptm160) cc_final: 0.6286 (ptp90) REVERT: E 754 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.7059 (pmm) REVERT: E 756 MET cc_start: 0.6600 (pmm) cc_final: 0.5386 (tpp) REVERT: E 827 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6823 (mtmt) outliers start: 185 outliers final: 94 residues processed: 497 average time/residue: 0.6747 time to fit residues: 404.1635 Evaluate side-chains 466 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 330 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 246 TRP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 89 LYS 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 166 MET Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 390 GLN Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 455 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 766 VAL Chi-restraints excluded: chain C residue 804 MET Chi-restraints excluded: chain C residue 814 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 825 SER Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 813 THR Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 253 GLU 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 579 MET Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 719 LYS Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 784 VAL Chi-restraints excluded: chain E residue 827 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 2 optimal weight: 4.9990 chunk 290 optimal weight: 20.0000 chunk 311 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 328 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 412 optimal weight: 0.8980 chunk 179 optimal weight: 9.9990 chunk 273 optimal weight: 8.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN D 649 GLN E 360 HIS E 394 ASN ** E 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104482 restraints weight = 46693.736| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.11 r_work: 0.3084 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35864 Z= 0.170 Angle : 0.616 13.427 48585 Z= 0.299 Chirality : 0.043 0.196 5022 Planarity : 0.004 0.057 6251 Dihedral : 8.545 153.960 4849 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.72 % Allowed : 28.49 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -0.60 (0.13), residues: 4235 helix: 0.64 (0.12), residues: 1765 sheet: -0.21 (0.21), residues: 631 loop : -1.47 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 741 TYR 0.025 0.001 TYR D 696 PHE 0.034 0.002 PHE C 845 TRP 0.024 0.001 TRP C 734 HIS 0.004 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00408 (35864) covalent geometry : angle 0.61581 (48585) hydrogen bonds : bond 0.03935 ( 1489) hydrogen bonds : angle 4.83945 ( 4185) *********************** 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 516 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 342 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.7969 (mmtt) cc_final: 0.7675 (mmmt) REVERT: A 161 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8277 (ttmp) REVERT: A 175 ASP cc_start: 0.8321 (t0) cc_final: 0.8031 (t0) REVERT: A 228 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7561 (p0) REVERT: A 232 GLU cc_start: 0.8492 (tp30) cc_final: 0.7730 (pm20) REVERT: A 233 PHE cc_start: 0.8404 (m-10) cc_final: 0.8189 (m-10) REVERT: A 235 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7454 (ttt180) REVERT: A 239 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.8297 (m-10) REVERT: A 340 GLN cc_start: 0.8262 (mt0) cc_final: 0.7847 (mm-40) REVERT: A 527 LYS cc_start: 0.8725 (mtpp) cc_final: 0.8396 (mtmt) REVERT: A 564 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7480 (mtp180) REVERT: A 583 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8425 (mtp180) REVERT: A 608 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8700 (mt-10) REVERT: A 674 LYS cc_start: 0.8724 (ttmm) cc_final: 0.8379 (pmtt) REVERT: A 754 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7634 (ttp) REVERT: A 756 MET cc_start: 0.8141 (tpp) cc_final: 0.7722 (mpp) REVERT: A 763 LYS cc_start: 0.8347 (mptt) cc_final: 0.7865 (mmmt) REVERT: A 792 ASP cc_start: 0.7570 (m-30) cc_final: 0.7144 (t70) REVERT: A 807 HIS cc_start: 0.6650 (OUTLIER) cc_final: 0.6377 (t-170) REVERT: A 837 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7740 (t0) REVERT: B 4 LYS cc_start: 0.6182 (OUTLIER) cc_final: 0.5666 (tptm) REVERT: B 12 GLN cc_start: 0.4177 (OUTLIER) cc_final: 0.3935 (pm20) REVERT: B 24 LYS cc_start: 0.8541 (mmmm) cc_final: 0.8125 (tttm) REVERT: B 36 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8096 (tpt) REVERT: B 149 CYS cc_start: 0.8425 (m) cc_final: 0.7693 (p) REVERT: B 166 MET cc_start: 0.6132 (tpp) cc_final: 0.5125 (tmm) REVERT: B 171 ILE cc_start: 0.7879 (mt) cc_final: 0.7649 (mm) REVERT: B 193 ASN cc_start: 0.7448 (t0) cc_final: 0.7208 (m-40) REVERT: B 209 TYR cc_start: 0.7513 (m-10) cc_final: 0.6960 (m-10) REVERT: B 245 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7112 (p0) REVERT: B 264 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8008 (mm) REVERT: B 265 LYS cc_start: 0.7615 (ptmt) cc_final: 0.7061 (mptt) REVERT: B 292 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6961 (m-80) REVERT: B 310 SER cc_start: 0.8293 (OUTLIER) cc_final: 0.7862 (p) REVERT: B 433 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8184 (tppt) REVERT: B 523 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7663 (pt0) REVERT: B 545 HIS cc_start: 0.7400 (t-90) cc_final: 0.7006 (t70) REVERT: B 561 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8223 (mp) REVERT: B 608 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8431 (pt0) REVERT: B 612 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8301 (mmm) REVERT: B 765 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7214 (mptt) REVERT: B 781 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7698 (tp) REVERT: C 1 MET cc_start: 0.5716 (ptt) cc_final: 0.4944 (tmm) REVERT: C 14 LYS cc_start: 0.7554 (mptt) cc_final: 0.6882 (mtpm) REVERT: C 82 LYS cc_start: 0.7992 (mmmt) cc_final: 0.7765 (ptmm) REVERT: C 116 GLU cc_start: 0.9341 (OUTLIER) cc_final: 0.8469 (pt0) REVERT: C 222 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8228 (mt) REVERT: C 233 PHE cc_start: 0.7900 (m-10) cc_final: 0.7437 (m-80) REVERT: C 298 LEU cc_start: 0.6824 (mt) cc_final: 0.6579 (tp) REVERT: C 612 MET cc_start: 0.7881 (mpt) cc_final: 0.7573 (mmp) REVERT: C 775 LEU cc_start: 0.7270 (mm) cc_final: 0.6897 (mp) REVERT: C 803 LYS cc_start: 0.7170 (tppp) cc_final: 0.6357 (ptpp) REVERT: C 804 MET cc_start: 0.5228 (OUTLIER) cc_final: 0.4380 (tpt) REVERT: C 815 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.6041 (tm-30) REVERT: C 817 GLU cc_start: 0.8048 (pt0) cc_final: 0.7604 (tp30) REVERT: D 3 ILE cc_start: 0.5295 (OUTLIER) cc_final: 0.5079 (tt) REVERT: D 15 GLU cc_start: 0.8129 (tt0) cc_final: 0.7840 (mp0) REVERT: D 51 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6181 (mp) REVERT: D 157 TYR cc_start: 0.8048 (m-80) cc_final: 0.7513 (m-80) REVERT: D 166 MET cc_start: 0.8103 (mtp) cc_final: 0.7390 (pmt) REVERT: D 294 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.4292 (mp0) REVERT: D 393 SER cc_start: 0.8529 (t) cc_final: 0.8266 (p) REVERT: D 433 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8007 (tptt) REVERT: D 477 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7210 (mm110) REVERT: D 494 GLU cc_start: 0.8357 (tp30) cc_final: 0.8086 (tp30) REVERT: D 545 HIS cc_start: 0.7685 (t-90) cc_final: 0.6872 (m-70) REVERT: D 590 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: D 724 ASP cc_start: 0.8190 (t0) cc_final: 0.7717 (t70) REVERT: D 727 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7391 (tm) REVERT: E 19 LYS cc_start: 0.7982 (mptp) cc_final: 0.7507 (mttt) REVERT: E 27 LYS cc_start: 0.8056 (tppt) cc_final: 0.7675 (tptp) REVERT: E 74 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7714 (tmt170) REVERT: E 76 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.5916 (mm-30) REVERT: E 106 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8023 (pttt) REVERT: E 229 MET cc_start: 0.8454 (mtp) cc_final: 0.8107 (mtm) REVERT: E 241 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8656 (tt) REVERT: E 356 ASN cc_start: 0.7386 (t0) cc_final: 0.6886 (p0) REVERT: E 508 ARG cc_start: 0.8712 (ttp-170) cc_final: 0.8069 (ttm110) REVERT: E 511 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7908 (p) REVERT: E 719 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7612 (ptpp) REVERT: E 724 ASP cc_start: 0.7635 (t0) cc_final: 0.7298 (OUTLIER) REVERT: E 733 LEU cc_start: 0.7225 (pp) cc_final: 0.6955 (mt) REVERT: E 754 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7064 (pmm) REVERT: E 756 MET cc_start: 0.6716 (pmm) cc_final: 0.5102 (tpt) REVERT: E 827 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6788 (mtmt) outliers start: 174 outliers final: 97 residues processed: 485 average time/residue: 0.6836 time to fit residues: 396.9012 Evaluate side-chains 469 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 333 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 246 TRP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 804 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 70 LEU 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 166 MET Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 766 VAL Chi-restraints excluded: chain C residue 804 MET Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 814 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 825 SER Chi-restraints excluded: chain C residue 835 LYS Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 253 GLU 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 579 MET Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 719 LYS Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 784 VAL Chi-restraints excluded: chain E residue 827 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 252 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 343 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 409 optimal weight: 6.9990 chunk 240 optimal weight: 8.9990 chunk 236 optimal weight: 7.9990 chunk 235 optimal weight: 7.9990 chunk 379 optimal weight: 8.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 HIS D 277 ASN D 649 GLN E 360 HIS E 394 ASN ** E 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.142904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101940 restraints weight = 46971.600| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.33 r_work: 0.3068 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 35864 Z= 0.228 Angle : 0.659 12.525 48585 Z= 0.322 Chirality : 0.045 0.173 5022 Planarity : 0.004 0.058 6251 Dihedral : 8.562 152.763 4846 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.45 % Allowed : 28.77 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -0.70 (0.12), residues: 4235 helix: 0.53 (0.12), residues: 1764 sheet: -0.27 (0.21), residues: 627 loop : -1.50 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 741 TYR 0.030 0.002 TYR D 696 PHE 0.028 0.002 PHE C 845 TRP 0.034 0.002 TRP C 734 HIS 0.004 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00551 (35864) covalent geometry : angle 0.65888 (48585) hydrogen bonds : bond 0.04308 ( 1489) hydrogen bonds : angle 4.97288 ( 4185) ********************** 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 500 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 336 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7277 (tptp) cc_final: 0.6808 (tppt) REVERT: A 106 LYS cc_start: 0.8041 (mmtt) cc_final: 0.7742 (mmmt) REVERT: A 175 ASP cc_start: 0.8374 (t0) cc_final: 0.8126 (t0) REVERT: A 228 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7652 (p0) REVERT: A 232 GLU cc_start: 0.8521 (tp30) cc_final: 0.7799 (pm20) REVERT: A 233 PHE cc_start: 0.8431 (m-10) cc_final: 0.8226 (m-10) REVERT: A 235 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7662 (ttt180) REVERT: A 340 GLN cc_start: 0.8342 (mt0) cc_final: 0.7885 (mm-40) REVERT: A 424 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8167 (mmm160) REVERT: A 527 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8536 (mtmt) REVERT: A 554 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8695 (tt) REVERT: A 564 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7136 (mtp180) REVERT: A 583 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8536 (mtp180) REVERT: A 608 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.8741 (mt-10) REVERT: A 674 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8389 (pmtt) REVERT: A 754 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7807 (ttp) REVERT: A 756 MET cc_start: 0.8104 (tpp) cc_final: 0.7804 (mpp) REVERT: A 763 LYS cc_start: 0.8379 (mptt) cc_final: 0.7922 (mmmt) REVERT: A 792 ASP cc_start: 0.7632 (m-30) cc_final: 0.7286 (t70) REVERT: A 807 HIS cc_start: 0.6706 (OUTLIER) cc_final: 0.6443 (t-170) REVERT: A 837 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7805 (t0) REVERT: B 4 LYS cc_start: 0.6197 (OUTLIER) cc_final: 0.5757 (tptm) REVERT: B 12 GLN cc_start: 0.4326 (OUTLIER) cc_final: 0.4073 (pm20) REVERT: B 24 LYS cc_start: 0.8525 (mmmm) cc_final: 0.8135 (tttm) REVERT: B 36 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8204 (tpt) REVERT: B 149 CYS cc_start: 0.8558 (m) cc_final: 0.7932 (p) REVERT: B 193 ASN cc_start: 0.7498 (t0) cc_final: 0.7246 (m-40) REVERT: B 209 TYR cc_start: 0.7638 (m-10) cc_final: 0.7097 (m-10) REVERT: B 245 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7188 (p0) REVERT: B 292 TYR cc_start: 0.7574 (OUTLIER) cc_final: 0.7081 (m-80) REVERT: B 310 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8082 (p) REVERT: B 433 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8192 (tppt) REVERT: B 523 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7869 (pt0) REVERT: B 545 HIS cc_start: 0.7461 (t-90) cc_final: 0.7076 (t70) REVERT: B 561 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8407 (mp) REVERT: B 608 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8537 (pt0) REVERT: B 612 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8451 (mmm) REVERT: B 765 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7387 (mptt) REVERT: B 781 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7890 (tp) REVERT: C 1 MET cc_start: 0.5784 (ptt) cc_final: 0.4932 (tmm) REVERT: C 14 LYS cc_start: 0.7786 (mptt) cc_final: 0.7094 (mtpm) REVERT: C 116 GLU cc_start: 0.9400 (OUTLIER) cc_final: 0.8608 (pt0) REVERT: C 222 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8429 (mt) REVERT: C 233 PHE cc_start: 0.7893 (m-10) cc_final: 0.7459 (m-80) REVERT: C 612 MET cc_start: 0.7928 (mpt) cc_final: 0.7653 (mmp) REVERT: C 735 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6646 (tptp) REVERT: C 803 LYS cc_start: 0.7207 (tppp) cc_final: 0.6382 (ptpp) REVERT: C 804 MET cc_start: 0.5373 (OUTLIER) cc_final: 0.4516 (tpt) REVERT: C 815 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.6015 (tm-30) REVERT: C 817 GLU cc_start: 0.7913 (pt0) cc_final: 0.7614 (tp30) REVERT: D 3 ILE cc_start: 0.5326 (OUTLIER) cc_final: 0.5064 (tt) REVERT: D 15 GLU cc_start: 0.8125 (tt0) cc_final: 0.7923 (mp0) REVERT: D 25 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6068 (tm-30) REVERT: D 51 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6308 (mp) REVERT: D 166 MET cc_start: 0.8177 (mtp) cc_final: 0.7464 (pmt) REVERT: D 294 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.4531 (mp0) REVERT: D 393 SER cc_start: 0.8548 (t) cc_final: 0.8287 (p) REVERT: D 433 LYS cc_start: 0.8517 (mmtt) cc_final: 0.7994 (tptt) REVERT: D 477 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7388 (mm110) REVERT: D 494 GLU cc_start: 0.8372 (tp30) cc_final: 0.8133 (tp30) REVERT: D 545 HIS cc_start: 0.7834 (t-90) cc_final: 0.7017 (m-70) REVERT: D 590 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8363 (m-30) REVERT: D 724 ASP cc_start: 0.8275 (t0) cc_final: 0.7827 (t70) REVERT: D 727 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7534 (tm) REVERT: E 19 LYS cc_start: 0.8112 (mptp) cc_final: 0.7630 (mttt) REVERT: E 27 LYS cc_start: 0.8069 (tppt) cc_final: 0.7754 (tptp) REVERT: E 74 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7751 (tmt170) REVERT: E 76 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6010 (mm-30) REVERT: E 106 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8057 (pttt) REVERT: E 229 MET cc_start: 0.8575 (mtp) cc_final: 0.8239 (mtm) REVERT: E 241 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8797 (tt) REVERT: E 356 ASN cc_start: 0.7541 (t0) cc_final: 0.7075 (p0) REVERT: E 508 ARG cc_start: 0.8785 (ttp-170) cc_final: 0.8160 (ttm170) REVERT: E 511 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.8027 (p) REVERT: E 719 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7812 (ptpp) REVERT: E 724 ASP cc_start: 0.7686 (t0) cc_final: 0.7391 (t70) REVERT: E 733 LEU cc_start: 0.7362 (pp) cc_final: 0.7084 (mt) REVERT: E 754 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7245 (pmm) REVERT: E 756 MET cc_start: 0.6703 (pmm) cc_final: 0.5030 (tpt) REVERT: E 827 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.7042 (mtmt) REVERT: E 831 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8139 (ttp-170) outliers start: 164 outliers final: 95 residues processed: 471 average time/residue: 0.6991 time to fit residues: 395.3407 Evaluate side-chains 461 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 324 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 451 VAL 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 564 ARG Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 246 TRP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 804 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 70 LEU 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 222 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 766 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 804 MET Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 814 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 825 SER Chi-restraints excluded: chain C residue 835 LYS Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 606 SER Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 253 GLU 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 579 MET Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 719 LYS Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 767 GLN Chi-restraints excluded: chain E residue 784 VAL Chi-restraints excluded: chain E residue 827 LYS Chi-restraints excluded: chain E residue 831 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 53 optimal weight: 0.9980 chunk 250 optimal weight: 5.9990 chunk 364 optimal weight: 10.0000 chunk 348 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 379 optimal weight: 7.9990 chunk 185 optimal weight: 3.9990 chunk 413 optimal weight: 0.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 HIS C 725 ASN D 277 ASN D 378 ASN D 649 GLN E 360 HIS E 394 ASN ** E 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.145307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.104658 restraints weight = 46543.326| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.35 r_work: 0.3107 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35864 Z= 0.133 Angle : 0.606 13.342 48585 Z= 0.293 Chirality : 0.043 0.165 5022 Planarity : 0.004 0.071 6251 Dihedral : 8.335 152.604 4846 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.64 % Allowed : 29.66 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.13), residues: 4235 helix: 0.75 (0.12), residues: 1755 sheet: -0.15 (0.21), residues: 629 loop : -1.40 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 741 TYR 0.024 0.001 TYR D 696 PHE 0.031 0.001 PHE B 300 TRP 0.037 0.001 TRP C 734 HIS 0.003 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00312 (35864) covalent geometry : angle 0.60634 (48585) hydrogen bonds : bond 0.03691 ( 1489) hydrogen bonds : angle 4.78601 ( 4185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13351.10 seconds wall clock time: 227 minutes 34.22 seconds (13654.22 seconds total)