Starting phenix.real_space_refine on Fri Aug 7 19:09:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10bu_75053/08_2026/10bu_75053.cif Found real_map, /net/cci-nas-00/data/ceres_data/10bu_75053/08_2026/10bu_75053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10bu_75053/08_2026/10bu_75053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10bu_75053/08_2026/10bu_75053.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10bu_75053/08_2026/10bu_75053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10bu_75053/08_2026/10bu_75053.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 14838 2.51 5 N 3977 2.21 5 O 4506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23438 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7820 Classifications: {'peptide': 990} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 51, 'TRANS': 934} Chain breaks: 2 Chain: "B" Number of atoms: 7819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7819 Classifications: {'peptide': 990} Link IDs: {'PCIS': 4, 'PTRANS': 51, 'TRANS': 934} Chain breaks: 1 Chain: "C" Number of atoms: 7799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7799 Classifications: {'peptide': 987} Link IDs: {'PCIS': 3, 'PTRANS': 52, 'TRANS': 931} Chain breaks: 1 Time building chain proxies: 5.27, per 1000 atoms: 0.22 Number of scatterers: 23438 At special positions: 0 Unit cell: (119.68, 116.864, 161.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 4506 8.00 N 3977 7.00 C 14838 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: 1.98 Conformation dependent library (CDL) restraints added in 1.2 seconds 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 46 sheets defined 16.5% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 8 through 12 Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.864A pdb=" N TYR A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 24' Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.749A pdb=" N LEU A 383 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN A 385 " --> pdb=" O MET A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.715A pdb=" N PHE A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 445 Processing helix chain 'A' and resid 533 through 546 Processing helix chain 'A' and resid 547 through 550 Processing helix chain 'A' and resid 551 through 555 removed outlier: 3.768A pdb=" N LYS A 555 " --> pdb=" O ASP A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 575 Processing helix chain 'A' and resid 579 through 583 Processing helix chain 'A' and resid 596 through 601 removed outlier: 3.632A pdb=" N ASN A 600 " --> pdb=" O TYR A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 618 removed outlier: 3.576A pdb=" N LEU A 618 " --> pdb=" O TYR A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 692 through 704 removed outlier: 3.562A pdb=" N ARG A 704 " --> pdb=" O GLU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 709 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 774 through 779 Processing helix chain 'A' and resid 831 through 842 Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 863 through 867 Processing helix chain 'A' and resid 960 through 964 Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 19 through 24 removed outlier: 4.285A pdb=" N TYR B 23 " --> pdb=" O ASP B 19 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 24' Processing helix chain 'B' and resid 25 through 34 removed outlier: 3.531A pdb=" N VAL B 29 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.530A pdb=" N LEU B 383 " --> pdb=" O LYS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 402 removed outlier: 3.659A pdb=" N PHE B 401 " --> pdb=" O ARG B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 445 removed outlier: 3.651A pdb=" N SER B 437 " --> pdb=" O ASN B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 544 Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 551 through 555 removed outlier: 3.814A pdb=" N LYS B 555 " --> pdb=" O ASP B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 575 Processing helix chain 'B' and resid 579 through 584 removed outlier: 3.829A pdb=" N ASP B 584 " --> pdb=" O GLY B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 601 removed outlier: 3.806A pdb=" N ASN B 600 " --> pdb=" O TYR B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 618 removed outlier: 3.527A pdb=" N LEU B 618 " --> pdb=" O TYR B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 692 through 704 Processing helix chain 'B' and resid 705 through 709 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 831 through 842 Processing helix chain 'B' and resid 854 through 858 removed outlier: 3.532A pdb=" N LYS B 857 " --> pdb=" O GLU B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 867 Processing helix chain 'B' and resid 955 through 959 Processing helix chain 'B' and resid 960 through 964 Processing helix chain 'C' and resid 7 through 12 removed outlier: 3.700A pdb=" N SER C 11 " --> pdb=" O MET C 7 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR C 12 " --> pdb=" O PRO C 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 12' Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.536A pdb=" N VAL C 29 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.755A pdb=" N LEU C 383 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN C 385 " --> pdb=" O MET C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 402 Processing helix chain 'C' and resid 433 through 445 removed outlier: 3.564A pdb=" N SER C 437 " --> pdb=" O ASN C 433 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 545 removed outlier: 3.501A pdb=" N ASN C 545 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.668A pdb=" N LYS C 555 " --> pdb=" O ASP C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 575 removed outlier: 3.940A pdb=" N MET C 573 " --> pdb=" O THR C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 584 removed outlier: 3.857A pdb=" N ASP C 584 " --> pdb=" O GLY C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 601 removed outlier: 3.785A pdb=" N ASN C 600 " --> pdb=" O TYR C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 618 Processing helix chain 'C' and resid 657 through 662 removed outlier: 3.743A pdb=" N VAL C 661 " --> pdb=" O ASP C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 673 Processing helix chain 'C' and resid 692 through 704 Processing helix chain 'C' and resid 705 through 709 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 774 through 779 Processing helix chain 'C' and resid 783 through 785 No H-bonds generated for 'chain 'C' and resid 783 through 785' Processing helix chain 'C' and resid 831 through 844 Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 863 through 867 Processing helix chain 'C' and resid 955 through 965 removed outlier: 4.438A pdb=" N GLN C 959 " --> pdb=" O THR C 955 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN C 960 " --> pdb=" O ASP C 956 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.492A pdb=" N ARG A 104 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ILE A 682 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASP A 102 " --> pdb=" O ILE A 682 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 removed outlier: 4.228A pdb=" N ASP A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 135 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 174 removed outlier: 3.960A pdb=" N ALA A 174 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE C 497 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N PHE A 272 " --> pdb=" O ILE C 497 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA A 226 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N TYR A 355 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLY A 228 " --> pdb=" O TYR A 355 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLU A 357 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 230 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY A 227 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 176 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 174 removed outlier: 3.960A pdb=" N ALA A 174 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS C 498 " --> pdb=" O ALA C 510 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA C 510 " --> pdb=" O LYS C 498 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 180 through 182 removed outlier: 3.870A pdb=" N ALA A 180 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA8, first strand: chain 'A' and resid 279 through 281 removed outlier: 7.983A pdb=" N LEU A 342 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL A 328 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS A 344 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB1, first strand: chain 'A' and resid 306 through 308 Processing sheet with id=AB2, first strand: chain 'A' and resid 366 through 367 Processing sheet with id=AB3, first strand: chain 'A' and resid 481 through 482 removed outlier: 3.662A pdb=" N MET A 529 " --> pdb=" O CYS A 482 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 509 through 511 removed outlier: 9.460A pdb=" N ALA B 174 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N GLY A 522 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 509 through 511 removed outlier: 3.858A pdb=" N ILE A 497 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N PHE B 272 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N ALA A 499 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 12.539A pdb=" N MET B 270 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 227 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE B 176 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 710 through 713 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 725 removed outlier: 3.675A pdb=" N GLY A 746 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 731 through 739 removed outlier: 4.453A pdb=" N SER A 738 " --> pdb=" O HIS A 968 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N HIS A 968 " --> pdb=" O SER A 738 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 794 " --> pdb=" O VAL A 798 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 868 through 875 Processing sheet with id=AC1, first strand: chain 'B' and resid 65 through 68 removed outlier: 7.393A pdb=" N ARG B 104 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE B 682 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP B 102 " --> pdb=" O ILE B 682 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU B 684 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR B 100 " --> pdb=" O LEU B 684 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 79 through 87 Processing sheet with id=AC3, first strand: chain 'B' and resid 133 through 136 Processing sheet with id=AC4, first strand: chain 'B' and resid 180 through 182 removed outlier: 4.422A pdb=" N ALA B 180 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 189 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 258 through 260 Processing sheet with id=AC6, first strand: chain 'B' and resid 279 through 281 removed outlier: 6.313A pdb=" N ILE B 280 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU B 342 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL B 328 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS B 344 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 304 through 308 removed outlier: 4.301A pdb=" N LEU B 306 " --> pdb=" O ILE B 317 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 366 through 368 Processing sheet with id=AC9, first strand: chain 'B' and resid 395 through 396 removed outlier: 3.985A pdb=" N ALA B 396 " --> pdb=" O GLN B 663 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 481 through 482 Processing sheet with id=AD2, first strand: chain 'B' and resid 509 through 511 removed outlier: 9.436A pdb=" N ALA C 174 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY B 522 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 509 through 511 removed outlier: 3.793A pdb=" N ILE B 497 " --> pdb=" O PHE C 272 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N PHE C 272 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N ALA B 499 " --> pdb=" O MET C 270 " (cutoff:3.500A) removed outlier: 11.982A pdb=" N MET C 270 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA C 226 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N TYR C 355 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY C 228 " --> pdb=" O TYR C 355 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY C 227 " --> pdb=" O PHE C 176 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE C 176 " --> pdb=" O GLY C 227 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 710 through 713 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 725 Processing sheet with id=AD6, first strand: chain 'B' and resid 731 through 739 removed outlier: 3.916A pdb=" N SER B 738 " --> pdb=" O HIS B 968 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS B 968 " --> pdb=" O SER B 738 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 868 through 875 Processing sheet with id=AD8, first strand: chain 'C' and resid 66 through 68 removed outlier: 5.579A pdb=" N ILE C 677 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASP C 108 " --> pdb=" O ILE C 677 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N PHE C 679 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL C 106 " --> pdb=" O PHE C 679 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 72 through 75 removed outlier: 4.026A pdb=" N ASP C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 133 through 136 Processing sheet with id=AE2, first strand: chain 'C' and resid 181 through 182 removed outlier: 3.790A pdb=" N ASN C 182 " --> pdb=" O GLY C 185 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 258 through 260 Processing sheet with id=AE4, first strand: chain 'C' and resid 279 through 281 Processing sheet with id=AE5, first strand: chain 'C' and resid 306 through 308 Processing sheet with id=AE6, first strand: chain 'C' and resid 366 through 368 Processing sheet with id=AE7, first strand: chain 'C' and resid 710 through 713 Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 725 removed outlier: 3.694A pdb=" N GLY C 746 " --> pdb=" O GLU C 990 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 731 through 739 removed outlier: 4.111A pdb=" N SER C 738 " --> pdb=" O HIS C 968 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N HIS C 968 " --> pdb=" O SER C 738 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 794 " --> pdb=" O VAL C 798 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 868 through 875 588 hydrogen bonds defined for protein. 1365 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: 5.23 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7741 1.34 - 1.46: 5216 1.46 - 1.58: 10855 1.58 - 1.69: 0 1.69 - 1.81: 213 Bond restraints: 24025 Sorted by residual: bond pdb=" CA ASN A 784 " pdb=" C ASN A 784 " ideal model delta sigma weight residual 1.524 1.443 0.080 2.25e-02 1.98e+03 1.28e+01 bond pdb=" C GLU C 210 " pdb=" N PRO C 211 " ideal model delta sigma weight residual 1.334 1.314 0.019 8.40e-03 1.42e+04 5.39e+00 bond pdb=" C GLU B 210 " pdb=" N PRO B 211 " ideal model delta sigma weight residual 1.334 1.314 0.019 8.40e-03 1.42e+04 5.27e+00 bond pdb=" CA PHE A 636 " pdb=" CB PHE A 636 " ideal model delta sigma weight residual 1.530 1.500 0.031 1.69e-02 3.50e+03 3.27e+00 bond pdb=" C ASN C 602 " pdb=" N PRO C 603 " ideal model delta sigma weight residual 1.335 1.312 0.022 1.28e-02 6.10e+03 3.06e+00 ... (remaining 24020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 31662 1.74 - 3.47: 886 3.47 - 5.21: 94 5.21 - 6.95: 11 6.95 - 8.69: 3 Bond angle restraints: 32656 Sorted by residual: angle pdb=" N GLY B 746 " pdb=" CA GLY B 746 " pdb=" C GLY B 746 " ideal model delta sigma weight residual 110.80 119.49 -8.69 1.71e+00 3.42e-01 2.58e+01 angle pdb=" C LEU C 548 " pdb=" N TYR C 549 " pdb=" CA TYR C 549 " ideal model delta sigma weight residual 122.56 115.09 7.47 1.72e+00 3.38e-01 1.89e+01 angle pdb=" N ILE B 638 " pdb=" CA ILE B 638 " pdb=" C ILE B 638 " ideal model delta sigma weight residual 113.20 109.58 3.62 9.60e-01 1.09e+00 1.42e+01 angle pdb=" N ALA A 420 " pdb=" CA ALA A 420 " pdb=" C ALA A 420 " ideal model delta sigma weight residual 114.75 110.52 4.23 1.26e+00 6.30e-01 1.13e+01 angle pdb=" C ARG B 745 " pdb=" N GLY B 746 " pdb=" CA GLY B 746 " ideal model delta sigma weight residual 121.38 117.37 4.01 1.22e+00 6.72e-01 1.08e+01 ... (remaining 32651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 12759 17.34 - 34.68: 1148 34.68 - 52.02: 279 52.02 - 69.36: 72 69.36 - 86.70: 10 Dihedral angle restraints: 14268 sinusoidal: 5653 harmonic: 8615 Sorted by residual: dihedral pdb=" CA VAL C 915 " pdb=" C VAL C 915 " pdb=" N PRO C 916 " pdb=" CA PRO C 916 " ideal model delta harmonic sigma weight residual -180.00 -124.62 -55.38 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CA LYS C 199 " pdb=" C LYS C 199 " pdb=" N GLU C 200 " pdb=" CA GLU C 200 " ideal model delta harmonic sigma weight residual -180.00 -146.70 -33.30 0 5.00e+00 4.00e-02 4.43e+01 dihedral pdb=" CA PHE B 863 " pdb=" C PHE B 863 " pdb=" N PHE B 864 " pdb=" CA PHE B 864 " ideal model delta harmonic sigma weight residual -180.00 -153.59 -26.41 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 14265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2382 0.044 - 0.087: 857 0.087 - 0.131: 225 0.131 - 0.175: 16 0.175 - 0.218: 2 Chirality restraints: 3482 Sorted by residual: chirality pdb=" CB VAL C 915 " pdb=" CA VAL C 915 " pdb=" CG1 VAL C 915 " pdb=" CG2 VAL C 915 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASN A 784 " pdb=" N ASN A 784 " pdb=" C ASN A 784 " pdb=" CB ASN A 784 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA ILE C 792 " pdb=" N ILE C 792 " pdb=" C ILE C 792 " pdb=" CB ILE C 792 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 3479 not shown) Planarity restraints: 4313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 915 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.02e+01 pdb=" N PRO C 916 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO C 916 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 916 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 774 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 775 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 775 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 775 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 911 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO B 912 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 912 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 912 " -0.022 5.00e-02 4.00e+02 ... (remaining 4310 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 490 2.60 - 3.17: 21203 3.17 - 3.75: 34464 3.75 - 4.32: 43622 4.32 - 4.90: 70083 Nonbonded interactions: 169862 Sorted by model distance: nonbonded pdb=" OG SER C 98 " pdb=" OG1 THR C 687 " model vdw 2.023 3.040 nonbonded pdb=" O MET C 96 " pdb=" OG1 THR C 99 " model vdw 2.081 3.040 nonbonded pdb=" OD1 ASN A 605 " pdb=" OG SER A 773 " model vdw 2.088 3.040 nonbonded pdb=" O MET B 96 " pdb=" OG1 THR B 99 " model vdw 2.096 3.040 nonbonded pdb=" N ASP C 460 " pdb=" OD1 ASP C 460 " model vdw 2.112 3.120 ... (remaining 169857 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 6 through 1017) selection = (chain 'B' and (resid 6 through 329 or resid 331 through 1017)) selection = (chain 'C' and (resid 6 through 329 or resid 331 through 1017)) } 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: 0.270 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: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.170 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 24025 Z= 0.257 Angle : 0.689 8.686 32656 Z= 0.390 Chirality : 0.046 0.218 3482 Planarity : 0.005 0.112 4313 Dihedral : 14.517 86.696 8784 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.07 % Favored : 84.93 % Rotamer: Outliers : 12.49 % Allowed : 12.65 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.04 % 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: -2.86 (0.15), residues: 2953 helix: 0.11 (0.33), residues: 269 sheet: -0.85 (0.21), residues: 592 loop : -2.71 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 92 TYR 0.020 0.002 TYR B 650 PHE 0.022 0.002 PHE C 749 TRP 0.015 0.002 TRP A 747 HIS 0.008 0.001 HIS C 968 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.26 (24025) covalent geometry : angle 0.68862 / 0.39 (32656) hydrogen bonds : bond 0.18278 / 12.16 ( 580) hydrogen bonds : angle 6.90401 / 4.69 ( 1365) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 316 poor density : 583 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.6107 (t80) REVERT: A 63 ARG cc_start: 0.6024 (mtt180) cc_final: 0.5791 (mtt180) REVERT: A 84 PHE cc_start: 0.7985 (m-80) cc_final: 0.7351 (m-10) REVERT: A 166 LYS cc_start: 0.7929 (mmtt) cc_final: 0.7652 (mmmt) REVERT: A 187 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7242 (pm20) REVERT: A 237 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7969 (mpp) REVERT: A 241 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.8777 (t80) REVERT: A 365 ASP cc_start: 0.8019 (p0) cc_final: 0.7533 (p0) REVERT: A 370 TYR cc_start: 0.8425 (t80) cc_final: 0.8057 (t80) REVERT: A 371 LYS cc_start: 0.8923 (mttt) cc_final: 0.8698 (mmmt) REVERT: A 385 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.6258 (mm-40) REVERT: A 386 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7820 (pm20) REVERT: A 422 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7551 (pp30) REVERT: A 465 ASP cc_start: 0.7705 (m-30) cc_final: 0.7352 (t0) REVERT: A 475 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.5612 (mt-10) REVERT: A 481 TYR cc_start: 0.8186 (m-80) cc_final: 0.7296 (m-10) REVERT: A 644 LEU cc_start: 0.7987 (mt) cc_final: 0.7556 (mt) REVERT: A 702 MET cc_start: 0.7833 (ttm) cc_final: 0.7541 (ttm) REVERT: A 744 PHE cc_start: 0.8241 (t80) cc_final: 0.7077 (t80) REVERT: A 768 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.6475 (t80) REVERT: A 774 ILE cc_start: 0.8247 (mt) cc_final: 0.8017 (mt) REVERT: A 787 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.5071 (m-10) REVERT: A 829 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8395 (m-40) REVERT: A 839 MET cc_start: 0.5680 (mmm) cc_final: 0.5332 (tpp) REVERT: A 860 MET cc_start: 0.7569 (ttm) cc_final: 0.7349 (ttp) REVERT: A 909 GLN cc_start: 0.7593 (pt0) cc_final: 0.7381 (pm20) REVERT: A 914 ASN cc_start: 0.7661 (p0) cc_final: 0.7277 (p0) REVERT: A 936 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: A 993 ASP cc_start: 0.7411 (t70) cc_final: 0.7137 (t70) REVERT: B 15 ILE cc_start: 0.8747 (mt) cc_final: 0.8535 (pt) REVERT: B 18 GLN cc_start: 0.7520 (mt0) cc_final: 0.7152 (mt0) REVERT: B 65 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8635 (p) REVERT: B 66 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7149 (tp) REVERT: B 167 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8078 (mttm) REVERT: B 232 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6440 (mtpp) REVERT: B 235 THR cc_start: 0.8627 (m) cc_final: 0.8323 (p) REVERT: B 244 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.6580 (t80) REVERT: B 251 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7644 (t0) REVERT: B 382 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.6714 (tmt) REVERT: B 406 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.5343 (t80) REVERT: B 465 ASP cc_start: 0.7435 (m-30) cc_final: 0.7021 (t70) REVERT: B 529 MET cc_start: 0.6442 (OUTLIER) cc_final: 0.6177 (mtt) REVERT: B 571 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7235 (m-30) REVERT: B 598 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7132 (tmm) REVERT: B 655 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7638 (tpp80) REVERT: B 787 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6572 (m-10) REVERT: B 824 ASN cc_start: 0.7422 (OUTLIER) cc_final: 0.7183 (m-40) REVERT: B 840 LEU cc_start: 0.7599 (mt) cc_final: 0.7277 (mt) REVERT: B 905 MET cc_start: 0.7744 (ptm) cc_final: 0.7146 (ptm) REVERT: B 917 TYR cc_start: 0.7355 (m-80) cc_final: 0.7048 (m-80) REVERT: B 937 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7811 (mmm160) REVERT: B 972 MET cc_start: 0.7457 (mtp) cc_final: 0.7228 (mtm) REVERT: C 12 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.6138 (t80) REVERT: C 21 SER cc_start: 0.8363 (p) cc_final: 0.7804 (t) REVERT: C 39 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.7189 (t80) REVERT: C 98 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8053 (t) REVERT: C 166 LYS cc_start: 0.8154 (ptpt) cc_final: 0.7886 (mtpt) REVERT: C 232 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6167 (mtpt) REVERT: C 235 THR cc_start: 0.8399 (m) cc_final: 0.8035 (p) REVERT: C 244 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.5994 (p90) REVERT: C 288 VAL cc_start: 0.7409 (OUTLIER) cc_final: 0.6841 (p) REVERT: C 371 LYS cc_start: 0.8844 (mttt) cc_final: 0.8404 (mmmt) REVERT: C 409 SER cc_start: 0.8011 (t) cc_final: 0.7474 (m) REVERT: C 412 ASN cc_start: 0.7332 (OUTLIER) cc_final: 0.6617 (p0) REVERT: C 483 PHE cc_start: 0.8339 (m-80) cc_final: 0.8126 (m-80) REVERT: C 529 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6273 (mtp) REVERT: C 554 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8736 (tt) REVERT: C 568 ASN cc_start: 0.8828 (m-40) cc_final: 0.8590 (m-40) REVERT: C 573 MET cc_start: 0.8083 (mmt) cc_final: 0.7684 (tpp) REVERT: C 644 LEU cc_start: 0.7899 (mt) cc_final: 0.7338 (mt) REVERT: C 671 ARG cc_start: 0.7455 (ttm170) cc_final: 0.6727 (ttt-90) REVERT: C 744 PHE cc_start: 0.8289 (t80) cc_final: 0.7489 (t80) REVERT: C 811 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: C 833 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7334 (p0) REVERT: C 882 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: C 914 ASN cc_start: 0.7491 (p0) cc_final: 0.7045 (t0) outliers start: 316 outliers final: 168 residues processed: 828 average time/residue: 0.1588 time to fit residues: 209.3788 Evaluate side-chains 658 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 451 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 829 ASN Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 834 TRP Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 GLN Chi-restraints excluded: chain A residue 873 GLN Chi-restraints excluded: chain A residue 889 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 937 ARG Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 955 THR Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 406 TYR Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 519 ASN Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 778 ASP Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 787 PHE Chi-restraints excluded: chain B residue 803 ASN Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain B residue 829 ASN Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 834 TRP Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 851 TYR Chi-restraints excluded: chain B residue 873 GLN Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 876 ASP Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 937 ARG Chi-restraints excluded: chain B residue 945 SER Chi-restraints excluded: chain B residue 947 ASN Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1001 HIS Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain C residue 12 TYR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 455 TRP Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 471 ASN Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain C residue 652 TRP Chi-restraints excluded: chain C residue 657 ASP Chi-restraints excluded: chain C residue 663 GLN Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 749 PHE Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 778 ASP Chi-restraints excluded: chain C residue 787 PHE Chi-restraints excluded: chain C residue 803 ASN Chi-restraints excluded: chain C residue 811 GLU Chi-restraints excluded: chain C residue 812 PHE Chi-restraints excluded: chain C residue 828 CYS Chi-restraints excluded: chain C residue 833 ASP Chi-restraints excluded: chain C residue 834 TRP Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 882 ASP Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 947 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN A 838 GLN B 173 GLN B 187 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN C 439 GLN C 456 ASN ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 588 ASN ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 668 ASN C 693 HIS C 838 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.158089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.122474 restraints weight = 33349.685| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 4.87 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24025 Z= 0.125 Angle : 0.610 8.341 32656 Z= 0.324 Chirality : 0.045 0.239 3482 Planarity : 0.005 0.097 4313 Dihedral : 10.939 63.737 3684 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 7.75 % Allowed : 19.17 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.04 % 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: -2.39 (0.15), residues: 2953 helix: 0.45 (0.34), residues: 274 sheet: -0.56 (0.22), residues: 578 loop : -2.36 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 246 TYR 0.022 0.001 TYR B 481 PHE 0.023 0.002 PHE A 483 TRP 0.017 0.002 TRP A 747 HIS 0.005 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (24025) covalent geometry : angle 0.60984 / 0.32 (32656) hydrogen bonds : bond 0.04167 / 2.80 ( 580) hydrogen bonds : angle 5.99233 / 4.11 ( 1365) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 546 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8811 (p) REVERT: A 84 PHE cc_start: 0.7974 (m-80) cc_final: 0.7306 (m-10) REVERT: A 94 LEU cc_start: 0.8105 (tp) cc_final: 0.7711 (tp) REVERT: A 166 LYS cc_start: 0.8435 (mmtt) cc_final: 0.8130 (mmmt) REVERT: A 187 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6054 (pp30) REVERT: A 222 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7220 (mm-30) REVERT: A 237 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8352 (mpp) REVERT: A 365 ASP cc_start: 0.8150 (p0) cc_final: 0.7747 (p0) REVERT: A 370 TYR cc_start: 0.8837 (t80) cc_final: 0.8035 (t80) REVERT: A 371 LYS cc_start: 0.9342 (mttt) cc_final: 0.8411 (mmmt) REVERT: A 422 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7383 (pp30) REVERT: A 465 ASP cc_start: 0.8375 (m-30) cc_final: 0.8088 (t70) REVERT: A 474 THR cc_start: 0.7082 (p) cc_final: 0.6701 (p) REVERT: A 475 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6018 (mt-10) REVERT: A 476 ASP cc_start: 0.8915 (t0) cc_final: 0.8310 (t0) REVERT: A 481 TYR cc_start: 0.8680 (m-80) cc_final: 0.7599 (m-10) REVERT: A 483 PHE cc_start: 0.8969 (m-80) cc_final: 0.8680 (m-80) REVERT: A 601 VAL cc_start: 0.8978 (t) cc_final: 0.8579 (p) REVERT: A 617 MET cc_start: 0.9047 (mtt) cc_final: 0.8746 (mmm) REVERT: A 644 LEU cc_start: 0.7972 (mt) cc_final: 0.7563 (mt) REVERT: A 668 ASN cc_start: 0.8250 (p0) cc_final: 0.7981 (p0) REVERT: A 691 MET cc_start: 0.8284 (ttm) cc_final: 0.7570 (tmm) REVERT: A 702 MET cc_start: 0.8089 (ttm) cc_final: 0.7702 (ttm) REVERT: A 744 PHE cc_start: 0.8442 (t80) cc_final: 0.7344 (t80) REVERT: A 768 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6427 (t80) REVERT: A 787 PHE cc_start: 0.7059 (OUTLIER) cc_final: 0.4727 (m-10) REVERT: A 833 ASP cc_start: 0.8286 (m-30) cc_final: 0.8080 (t0) REVERT: A 837 VAL cc_start: 0.8205 (t) cc_final: 0.7962 (t) REVERT: A 839 MET cc_start: 0.4452 (mmm) cc_final: 0.4115 (mmm) REVERT: A 882 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7738 (t0) REVERT: A 907 GLU cc_start: 0.6995 (pm20) cc_final: 0.6681 (pm20) REVERT: A 909 GLN cc_start: 0.7806 (pt0) cc_final: 0.7352 (pm20) REVERT: A 914 ASN cc_start: 0.8134 (p0) cc_final: 0.7614 (t0) REVERT: A 965 ASN cc_start: 0.9333 (m-40) cc_final: 0.8289 (t0) REVERT: A 979 MET cc_start: 0.7545 (mtp) cc_final: 0.7343 (mtt) REVERT: A 993 ASP cc_start: 0.7940 (t70) cc_final: 0.7434 (t0) REVERT: B 15 ILE cc_start: 0.8461 (mt) cc_final: 0.8124 (pt) REVERT: B 18 GLN cc_start: 0.7821 (mt0) cc_final: 0.7367 (mt0) REVERT: B 66 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6492 (tp) REVERT: B 219 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8812 (p0) REVERT: B 232 LYS cc_start: 0.6794 (OUTLIER) cc_final: 0.5973 (mtpp) REVERT: B 235 THR cc_start: 0.8939 (m) cc_final: 0.8278 (p) REVERT: B 251 ASN cc_start: 0.7210 (OUTLIER) cc_final: 0.6941 (t0) REVERT: B 260 GLN cc_start: 0.8324 (pt0) cc_final: 0.8098 (pp30) REVERT: B 270 MET cc_start: 0.7627 (mtt) cc_final: 0.7372 (mtt) REVERT: B 357 GLU cc_start: 0.8663 (pt0) cc_final: 0.8308 (pm20) REVERT: B 365 ASP cc_start: 0.8951 (p0) cc_final: 0.8246 (p0) REVERT: B 371 LYS cc_start: 0.9211 (mmtt) cc_final: 0.8344 (mmmt) REVERT: B 406 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.5532 (t80) REVERT: B 465 ASP cc_start: 0.7878 (m-30) cc_final: 0.7478 (t70) REVERT: B 526 ASN cc_start: 0.8516 (p0) cc_final: 0.8241 (p0) REVERT: B 529 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6177 (mtt) REVERT: B 573 MET cc_start: 0.8355 (mmt) cc_final: 0.7948 (tpp) REVERT: B 655 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7418 (tpp80) REVERT: B 668 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7588 (p0) REVERT: B 689 PHE cc_start: 0.8930 (t80) cc_final: 0.8447 (t80) REVERT: B 730 THR cc_start: 0.9149 (p) cc_final: 0.8784 (m) REVERT: B 741 TRP cc_start: 0.8748 (m100) cc_final: 0.7174 (m100) REVERT: B 840 LEU cc_start: 0.8197 (mt) cc_final: 0.7888 (mt) REVERT: B 889 ILE cc_start: 0.8433 (mt) cc_final: 0.8200 (tp) REVERT: B 907 GLU cc_start: 0.7382 (pm20) cc_final: 0.7104 (pm20) REVERT: B 917 TYR cc_start: 0.6994 (m-80) cc_final: 0.6755 (m-80) REVERT: B 936 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: B 937 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6616 (mmm160) REVERT: B 949 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8239 (ttt) REVERT: B 979 MET cc_start: 0.7939 (mtp) cc_final: 0.7696 (mtt) REVERT: C 22 GLU cc_start: 0.7652 (mp0) cc_final: 0.7210 (mp0) REVERT: C 90 ASP cc_start: 0.9176 (p0) cc_final: 0.8843 (p0) REVERT: C 232 LYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5291 (mtpt) REVERT: C 235 THR cc_start: 0.8801 (m) cc_final: 0.8099 (p) REVERT: C 260 GLN cc_start: 0.8122 (tt0) cc_final: 0.7769 (tm-30) REVERT: C 270 MET cc_start: 0.7605 (mtp) cc_final: 0.7217 (mtt) REVERT: C 329 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.5918 (pp) REVERT: C 412 ASN cc_start: 0.6511 (OUTLIER) cc_final: 0.5965 (p0) REVERT: C 529 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.6577 (mtp) REVERT: C 573 MET cc_start: 0.8163 (mmt) cc_final: 0.7835 (tpp) REVERT: C 644 LEU cc_start: 0.8004 (mt) cc_final: 0.7412 (mt) REVERT: C 671 ARG cc_start: 0.6918 (ttm170) cc_final: 0.6543 (ttt-90) REVERT: C 744 PHE cc_start: 0.8234 (t80) cc_final: 0.6762 (t80) REVERT: C 756 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8362 (mt-10) REVERT: C 786 THR cc_start: 0.9020 (p) cc_final: 0.8790 (t) REVERT: C 845 ILE cc_start: 0.8866 (mt) cc_final: 0.8561 (mt) REVERT: C 860 MET cc_start: 0.8408 (ttp) cc_final: 0.8055 (ttp) REVERT: C 889 ILE cc_start: 0.8667 (mt) cc_final: 0.8405 (tp) REVERT: C 909 GLN cc_start: 0.7520 (pm20) cc_final: 0.7312 (pm20) REVERT: C 914 ASN cc_start: 0.7774 (p0) cc_final: 0.7488 (p0) REVERT: C 927 SER cc_start: 0.8017 (p) cc_final: 0.7626 (t) REVERT: C 955 THR cc_start: 0.8429 (t) cc_final: 0.8147 (t) outliers start: 196 outliers final: 114 residues processed: 696 average time/residue: 0.1593 time to fit residues: 176.2822 Evaluate side-chains 602 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 465 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 834 TRP Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 GLN Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 937 ARG Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 406 TYR Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 757 THR Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 834 TRP Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 851 TYR Chi-restraints excluded: chain B residue 873 GLN Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 937 ARG Chi-restraints excluded: chain B residue 949 MET Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1001 HIS Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 455 TRP Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 652 TRP Chi-restraints excluded: chain C residue 663 GLN Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 778 ASP Chi-restraints excluded: chain C residue 787 PHE Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 834 TRP Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 1001 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 0.9980 chunk 230 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 179 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 216 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 124 optimal weight: 50.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN A 838 GLN B 42 ASN B 173 GLN ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 ASN ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 GLN ** 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 = 0.4201 r_free = 0.4201 target = 0.161329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.123619 restraints weight = 33833.769| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 4.96 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24025 Z= 0.133 Angle : 0.589 9.387 32656 Z= 0.312 Chirality : 0.046 0.352 3482 Planarity : 0.005 0.104 4313 Dihedral : 9.522 64.052 3502 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 7.87 % Allowed : 20.51 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.04 % 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: -2.26 (0.15), residues: 2953 helix: 0.50 (0.34), residues: 280 sheet: -0.45 (0.22), residues: 576 loop : -2.27 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 246 TYR 0.017 0.001 TYR C 650 PHE 0.018 0.001 PHE C 483 TRP 0.019 0.002 TRP B 455 HIS 0.008 0.001 HIS C 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (24025) covalent geometry : angle 0.58916 / 0.31 (32656) hydrogen bonds : bond 0.03959 / 2.67 ( 580) hydrogen bonds : angle 5.81780 / 3.96 ( 1365) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 491 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.6223 (OUTLIER) cc_final: 0.5628 (t80) REVERT: A 49 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8806 (p) REVERT: A 84 PHE cc_start: 0.7887 (m-80) cc_final: 0.7271 (m-10) REVERT: A 166 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8031 (mmmt) REVERT: A 187 GLN cc_start: 0.6631 (OUTLIER) cc_final: 0.6010 (pp30) REVERT: A 205 LYS cc_start: 0.8958 (pttt) cc_final: 0.8601 (ptpp) REVERT: A 219 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8568 (p0) REVERT: A 220 GLU cc_start: 0.8514 (pm20) cc_final: 0.8290 (pm20) REVERT: A 222 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7124 (mm-30) REVERT: A 237 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8158 (mpp) REVERT: A 257 MET cc_start: 0.7577 (mmp) cc_final: 0.7006 (tpp) REVERT: A 270 MET cc_start: 0.7286 (mtt) cc_final: 0.7064 (mtt) REVERT: A 365 ASP cc_start: 0.8189 (p0) cc_final: 0.7685 (p0) REVERT: A 370 TYR cc_start: 0.8658 (t80) cc_final: 0.7772 (t80) REVERT: A 371 LYS cc_start: 0.9315 (mttt) cc_final: 0.8276 (mmmt) REVERT: A 385 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.6939 (mm-40) REVERT: A 422 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7259 (pp30) REVERT: A 465 ASP cc_start: 0.8329 (m-30) cc_final: 0.8045 (t70) REVERT: A 474 THR cc_start: 0.7147 (p) cc_final: 0.6809 (p) REVERT: A 476 ASP cc_start: 0.8895 (t0) cc_final: 0.8377 (t0) REVERT: A 481 TYR cc_start: 0.8657 (m-80) cc_final: 0.7613 (m-10) REVERT: A 614 TYR cc_start: 0.8375 (t80) cc_final: 0.7616 (t80) REVERT: A 644 LEU cc_start: 0.7926 (mt) cc_final: 0.7492 (mt) REVERT: A 651 GLU cc_start: 0.6701 (tt0) cc_final: 0.6133 (pt0) REVERT: A 668 ASN cc_start: 0.8341 (p0) cc_final: 0.8027 (p0) REVERT: A 691 MET cc_start: 0.8143 (ttm) cc_final: 0.7454 (tmm) REVERT: A 702 MET cc_start: 0.7940 (ttm) cc_final: 0.7510 (ttm) REVERT: A 714 ASP cc_start: 0.8927 (t70) cc_final: 0.8627 (t70) REVERT: A 744 PHE cc_start: 0.8438 (t80) cc_final: 0.7477 (t80) REVERT: A 768 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6535 (t80) REVERT: A 787 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.4616 (m-10) REVERT: A 833 ASP cc_start: 0.8533 (m-30) cc_final: 0.8072 (t0) REVERT: A 837 VAL cc_start: 0.8295 (t) cc_final: 0.7861 (m) REVERT: A 839 MET cc_start: 0.4174 (mmm) cc_final: 0.3832 (mmm) REVERT: A 858 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7328 (p0) REVERT: A 882 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7673 (t0) REVERT: A 909 GLN cc_start: 0.7881 (pt0) cc_final: 0.7011 (pm20) REVERT: A 914 ASN cc_start: 0.8002 (p0) cc_final: 0.7341 (p0) REVERT: A 965 ASN cc_start: 0.9338 (m-40) cc_final: 0.8346 (t0) REVERT: A 979 MET cc_start: 0.7497 (mtp) cc_final: 0.7034 (mtp) REVERT: A 993 ASP cc_start: 0.7884 (t70) cc_final: 0.7417 (t0) REVERT: B 15 ILE cc_start: 0.8398 (mt) cc_final: 0.8049 (pt) REVERT: B 18 GLN cc_start: 0.7587 (mt0) cc_final: 0.7127 (mt0) REVERT: B 66 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6165 (tp) REVERT: B 173 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7981 (mp10) REVERT: B 219 ASN cc_start: 0.9025 (OUTLIER) cc_final: 0.8665 (p0) REVERT: B 232 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.5818 (mtpp) REVERT: B 235 THR cc_start: 0.8837 (m) cc_final: 0.8249 (p) REVERT: B 251 ASN cc_start: 0.7136 (OUTLIER) cc_final: 0.6874 (t0) REVERT: B 270 MET cc_start: 0.7447 (mtt) cc_final: 0.7141 (mtt) REVERT: B 365 ASP cc_start: 0.8850 (p0) cc_final: 0.8458 (p0) REVERT: B 371 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8340 (mmmt) REVERT: B 391 ARG cc_start: 0.8208 (mtp180) cc_final: 0.7809 (mtp180) REVERT: B 406 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.5414 (t80) REVERT: B 413 MET cc_start: 0.7057 (ttp) cc_final: 0.6737 (ttp) REVERT: B 509 TRP cc_start: 0.7335 (m100) cc_final: 0.7116 (m100) REVERT: B 529 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.5817 (mtt) REVERT: B 573 MET cc_start: 0.8395 (mmt) cc_final: 0.8063 (tpp) REVERT: B 617 MET cc_start: 0.8811 (tpp) cc_final: 0.8489 (tpp) REVERT: B 652 TRP cc_start: 0.7652 (OUTLIER) cc_final: 0.7441 (t-100) REVERT: B 655 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7260 (tpp80) REVERT: B 689 PHE cc_start: 0.8967 (t80) cc_final: 0.8489 (t80) REVERT: B 730 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8618 (m) REVERT: B 739 ARG cc_start: 0.7693 (tmm-80) cc_final: 0.7346 (tmm-80) REVERT: B 833 ASP cc_start: 0.8231 (m-30) cc_final: 0.8015 (t0) REVERT: B 840 LEU cc_start: 0.8195 (mt) cc_final: 0.7887 (mt) REVERT: B 889 ILE cc_start: 0.8326 (mt) cc_final: 0.8083 (tp) REVERT: B 907 GLU cc_start: 0.7484 (pm20) cc_final: 0.7253 (pm20) REVERT: B 917 TYR cc_start: 0.6871 (m-80) cc_final: 0.6651 (m-80) REVERT: B 936 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8171 (m-30) REVERT: B 979 MET cc_start: 0.7710 (mtp) cc_final: 0.7321 (mtt) REVERT: C 18 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7341 (mm-40) REVERT: C 22 GLU cc_start: 0.7987 (mp0) cc_final: 0.7705 (mp0) REVERT: C 90 ASP cc_start: 0.9077 (p0) cc_final: 0.8811 (p0) REVERT: C 166 LYS cc_start: 0.8635 (ptpt) cc_final: 0.8385 (mtpt) REVERT: C 219 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8209 (p0) REVERT: C 232 LYS cc_start: 0.6032 (OUTLIER) cc_final: 0.5155 (mtpt) REVERT: C 235 THR cc_start: 0.8744 (m) cc_final: 0.8029 (p) REVERT: C 270 MET cc_start: 0.7440 (mtp) cc_final: 0.6976 (mtt) REVERT: C 329 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6416 (pp) REVERT: C 365 ASP cc_start: 0.8792 (p0) cc_final: 0.8442 (p0) REVERT: C 371 LYS cc_start: 0.9233 (mtpt) cc_final: 0.8846 (mtpp) REVERT: C 374 LYS cc_start: 0.8851 (mmmt) cc_final: 0.8418 (tppt) REVERT: C 412 ASN cc_start: 0.6660 (OUTLIER) cc_final: 0.6225 (p0) REVERT: C 512 ASP cc_start: 0.8880 (t0) cc_final: 0.8345 (t70) REVERT: C 529 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.6545 (mtp) REVERT: C 554 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9110 (tt) REVERT: C 573 MET cc_start: 0.8124 (mmt) cc_final: 0.7819 (tpp) REVERT: C 617 MET cc_start: 0.9057 (tpp) cc_final: 0.8791 (tpt) REVERT: C 644 LEU cc_start: 0.7900 (mt) cc_final: 0.7317 (mt) REVERT: C 669 ASP cc_start: 0.8773 (t70) cc_final: 0.8252 (t70) REVERT: C 671 ARG cc_start: 0.6952 (ttm170) cc_final: 0.6536 (ttp80) REVERT: C 744 PHE cc_start: 0.8144 (t80) cc_final: 0.6494 (t80) REVERT: C 756 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8372 (mt-10) REVERT: C 839 MET cc_start: 0.5384 (mmm) cc_final: 0.5053 (mmm) REVERT: C 860 MET cc_start: 0.8254 (ttp) cc_final: 0.7879 (ttp) REVERT: C 889 ILE cc_start: 0.8590 (mt) cc_final: 0.8282 (tp) REVERT: C 905 MET cc_start: 0.7478 (ptm) cc_final: 0.7195 (ptp) REVERT: C 907 GLU cc_start: 0.7521 (pm20) cc_final: 0.7280 (pm20) REVERT: C 909 GLN cc_start: 0.7491 (pm20) cc_final: 0.7190 (pm20) REVERT: C 914 ASN cc_start: 0.7822 (p0) cc_final: 0.7483 (p0) REVERT: C 927 SER cc_start: 0.7960 (p) cc_final: 0.7589 (t) REVERT: C 941 ARG cc_start: 0.6674 (OUTLIER) cc_final: 0.6138 (mtp-110) REVERT: C 955 THR cc_start: 0.8194 (t) cc_final: 0.7837 (t) REVERT: C 979 MET cc_start: 0.8307 (mtt) cc_final: 0.8080 (mtp) REVERT: C 993 ASP cc_start: 0.7158 (t70) cc_final: 0.6713 (t0) outliers start: 199 outliers final: 128 residues processed: 642 average time/residue: 0.1613 time to fit residues: 165.1283 Evaluate side-chains 616 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 459 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 834 TRP Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 GLN Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 937 ARG Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 406 TYR Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 652 TRP Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 757 THR Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 834 TRP Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 851 TYR Chi-restraints excluded: chain B residue 873 GLN Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 455 TRP Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 471 ASN Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 652 TRP Chi-restraints excluded: chain C residue 663 GLN Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 698 THR Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 778 ASP Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 817 SER Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 834 TRP Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 935 CYS Chi-restraints excluded: chain C residue 941 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 94 optimal weight: 9.9990 chunk 286 optimal weight: 0.9990 chunk 292 optimal weight: 3.9990 chunk 231 optimal weight: 0.8980 chunk 218 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 chunk 274 optimal weight: 0.9980 chunk 271 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 GLN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 HIS B 386 GLN ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.159743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.124061 restraints weight = 32593.841| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 4.85 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24025 Z= 0.135 Angle : 0.591 10.357 32656 Z= 0.309 Chirality : 0.045 0.320 3482 Planarity : 0.005 0.112 4313 Dihedral : 9.125 65.821 3478 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 8.02 % Allowed : 21.26 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.04 % 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: -2.21 (0.15), residues: 2953 helix: 0.51 (0.34), residues: 281 sheet: -0.43 (0.22), residues: 584 loop : -2.23 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 92 TYR 0.017 0.001 TYR C 650 PHE 0.031 0.001 PHE C 113 TRP 0.019 0.002 TRP B 455 HIS 0.008 0.001 HIS A 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (24025) covalent geometry : angle 0.59115 / 0.31 (32656) hydrogen bonds : bond 0.03883 / 2.62 ( 580) hydrogen bonds : angle 5.74461 / 3.90 ( 1365) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 481 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.6386 (OUTLIER) cc_final: 0.5781 (t80) REVERT: A 49 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8863 (p) REVERT: A 84 PHE cc_start: 0.8045 (m-80) cc_final: 0.7428 (m-10) REVERT: A 94 LEU cc_start: 0.8034 (tp) cc_final: 0.7698 (tp) REVERT: A 166 LYS cc_start: 0.8421 (mmtt) cc_final: 0.8029 (mmmt) REVERT: A 187 GLN cc_start: 0.6708 (OUTLIER) cc_final: 0.6092 (pp30) REVERT: A 205 LYS cc_start: 0.8914 (pttt) cc_final: 0.8528 (ptpp) REVERT: A 219 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8599 (p0) REVERT: A 246 ARG cc_start: 0.8361 (ptt-90) cc_final: 0.8101 (mtm-85) REVERT: A 270 MET cc_start: 0.7416 (mtt) cc_final: 0.7169 (mtt) REVERT: A 365 ASP cc_start: 0.8201 (p0) cc_final: 0.7703 (p0) REVERT: A 370 TYR cc_start: 0.8655 (t80) cc_final: 0.7410 (t80) REVERT: A 371 LYS cc_start: 0.9326 (mttt) cc_final: 0.8386 (mmmt) REVERT: A 400 ASN cc_start: 0.8815 (m110) cc_final: 0.8588 (m110) REVERT: A 422 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7278 (pp30) REVERT: A 465 ASP cc_start: 0.8345 (m-30) cc_final: 0.8076 (t70) REVERT: A 474 THR cc_start: 0.7251 (p) cc_final: 0.6915 (p) REVERT: A 475 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6154 (mt-10) REVERT: A 476 ASP cc_start: 0.8829 (t0) cc_final: 0.8349 (t0) REVERT: A 481 TYR cc_start: 0.8601 (m-80) cc_final: 0.8396 (m-10) REVERT: A 614 TYR cc_start: 0.8388 (t80) cc_final: 0.7671 (t80) REVERT: A 644 LEU cc_start: 0.7942 (mt) cc_final: 0.7506 (mt) REVERT: A 668 ASN cc_start: 0.8338 (p0) cc_final: 0.8003 (p0) REVERT: A 691 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7452 (tmm) REVERT: A 702 MET cc_start: 0.7994 (ttm) cc_final: 0.7554 (ttm) REVERT: A 714 ASP cc_start: 0.9029 (t70) cc_final: 0.8722 (t70) REVERT: A 744 PHE cc_start: 0.8584 (t80) cc_final: 0.7341 (t80) REVERT: A 747 TRP cc_start: 0.7287 (m-90) cc_final: 0.7008 (m-90) REVERT: A 768 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.6459 (t80) REVERT: A 787 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.4670 (m-10) REVERT: A 793 THR cc_start: 0.7242 (OUTLIER) cc_final: 0.6906 (p) REVERT: A 833 ASP cc_start: 0.8375 (m-30) cc_final: 0.7978 (t0) REVERT: A 837 VAL cc_start: 0.8370 (t) cc_final: 0.8081 (t) REVERT: A 839 MET cc_start: 0.4288 (mmm) cc_final: 0.3953 (mmm) REVERT: A 848 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8207 (mm-40) REVERT: A 882 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7677 (t0) REVERT: A 909 GLN cc_start: 0.7738 (pt0) cc_final: 0.6981 (pm20) REVERT: A 914 ASN cc_start: 0.8042 (p0) cc_final: 0.7365 (p0) REVERT: A 949 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7539 (mtt) REVERT: A 979 MET cc_start: 0.7350 (mtp) cc_final: 0.6942 (mtp) REVERT: A 993 ASP cc_start: 0.7806 (t70) cc_final: 0.7401 (t0) REVERT: B 15 ILE cc_start: 0.8421 (mt) cc_final: 0.8062 (pt) REVERT: B 18 GLN cc_start: 0.7693 (mt0) cc_final: 0.7224 (mt0) REVERT: B 60 ARG cc_start: 0.5722 (mtt180) cc_final: 0.5438 (mtt90) REVERT: B 66 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6262 (tp) REVERT: B 200 GLU cc_start: 0.8037 (pm20) cc_final: 0.6686 (pm20) REVERT: B 219 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8571 (p0) REVERT: B 232 LYS cc_start: 0.6702 (OUTLIER) cc_final: 0.5930 (mtpp) REVERT: B 235 THR cc_start: 0.8887 (m) cc_final: 0.8303 (p) REVERT: B 251 ASN cc_start: 0.7263 (OUTLIER) cc_final: 0.6997 (t0) REVERT: B 267 GLN cc_start: 0.8130 (tp40) cc_final: 0.7896 (tp40) REVERT: B 270 MET cc_start: 0.7527 (mtt) cc_final: 0.7228 (mtt) REVERT: B 357 GLU cc_start: 0.8608 (pt0) cc_final: 0.8366 (pt0) REVERT: B 365 ASP cc_start: 0.8917 (p0) cc_final: 0.8511 (p0) REVERT: B 371 LYS cc_start: 0.9089 (mmtt) cc_final: 0.8259 (mmmt) REVERT: B 391 ARG cc_start: 0.8180 (mtp180) cc_final: 0.7814 (mtp180) REVERT: B 406 TYR cc_start: 0.7190 (OUTLIER) cc_final: 0.5391 (t80) REVERT: B 413 MET cc_start: 0.7109 (ttp) cc_final: 0.6782 (ttp) REVERT: B 481 TYR cc_start: 0.8700 (m-10) cc_final: 0.8401 (m-10) REVERT: B 498 LYS cc_start: 0.8030 (tppp) cc_final: 0.7253 (ttpt) REVERT: B 529 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.5908 (mtt) REVERT: B 573 MET cc_start: 0.8421 (mmt) cc_final: 0.8117 (tpp) REVERT: B 617 MET cc_start: 0.8760 (tpp) cc_final: 0.8394 (tpp) REVERT: B 652 TRP cc_start: 0.7751 (OUTLIER) cc_final: 0.7488 (t-100) REVERT: B 655 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7232 (tpp80) REVERT: B 689 PHE cc_start: 0.8903 (t80) cc_final: 0.8381 (t80) REVERT: B 739 ARG cc_start: 0.7867 (tmm-80) cc_final: 0.7482 (tmm-80) REVERT: B 747 TRP cc_start: 0.8194 (OUTLIER) cc_final: 0.7886 (m-10) REVERT: B 756 GLU cc_start: 0.8608 (pt0) cc_final: 0.8289 (pt0) REVERT: B 770 TYR cc_start: 0.7630 (t80) cc_final: 0.7422 (t80) REVERT: B 840 LEU cc_start: 0.8199 (mt) cc_final: 0.7893 (mt) REVERT: B 889 ILE cc_start: 0.8280 (mt) cc_final: 0.8001 (tp) REVERT: B 907 GLU cc_start: 0.7463 (pm20) cc_final: 0.7251 (pm20) REVERT: B 917 TYR cc_start: 0.6853 (m-80) cc_final: 0.6632 (m-80) REVERT: B 977 ASP cc_start: 0.8514 (t70) cc_final: 0.8217 (t70) REVERT: B 979 MET cc_start: 0.7874 (mtp) cc_final: 0.7497 (mtt) REVERT: C 18 GLN cc_start: 0.7611 (mm-40) cc_final: 0.7120 (mm-40) REVERT: C 22 GLU cc_start: 0.7963 (mp0) cc_final: 0.7718 (mp0) REVERT: C 90 ASP cc_start: 0.9044 (p0) cc_final: 0.8824 (p0) REVERT: C 166 LYS cc_start: 0.8581 (ptpt) cc_final: 0.8296 (mtpt) REVERT: C 219 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8789 (p0) REVERT: C 232 LYS cc_start: 0.5938 (OUTLIER) cc_final: 0.4931 (mtpt) REVERT: C 235 THR cc_start: 0.8779 (m) cc_final: 0.8076 (p) REVERT: C 270 MET cc_start: 0.7474 (mtp) cc_final: 0.7084 (mtt) REVERT: C 329 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6284 (pp) REVERT: C 365 ASP cc_start: 0.8789 (p0) cc_final: 0.8400 (p0) REVERT: C 371 LYS cc_start: 0.9243 (mtpt) cc_final: 0.8937 (mtpp) REVERT: C 529 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.6605 (mtp) REVERT: C 573 MET cc_start: 0.8138 (mmt) cc_final: 0.7832 (tpp) REVERT: C 644 LEU cc_start: 0.7902 (mt) cc_final: 0.7335 (mt) REVERT: C 669 ASP cc_start: 0.8817 (t70) cc_final: 0.8442 (t70) REVERT: C 671 ARG cc_start: 0.7188 (ttm170) cc_final: 0.6654 (ttp80) REVERT: C 744 PHE cc_start: 0.8176 (t80) cc_final: 0.6511 (t80) REVERT: C 756 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8134 (mt-10) REVERT: C 786 THR cc_start: 0.8931 (p) cc_final: 0.8660 (t) REVERT: C 839 MET cc_start: 0.5587 (mmm) cc_final: 0.5186 (mmm) REVERT: C 860 MET cc_start: 0.8327 (ttp) cc_final: 0.7954 (ttp) REVERT: C 889 ILE cc_start: 0.8601 (mt) cc_final: 0.8303 (tp) REVERT: C 905 MET cc_start: 0.7579 (ptm) cc_final: 0.7278 (ptp) REVERT: C 909 GLN cc_start: 0.7404 (pm20) cc_final: 0.7143 (pm20) REVERT: C 914 ASN cc_start: 0.7961 (p0) cc_final: 0.7600 (p0) REVERT: C 927 SER cc_start: 0.7957 (p) cc_final: 0.7570 (t) REVERT: C 941 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.6304 (mtp-110) REVERT: C 955 THR cc_start: 0.8219 (t) cc_final: 0.7840 (t) outliers start: 203 outliers final: 139 residues processed: 639 average time/residue: 0.1594 time to fit residues: 163.0266 Evaluate side-chains 628 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 462 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 834 TRP Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 GLN Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1001 HIS Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 400 ASN Chi-restraints excluded: chain B residue 406 TYR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 652 TRP Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 747 TRP Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 757 THR Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 834 TRP Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 851 TYR Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 455 TRP Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 471 ASN Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 652 TRP Chi-restraints excluded: chain C residue 663 GLN Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 698 THR Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 778 ASP Chi-restraints excluded: chain C residue 787 PHE Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 799 SER Chi-restraints excluded: chain C residue 817 SER Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 834 TRP Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 935 CYS Chi-restraints excluded: chain C residue 941 ARG Chi-restraints excluded: chain C residue 947 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 86 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 GLN A 439 GLN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN A 568 ASN ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 545 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.149015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.112602 restraints weight = 35711.921| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 4.85 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 24025 Z= 0.304 Angle : 0.734 12.301 32656 Z= 0.383 Chirality : 0.049 0.361 3482 Planarity : 0.005 0.123 4313 Dihedral : 9.481 65.948 3455 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer: Outliers : 9.41 % Allowed : 21.19 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.04 % 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: -2.50 (0.15), residues: 2953 helix: 0.01 (0.33), residues: 282 sheet: -0.52 (0.22), residues: 585 loop : -2.43 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 92 TYR 0.024 0.002 TYR C 650 PHE 0.033 0.002 PHE C 749 TRP 0.019 0.002 TRP A 455 HIS 0.010 0.002 HIS C 968 Details of bonding type rmsd/Z covalent geometry : bond 0.00694 / 0.30 (24025) covalent geometry : angle 0.73359 / 0.38 (32656) hydrogen bonds : bond 0.05645 / 3.78 ( 580) hydrogen bonds : angle 6.26762 / 4.24 ( 1365) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 445 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.6511 (OUTLIER) cc_final: 0.5694 (t80) REVERT: A 49 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8840 (p) REVERT: A 84 PHE cc_start: 0.8172 (m-80) cc_final: 0.7439 (m-10) REVERT: A 166 LYS cc_start: 0.8470 (mmtt) cc_final: 0.8100 (mmmt) REVERT: A 187 GLN cc_start: 0.6677 (OUTLIER) cc_final: 0.5683 (pp30) REVERT: A 205 LYS cc_start: 0.8872 (pttt) cc_final: 0.8452 (ptpp) REVERT: A 219 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8563 (p0) REVERT: A 220 GLU cc_start: 0.8317 (pm20) cc_final: 0.8115 (pm20) REVERT: A 222 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6586 (mm-30) REVERT: A 257 MET cc_start: 0.7833 (mmm) cc_final: 0.7243 (tpp) REVERT: A 270 MET cc_start: 0.7811 (mtt) cc_final: 0.7565 (mtt) REVERT: A 322 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8276 (m-30) REVERT: A 365 ASP cc_start: 0.8338 (p0) cc_final: 0.8020 (p0) REVERT: A 371 LYS cc_start: 0.9412 (mttt) cc_final: 0.8652 (mmtt) REVERT: A 400 ASN cc_start: 0.8912 (m110) cc_final: 0.8568 (m110) REVERT: A 422 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7428 (pp30) REVERT: A 474 THR cc_start: 0.7352 (p) cc_final: 0.6945 (p) REVERT: A 475 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6277 (mt-10) REVERT: A 476 ASP cc_start: 0.8774 (t0) cc_final: 0.8348 (t0) REVERT: A 481 TYR cc_start: 0.8905 (m-80) cc_final: 0.8609 (m-10) REVERT: A 529 MET cc_start: 0.7967 (mmm) cc_final: 0.7430 (tpp) REVERT: A 545 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8144 (t0) REVERT: A 644 LEU cc_start: 0.8125 (mt) cc_final: 0.7643 (mt) REVERT: A 668 ASN cc_start: 0.8412 (p0) cc_final: 0.8051 (p0) REVERT: A 669 ASP cc_start: 0.8739 (t0) cc_final: 0.8486 (t70) REVERT: A 691 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7855 (ttm) REVERT: A 702 MET cc_start: 0.8095 (ttm) cc_final: 0.7688 (ttm) REVERT: A 714 ASP cc_start: 0.8990 (t70) cc_final: 0.8732 (t70) REVERT: A 768 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.6707 (t80) REVERT: A 787 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.5007 (m-10) REVERT: A 793 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7546 (p) REVERT: A 839 MET cc_start: 0.4771 (mmm) cc_final: 0.4358 (mmm) REVERT: A 882 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7752 (t0) REVERT: A 909 GLN cc_start: 0.7935 (pt0) cc_final: 0.7267 (pm20) REVERT: A 914 ASN cc_start: 0.8066 (p0) cc_final: 0.7528 (p0) REVERT: A 949 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7567 (ttt) REVERT: A 979 MET cc_start: 0.7630 (mtp) cc_final: 0.7169 (mtt) REVERT: A 993 ASP cc_start: 0.7954 (t70) cc_final: 0.7618 (t0) REVERT: B 18 GLN cc_start: 0.7699 (mt0) cc_final: 0.7219 (mt0) REVERT: B 65 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8391 (p) REVERT: B 66 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6624 (tp) REVERT: B 200 GLU cc_start: 0.8209 (pm20) cc_final: 0.6914 (pm20) REVERT: B 219 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8397 (p0) REVERT: B 232 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.5873 (mtpp) REVERT: B 235 THR cc_start: 0.8958 (m) cc_final: 0.8364 (p) REVERT: B 251 ASN cc_start: 0.7154 (OUTLIER) cc_final: 0.6952 (t0) REVERT: B 365 ASP cc_start: 0.8696 (p0) cc_final: 0.8315 (p0) REVERT: B 371 LYS cc_start: 0.9152 (mmtt) cc_final: 0.8402 (mmmt) REVERT: B 406 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.5720 (t80) REVERT: B 413 MET cc_start: 0.7298 (ttp) cc_final: 0.6909 (ttp) REVERT: B 481 TYR cc_start: 0.8887 (m-10) cc_final: 0.8488 (m-10) REVERT: B 529 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6168 (mmm) REVERT: B 655 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7542 (tpp80) REVERT: B 689 PHE cc_start: 0.8910 (t80) cc_final: 0.8339 (t80) REVERT: B 739 ARG cc_start: 0.7993 (tmm-80) cc_final: 0.7578 (tmm-80) REVERT: B 747 TRP cc_start: 0.8377 (OUTLIER) cc_final: 0.7720 (m-10) REVERT: B 770 TYR cc_start: 0.7913 (t80) cc_final: 0.7629 (t80) REVERT: B 840 LEU cc_start: 0.8249 (mt) cc_final: 0.7903 (mt) REVERT: B 917 TYR cc_start: 0.7019 (m-80) cc_final: 0.6797 (m-80) REVERT: B 979 MET cc_start: 0.8034 (mtp) cc_final: 0.7627 (mtt) REVERT: C 18 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7287 (mm-40) REVERT: C 22 GLU cc_start: 0.8060 (mp0) cc_final: 0.7740 (mp0) REVERT: C 166 LYS cc_start: 0.8608 (ptpt) cc_final: 0.8337 (mtpt) REVERT: C 216 SER cc_start: 0.9278 (m) cc_final: 0.8750 (t) REVERT: C 232 LYS cc_start: 0.6490 (OUTLIER) cc_final: 0.5407 (mtpt) REVERT: C 235 THR cc_start: 0.8921 (m) cc_final: 0.8310 (p) REVERT: C 267 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7990 (mm110) REVERT: C 270 MET cc_start: 0.7734 (mtp) cc_final: 0.7371 (mtt) REVERT: C 329 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6381 (pp) REVERT: C 365 ASP cc_start: 0.8772 (p0) cc_final: 0.8424 (p0) REVERT: C 371 LYS cc_start: 0.9471 (mtpt) cc_final: 0.9183 (mtpp) REVERT: C 374 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8442 (tppt) REVERT: C 529 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7315 (mmt) REVERT: C 573 MET cc_start: 0.8290 (mmt) cc_final: 0.7884 (tpp) REVERT: C 617 MET cc_start: 0.9040 (tpp) cc_final: 0.8673 (tpt) REVERT: C 644 LEU cc_start: 0.8095 (mt) cc_final: 0.7532 (mt) REVERT: C 671 ARG cc_start: 0.7319 (ttm170) cc_final: 0.6699 (ttp80) REVERT: C 744 PHE cc_start: 0.8498 (t80) cc_final: 0.6774 (t80) REVERT: C 786 THR cc_start: 0.9031 (p) cc_final: 0.8753 (t) REVERT: C 860 MET cc_start: 0.8270 (ttp) cc_final: 0.7921 (ttp) REVERT: C 889 ILE cc_start: 0.8724 (mt) cc_final: 0.8386 (tp) REVERT: C 909 GLN cc_start: 0.7491 (pm20) cc_final: 0.7174 (pm20) REVERT: C 914 ASN cc_start: 0.7640 (p0) cc_final: 0.7194 (p0) REVERT: C 936 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.7683 (m-30) REVERT: C 941 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.6403 (mtp-110) REVERT: C 955 THR cc_start: 0.8523 (t) cc_final: 0.8185 (t) outliers start: 238 outliers final: 178 residues processed: 624 average time/residue: 0.1553 time to fit residues: 156.5258 Evaluate side-chains 636 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 430 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 834 TRP Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 GLN Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1001 HIS Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 400 ASN Chi-restraints excluded: chain B residue 406 TYR Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 652 TRP Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 747 TRP Chi-restraints excluded: chain B residue 749 PHE Chi-restraints excluded: chain B residue 757 THR Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 833 ASP Chi-restraints excluded: chain B residue 834 TRP Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 851 TYR Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1001 HIS Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 455 TRP Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 471 ASN Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 652 TRP Chi-restraints excluded: chain C residue 663 GLN Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 698 THR Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 749 PHE Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 778 ASP Chi-restraints excluded: chain C residue 787 PHE Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 812 PHE Chi-restraints excluded: chain C residue 817 SER Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 834 TRP Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 935 CYS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 941 ARG Chi-restraints excluded: chain C residue 947 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 46 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 273 optimal weight: 0.6980 chunk 121 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 ASN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 GLN ** C 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 866 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.159315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.123558 restraints weight = 32835.671| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 4.88 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24025 Z= 0.122 Angle : 0.595 10.711 32656 Z= 0.312 Chirality : 0.045 0.206 3482 Planarity : 0.005 0.102 4313 Dihedral : 8.863 71.623 3449 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 7.59 % Allowed : 23.99 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.04 % 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: -2.24 (0.15), residues: 2953 helix: 0.46 (0.35), residues: 270 sheet: -0.40 (0.22), residues: 582 loop : -2.25 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 92 TYR 0.023 0.001 TYR A 856 PHE 0.025 0.001 PHE C 113 TRP 0.019 0.002 TRP A 747 HIS 0.006 0.001 HIS C 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (24025) covalent geometry : angle 0.59490 / 0.31 (32656) hydrogen bonds : bond 0.03702 / 2.49 ( 580) hydrogen bonds : angle 5.77383 / 3.90 ( 1365) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 469 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.6311 (OUTLIER) cc_final: 0.5734 (t80) REVERT: A 49 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8826 (p) REVERT: A 84 PHE cc_start: 0.8083 (m-80) cc_final: 0.7440 (m-10) REVERT: A 166 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8056 (mmmt) REVERT: A 187 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6296 (pp30) REVERT: A 205 LYS cc_start: 0.8940 (pttt) cc_final: 0.8548 (ptpp) REVERT: A 219 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8602 (p0) REVERT: A 270 MET cc_start: 0.7862 (mtt) cc_final: 0.7528 (mtt) REVERT: A 322 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8313 (m-30) REVERT: A 357 GLU cc_start: 0.8172 (pt0) cc_final: 0.7176 (pm20) REVERT: A 365 ASP cc_start: 0.8298 (p0) cc_final: 0.7856 (p0) REVERT: A 370 TYR cc_start: 0.8475 (t80) cc_final: 0.7710 (t80) REVERT: A 371 LYS cc_start: 0.9322 (mttt) cc_final: 0.8964 (mtpt) REVERT: A 382 MET cc_start: 0.8108 (tpt) cc_final: 0.7772 (tpp) REVERT: A 400 ASN cc_start: 0.8841 (m110) cc_final: 0.8520 (m110) REVERT: A 422 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7367 (pp30) REVERT: A 428 ASP cc_start: 0.8400 (t0) cc_final: 0.8106 (t0) REVERT: A 474 THR cc_start: 0.7140 (p) cc_final: 0.6794 (p) REVERT: A 475 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6148 (mt-10) REVERT: A 481 TYR cc_start: 0.8736 (m-80) cc_final: 0.8436 (m-10) REVERT: A 545 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.7882 (t0) REVERT: A 614 TYR cc_start: 0.8374 (t80) cc_final: 0.7686 (t80) REVERT: A 617 MET cc_start: 0.8964 (mtt) cc_final: 0.8396 (tpt) REVERT: A 644 LEU cc_start: 0.8019 (mt) cc_final: 0.7581 (mt) REVERT: A 668 ASN cc_start: 0.8255 (p0) cc_final: 0.7887 (p0) REVERT: A 691 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7404 (tmm) REVERT: A 702 MET cc_start: 0.8017 (ttm) cc_final: 0.7638 (ttm) REVERT: A 714 ASP cc_start: 0.8911 (t70) cc_final: 0.8656 (t0) REVERT: A 744 PHE cc_start: 0.8621 (t80) cc_final: 0.7479 (t80) REVERT: A 768 TYR cc_start: 0.7598 (OUTLIER) cc_final: 0.6712 (t80) REVERT: A 787 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.4597 (m-10) REVERT: A 793 THR cc_start: 0.7315 (OUTLIER) cc_final: 0.6966 (p) REVERT: A 839 MET cc_start: 0.4037 (mmm) cc_final: 0.3739 (mmm) REVERT: A 848 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8256 (mm-40) REVERT: A 882 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7595 (t0) REVERT: A 909 GLN cc_start: 0.7745 (pt0) cc_final: 0.6982 (pm20) REVERT: A 914 ASN cc_start: 0.7975 (p0) cc_final: 0.7243 (p0) REVERT: A 979 MET cc_start: 0.7400 (mtp) cc_final: 0.7015 (mtp) REVERT: A 993 ASP cc_start: 0.7772 (t70) cc_final: 0.7387 (t0) REVERT: B 18 GLN cc_start: 0.7603 (mt0) cc_final: 0.7179 (mt0) REVERT: B 66 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6196 (tp) REVERT: B 200 GLU cc_start: 0.8165 (pm20) cc_final: 0.6842 (pm20) REVERT: B 219 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8425 (p0) REVERT: B 232 LYS cc_start: 0.6708 (OUTLIER) cc_final: 0.5926 (mtpp) REVERT: B 235 THR cc_start: 0.8876 (m) cc_final: 0.8268 (p) REVERT: B 251 ASN cc_start: 0.7217 (OUTLIER) cc_final: 0.6944 (t0) REVERT: B 357 GLU cc_start: 0.8549 (pt0) cc_final: 0.8310 (pt0) REVERT: B 365 ASP cc_start: 0.8681 (p0) cc_final: 0.8285 (p0) REVERT: B 371 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8375 (mmmt) REVERT: B 386 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8323 (mm110) REVERT: B 406 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.5247 (t80) REVERT: B 413 MET cc_start: 0.7128 (ttp) cc_final: 0.6767 (ttp) REVERT: B 498 LYS cc_start: 0.7890 (tppp) cc_final: 0.7160 (ttpt) REVERT: B 529 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.5956 (mtt) REVERT: B 573 MET cc_start: 0.8460 (mmt) cc_final: 0.8122 (tpp) REVERT: B 617 MET cc_start: 0.8805 (tpp) cc_final: 0.8595 (tpp) REVERT: B 652 TRP cc_start: 0.7715 (OUTLIER) cc_final: 0.7368 (t60) REVERT: B 655 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7442 (tpp80) REVERT: B 689 PHE cc_start: 0.8900 (t80) cc_final: 0.8290 (t80) REVERT: B 741 TRP cc_start: 0.8687 (m100) cc_final: 0.7260 (m100) REVERT: B 747 TRP cc_start: 0.8238 (OUTLIER) cc_final: 0.7818 (m-10) REVERT: B 834 TRP cc_start: 0.6700 (OUTLIER) cc_final: 0.6335 (m100) REVERT: B 840 LEU cc_start: 0.8210 (mt) cc_final: 0.7912 (mt) REVERT: B 907 GLU cc_start: 0.7407 (pm20) cc_final: 0.7077 (pm20) REVERT: B 917 TYR cc_start: 0.6797 (m-80) cc_final: 0.6570 (m-80) REVERT: B 936 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8162 (m-30) REVERT: B 977 ASP cc_start: 0.8419 (t70) cc_final: 0.8152 (t70) REVERT: C 18 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7260 (mm-40) REVERT: C 22 GLU cc_start: 0.7944 (mp0) cc_final: 0.7723 (mp0) REVERT: C 166 LYS cc_start: 0.8597 (ptpt) cc_final: 0.8315 (mtpt) REVERT: C 173 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7546 (mm-40) REVERT: C 216 SER cc_start: 0.9210 (m) cc_final: 0.8622 (t) REVERT: C 232 LYS cc_start: 0.6114 (OUTLIER) cc_final: 0.5127 (mtpt) REVERT: C 235 THR cc_start: 0.8890 (m) cc_final: 0.8261 (p) REVERT: C 254 GLN cc_start: 0.7808 (mp10) cc_final: 0.7456 (mp10) REVERT: C 270 MET cc_start: 0.7632 (mtp) cc_final: 0.7197 (mtt) REVERT: C 329 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6305 (pp) REVERT: C 365 ASP cc_start: 0.8681 (p0) cc_final: 0.8349 (p0) REVERT: C 371 LYS cc_start: 0.9265 (mtpt) cc_final: 0.8984 (mtpp) REVERT: C 529 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.6489 (mtp) REVERT: C 573 MET cc_start: 0.8080 (mmt) cc_final: 0.7757 (tpp) REVERT: C 617 MET cc_start: 0.9090 (tpp) cc_final: 0.8573 (tpt) REVERT: C 644 LEU cc_start: 0.7934 (mt) cc_final: 0.7404 (mt) REVERT: C 671 ARG cc_start: 0.7139 (ttm170) cc_final: 0.6671 (ttp80) REVERT: C 702 MET cc_start: 0.8370 (ttm) cc_final: 0.7640 (tmm) REVERT: C 744 PHE cc_start: 0.8158 (t80) cc_final: 0.6644 (t80) REVERT: C 756 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8371 (mt-10) REVERT: C 786 THR cc_start: 0.9039 (p) cc_final: 0.8687 (t) REVERT: C 839 MET cc_start: 0.5425 (mmm) cc_final: 0.5098 (mmm) REVERT: C 860 MET cc_start: 0.8232 (ttp) cc_final: 0.7895 (ttp) REVERT: C 882 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8213 (m-30) REVERT: C 889 ILE cc_start: 0.8619 (mt) cc_final: 0.8319 (tp) REVERT: C 909 GLN cc_start: 0.7236 (pm20) cc_final: 0.6863 (pm20) REVERT: C 914 ASN cc_start: 0.7970 (p0) cc_final: 0.7647 (p0) REVERT: C 927 SER cc_start: 0.8092 (p) cc_final: 0.7716 (t) REVERT: C 941 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6223 (mtp-110) REVERT: C 962 LEU cc_start: 0.8471 (tp) cc_final: 0.8260 (tt) outliers start: 192 outliers final: 132 residues processed: 612 average time/residue: 0.1551 time to fit residues: 153.3406 Evaluate side-chains 608 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 444 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 834 TRP Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 GLN Chi-restraints excluded: chain A residue 881 LYS Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1001 HIS Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 406 TYR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 652 TRP Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 747 TRP Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 833 ASP Chi-restraints excluded: chain B residue 834 TRP Chi-restraints excluded: chain B residue 851 TYR Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1001 HIS Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 455 TRP Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 471 ASN Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 652 TRP Chi-restraints excluded: chain C residue 663 GLN Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 698 THR Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 778 ASP Chi-restraints excluded: chain C residue 787 PHE Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 799 SER Chi-restraints excluded: chain C residue 817 SER Chi-restraints excluded: chain C residue 834 TRP Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 882 ASP Chi-restraints excluded: chain C residue 911 TYR Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 935 CYS Chi-restraints excluded: chain C residue 941 ARG Chi-restraints excluded: chain C residue 1010 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 125 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 277 optimal weight: 0.0020 chunk 183 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 288 optimal weight: 5.9990 chunk 190 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 259 optimal weight: 0.9980 overall best weight: 3.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** B 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 GLN ** C 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 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 = 0.4133 r_free = 0.4133 target = 0.153959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.116841 restraints weight = 34614.552| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 4.89 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24025 Z= 0.204 Angle : 0.659 11.975 32656 Z= 0.344 Chirality : 0.047 0.401 3482 Planarity : 0.005 0.110 4313 Dihedral : 8.942 71.671 3444 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.75 % Favored : 88.22 % Rotamer: Outliers : 7.75 % Allowed : 24.03 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.04 % 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: -2.28 (0.15), residues: 2953 helix: 0.47 (0.35), residues: 269 sheet: -0.39 (0.22), residues: 577 loop : -2.30 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 92 TYR 0.024 0.002 TYR A 856 PHE 0.024 0.002 PHE C 749 TRP 0.020 0.002 TRP B 509 HIS 0.007 0.001 HIS C 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (24025) covalent geometry : angle 0.65943 / 0.34 (32656) hydrogen bonds : bond 0.04572 / 3.06 ( 580) hydrogen bonds : angle 5.92014 / 4.00 ( 1365) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 439 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.5496 (t80) REVERT: A 49 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8751 (p) REVERT: A 84 PHE cc_start: 0.7938 (m-80) cc_final: 0.7338 (m-10) REVERT: A 166 LYS cc_start: 0.8329 (mmtt) cc_final: 0.7977 (mmmt) REVERT: A 187 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.6194 (pp30) REVERT: A 205 LYS cc_start: 0.8798 (pttt) cc_final: 0.8403 (ptpp) REVERT: A 219 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8468 (p0) REVERT: A 270 MET cc_start: 0.7783 (mtt) cc_final: 0.7433 (mtt) REVERT: A 322 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8260 (m-30) REVERT: A 365 ASP cc_start: 0.8306 (p0) cc_final: 0.7913 (p0) REVERT: A 370 TYR cc_start: 0.8498 (t80) cc_final: 0.7517 (t80) REVERT: A 371 LYS cc_start: 0.9312 (mttt) cc_final: 0.8455 (mmmt) REVERT: A 400 ASN cc_start: 0.8883 (m110) cc_final: 0.8516 (m110) REVERT: A 422 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7356 (pp30) REVERT: A 428 ASP cc_start: 0.8457 (t0) cc_final: 0.8068 (t0) REVERT: A 475 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6274 (mt-10) REVERT: A 481 TYR cc_start: 0.8879 (m-80) cc_final: 0.8560 (m-10) REVERT: A 529 MET cc_start: 0.7848 (mmm) cc_final: 0.7299 (tpp) REVERT: A 545 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8048 (t0) REVERT: A 617 MET cc_start: 0.9031 (mtt) cc_final: 0.8545 (tpp) REVERT: A 644 LEU cc_start: 0.7989 (mt) cc_final: 0.7520 (mt) REVERT: A 668 ASN cc_start: 0.8304 (p0) cc_final: 0.7932 (p0) REVERT: A 669 ASP cc_start: 0.8595 (t0) cc_final: 0.8269 (t70) REVERT: A 691 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7429 (tmm) REVERT: A 702 MET cc_start: 0.7974 (ttm) cc_final: 0.7618 (ttm) REVERT: A 714 ASP cc_start: 0.8928 (t70) cc_final: 0.8672 (t0) REVERT: A 744 PHE cc_start: 0.8730 (t80) cc_final: 0.7033 (t80) REVERT: A 747 TRP cc_start: 0.7311 (m-90) cc_final: 0.6950 (m-90) REVERT: A 768 TYR cc_start: 0.7479 (OUTLIER) cc_final: 0.6549 (t80) REVERT: A 787 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.4719 (m-10) REVERT: A 793 THR cc_start: 0.7409 (OUTLIER) cc_final: 0.6975 (p) REVERT: A 833 ASP cc_start: 0.8687 (m-30) cc_final: 0.8434 (t0) REVERT: A 839 MET cc_start: 0.3845 (mmm) cc_final: 0.3398 (mmm) REVERT: A 882 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7460 (t0) REVERT: A 889 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8112 (tp) REVERT: A 909 GLN cc_start: 0.7784 (pt0) cc_final: 0.7025 (pm20) REVERT: A 977 ASP cc_start: 0.8591 (t70) cc_final: 0.8165 (t70) REVERT: A 979 MET cc_start: 0.7394 (mtp) cc_final: 0.6800 (mtt) REVERT: A 993 ASP cc_start: 0.7856 (t70) cc_final: 0.7456 (t0) REVERT: B 18 GLN cc_start: 0.7559 (mt0) cc_final: 0.7091 (mt0) REVERT: B 66 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6118 (tp) REVERT: B 200 GLU cc_start: 0.8148 (pm20) cc_final: 0.7808 (pm20) REVERT: B 219 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8316 (p0) REVERT: B 232 LYS cc_start: 0.6456 (OUTLIER) cc_final: 0.5582 (mtpp) REVERT: B 235 THR cc_start: 0.8817 (m) cc_final: 0.8190 (p) REVERT: B 251 ASN cc_start: 0.6983 (OUTLIER) cc_final: 0.6757 (t0) REVERT: B 313 MET cc_start: 0.7601 (tpt) cc_final: 0.7331 (mpp) REVERT: B 365 ASP cc_start: 0.8699 (p0) cc_final: 0.8279 (p0) REVERT: B 371 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8244 (mmmt) REVERT: B 386 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7986 (mm110) REVERT: B 413 MET cc_start: 0.7094 (ttp) cc_final: 0.6692 (ttp) REVERT: B 494 TYR cc_start: 0.7563 (m-80) cc_final: 0.7266 (m-10) REVERT: B 573 MET cc_start: 0.8484 (mmt) cc_final: 0.8133 (tpp) REVERT: B 617 MET cc_start: 0.8782 (tpp) cc_final: 0.8285 (tpp) REVERT: B 652 TRP cc_start: 0.7554 (OUTLIER) cc_final: 0.7176 (t60) REVERT: B 655 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7388 (tpp80) REVERT: B 689 PHE cc_start: 0.8848 (t80) cc_final: 0.8152 (t80) REVERT: B 739 ARG cc_start: 0.7739 (tmm-80) cc_final: 0.7510 (tmm-80) REVERT: B 747 TRP cc_start: 0.8210 (OUTLIER) cc_final: 0.7715 (m-10) REVERT: B 840 LEU cc_start: 0.8230 (mt) cc_final: 0.7929 (mt) REVERT: B 860 MET cc_start: 0.8093 (ttp) cc_final: 0.7889 (ttp) REVERT: B 907 GLU cc_start: 0.7327 (pm20) cc_final: 0.7103 (pm20) REVERT: B 917 TYR cc_start: 0.6793 (m-80) cc_final: 0.6584 (m-80) REVERT: B 977 ASP cc_start: 0.8397 (t70) cc_final: 0.8125 (t70) REVERT: C 18 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7187 (mm-40) REVERT: C 166 LYS cc_start: 0.8468 (ptpt) cc_final: 0.8225 (mtpt) REVERT: C 216 SER cc_start: 0.8900 (m) cc_final: 0.8403 (t) REVERT: C 232 LYS cc_start: 0.6239 (OUTLIER) cc_final: 0.5231 (mtpt) REVERT: C 235 THR cc_start: 0.8809 (m) cc_final: 0.8160 (p) REVERT: C 270 MET cc_start: 0.7677 (mtp) cc_final: 0.7213 (mtt) REVERT: C 329 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6414 (pp) REVERT: C 365 ASP cc_start: 0.8811 (p0) cc_final: 0.8387 (p0) REVERT: C 371 LYS cc_start: 0.9440 (mtpt) cc_final: 0.9132 (mtpp) REVERT: C 374 LYS cc_start: 0.8657 (mmmt) cc_final: 0.8149 (tppt) REVERT: C 481 TYR cc_start: 0.9067 (m-80) cc_final: 0.7752 (m-80) REVERT: C 529 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.6805 (mtp) REVERT: C 573 MET cc_start: 0.8119 (mmt) cc_final: 0.7720 (tpp) REVERT: C 617 MET cc_start: 0.9131 (tpp) cc_final: 0.8686 (tpt) REVERT: C 644 LEU cc_start: 0.7936 (mt) cc_final: 0.7394 (mt) REVERT: C 671 ARG cc_start: 0.7123 (ttm170) cc_final: 0.6610 (ttp80) REVERT: C 744 PHE cc_start: 0.8169 (t80) cc_final: 0.6366 (t80) REVERT: C 756 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8183 (mt-10) REVERT: C 786 THR cc_start: 0.8937 (p) cc_final: 0.8610 (t) REVERT: C 839 MET cc_start: 0.5308 (mmm) cc_final: 0.4975 (mmm) REVERT: C 860 MET cc_start: 0.8016 (ttp) cc_final: 0.7675 (ttp) REVERT: C 889 ILE cc_start: 0.8527 (mt) cc_final: 0.8220 (tp) REVERT: C 905 MET cc_start: 0.7616 (ptp) cc_final: 0.7398 (ptp) REVERT: C 909 GLN cc_start: 0.6946 (pm20) cc_final: 0.6549 (pm20) REVERT: C 936 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: C 941 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.6226 (mtp-110) outliers start: 196 outliers final: 147 residues processed: 596 average time/residue: 0.1531 time to fit residues: 147.0943 Evaluate side-chains 606 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 432 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 834 TRP Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 GLN Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 889 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1001 HIS Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 400 ASN Chi-restraints excluded: chain B residue 406 TYR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 652 TRP Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 747 TRP Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 834 TRP Chi-restraints excluded: chain B residue 851 TYR Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1001 HIS Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 455 TRP Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 471 ASN Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 652 TRP Chi-restraints excluded: chain C residue 663 GLN Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 698 THR Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 778 ASP Chi-restraints excluded: chain C residue 787 PHE Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 799 SER Chi-restraints excluded: chain C residue 812 PHE Chi-restraints excluded: chain C residue 817 SER Chi-restraints excluded: chain C residue 834 TRP Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 911 TYR Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 935 CYS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 941 ARG Chi-restraints excluded: chain C residue 1010 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 177 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 130 optimal weight: 50.0000 chunk 200 optimal weight: 5.9990 chunk 223 optimal weight: 50.0000 chunk 189 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 287 optimal weight: 5.9990 chunk 285 optimal weight: 0.8980 chunk 229 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.155365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.119973 restraints weight = 33609.381| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 4.82 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24025 Z= 0.185 Angle : 0.654 12.436 32656 Z= 0.339 Chirality : 0.047 0.368 3482 Planarity : 0.005 0.122 4313 Dihedral : 8.855 73.887 3438 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 7.83 % Allowed : 24.74 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: -2.27 (0.15), residues: 2953 helix: 0.44 (0.35), residues: 269 sheet: -0.39 (0.22), residues: 573 loop : -2.27 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.024 0.002 TYR A 856 PHE 0.022 0.002 PHE C 749 TRP 0.023 0.002 TRP B 509 HIS 0.007 0.001 HIS C 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (24025) covalent geometry : angle 0.65419 / 0.34 (32656) hydrogen bonds : bond 0.04372 / 2.93 ( 580) hydrogen bonds : angle 5.90048 / 3.99 ( 1365) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 441 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.6136 (OUTLIER) cc_final: 0.5519 (t80) REVERT: A 49 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8734 (p) REVERT: A 84 PHE cc_start: 0.7914 (m-80) cc_final: 0.7305 (m-10) REVERT: A 166 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7994 (mmmt) REVERT: A 187 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.6209 (pp30) REVERT: A 205 LYS cc_start: 0.8794 (pttt) cc_final: 0.8404 (ptpp) REVERT: A 216 SER cc_start: 0.8687 (m) cc_final: 0.7809 (t) REVERT: A 219 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8526 (p0) REVERT: A 270 MET cc_start: 0.7789 (mtt) cc_final: 0.7416 (mtt) REVERT: A 322 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8364 (m-30) REVERT: A 365 ASP cc_start: 0.8371 (p0) cc_final: 0.7888 (p0) REVERT: A 370 TYR cc_start: 0.8509 (t80) cc_final: 0.7541 (t80) REVERT: A 371 LYS cc_start: 0.9327 (mttt) cc_final: 0.8460 (mmmt) REVERT: A 400 ASN cc_start: 0.8876 (m110) cc_final: 0.8505 (m110) REVERT: A 422 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7340 (pp30) REVERT: A 474 THR cc_start: 0.7011 (p) cc_final: 0.6674 (p) REVERT: A 475 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6190 (mt-10) REVERT: A 481 TYR cc_start: 0.8886 (m-80) cc_final: 0.8551 (m-10) REVERT: A 529 MET cc_start: 0.7773 (mmm) cc_final: 0.6373 (tpp) REVERT: A 545 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.7627 (t0) REVERT: A 576 ARG cc_start: 0.8590 (mmt180) cc_final: 0.7196 (mmt180) REVERT: A 614 TYR cc_start: 0.8293 (t80) cc_final: 0.7661 (t80) REVERT: A 617 MET cc_start: 0.9072 (mtt) cc_final: 0.8396 (ttm) REVERT: A 644 LEU cc_start: 0.7957 (mt) cc_final: 0.7499 (mt) REVERT: A 668 ASN cc_start: 0.8273 (p0) cc_final: 0.7890 (p0) REVERT: A 691 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7371 (tmm) REVERT: A 702 MET cc_start: 0.7958 (ttm) cc_final: 0.7585 (ttm) REVERT: A 714 ASP cc_start: 0.8922 (t70) cc_final: 0.8669 (t0) REVERT: A 744 PHE cc_start: 0.8672 (t80) cc_final: 0.7335 (t80) REVERT: A 747 TRP cc_start: 0.7265 (m-90) cc_final: 0.7009 (m-90) REVERT: A 768 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.6548 (t80) REVERT: A 787 PHE cc_start: 0.6996 (OUTLIER) cc_final: 0.4615 (m-10) REVERT: A 793 THR cc_start: 0.7377 (OUTLIER) cc_final: 0.6944 (p) REVERT: A 833 ASP cc_start: 0.8705 (m-30) cc_final: 0.8497 (t0) REVERT: A 839 MET cc_start: 0.3750 (mmm) cc_final: 0.3334 (mmm) REVERT: A 882 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7455 (t0) REVERT: A 909 GLN cc_start: 0.7557 (pt0) cc_final: 0.6993 (pm20) REVERT: A 914 ASN cc_start: 0.7853 (p0) cc_final: 0.7185 (p0) REVERT: A 977 ASP cc_start: 0.8589 (t70) cc_final: 0.8168 (t70) REVERT: A 979 MET cc_start: 0.7375 (mtp) cc_final: 0.6758 (mtt) REVERT: A 993 ASP cc_start: 0.7859 (t70) cc_final: 0.7447 (t0) REVERT: B 18 GLN cc_start: 0.7561 (mt0) cc_final: 0.7085 (mt0) REVERT: B 66 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.6078 (tp) REVERT: B 200 GLU cc_start: 0.8104 (pm20) cc_final: 0.7789 (pm20) REVERT: B 219 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8345 (p0) REVERT: B 232 LYS cc_start: 0.6448 (OUTLIER) cc_final: 0.5630 (mtpp) REVERT: B 235 THR cc_start: 0.8812 (m) cc_final: 0.8186 (p) REVERT: B 251 ASN cc_start: 0.6847 (OUTLIER) cc_final: 0.6619 (t0) REVERT: B 365 ASP cc_start: 0.8696 (p0) cc_final: 0.8270 (p0) REVERT: B 371 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8248 (mmmt) REVERT: B 386 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8092 (mm110) REVERT: B 413 MET cc_start: 0.7097 (ttp) cc_final: 0.6689 (ttp) REVERT: B 494 TYR cc_start: 0.7710 (m-80) cc_final: 0.7464 (m-10) REVERT: B 498 LYS cc_start: 0.7810 (tppp) cc_final: 0.7119 (ttpt) REVERT: B 573 MET cc_start: 0.8458 (mmt) cc_final: 0.8109 (tpp) REVERT: B 617 MET cc_start: 0.8804 (tpp) cc_final: 0.8462 (tpp) REVERT: B 652 TRP cc_start: 0.7557 (OUTLIER) cc_final: 0.7184 (t60) REVERT: B 655 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7417 (tpp80) REVERT: B 689 PHE cc_start: 0.8785 (t80) cc_final: 0.8120 (t80) REVERT: B 739 ARG cc_start: 0.7657 (tmm-80) cc_final: 0.7445 (tmm-80) REVERT: B 747 TRP cc_start: 0.8188 (OUTLIER) cc_final: 0.7696 (m-10) REVERT: B 834 TRP cc_start: 0.6406 (OUTLIER) cc_final: 0.6095 (m100) REVERT: B 840 LEU cc_start: 0.8203 (mt) cc_final: 0.7912 (mt) REVERT: B 860 MET cc_start: 0.7931 (ttp) cc_final: 0.7703 (ttp) REVERT: B 907 GLU cc_start: 0.7201 (pm20) cc_final: 0.6957 (pm20) REVERT: B 917 TYR cc_start: 0.6746 (m-80) cc_final: 0.6542 (m-80) REVERT: B 977 ASP cc_start: 0.8404 (t70) cc_final: 0.8127 (t70) REVERT: C 134 GLU cc_start: 0.7856 (pt0) cc_final: 0.7648 (mt-10) REVERT: C 166 LYS cc_start: 0.8485 (ptpt) cc_final: 0.8245 (mtpt) REVERT: C 216 SER cc_start: 0.8769 (m) cc_final: 0.8249 (t) REVERT: C 219 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8491 (p0) REVERT: C 232 LYS cc_start: 0.6111 (OUTLIER) cc_final: 0.5239 (mtpt) REVERT: C 235 THR cc_start: 0.8722 (m) cc_final: 0.7974 (p) REVERT: C 270 MET cc_start: 0.7681 (mtp) cc_final: 0.7265 (mtt) REVERT: C 329 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6365 (pp) REVERT: C 365 ASP cc_start: 0.8795 (p0) cc_final: 0.8376 (p0) REVERT: C 371 LYS cc_start: 0.9442 (mtpt) cc_final: 0.9145 (mtpp) REVERT: C 378 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7888 (m110) REVERT: C 481 TYR cc_start: 0.9033 (m-80) cc_final: 0.7870 (m-80) REVERT: C 617 MET cc_start: 0.9157 (tpp) cc_final: 0.8681 (tpt) REVERT: C 644 LEU cc_start: 0.7929 (mt) cc_final: 0.7397 (mt) REVERT: C 744 PHE cc_start: 0.8142 (t80) cc_final: 0.6395 (t80) REVERT: C 756 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8169 (mt-10) REVERT: C 839 MET cc_start: 0.5243 (mmm) cc_final: 0.4904 (mmm) REVERT: C 860 MET cc_start: 0.7999 (ttp) cc_final: 0.7649 (ttp) REVERT: C 889 ILE cc_start: 0.8523 (mt) cc_final: 0.8217 (tp) REVERT: C 905 MET cc_start: 0.7624 (ptp) cc_final: 0.7394 (ptp) REVERT: C 909 GLN cc_start: 0.6959 (pm20) cc_final: 0.6549 (pm20) REVERT: C 914 ASN cc_start: 0.7832 (OUTLIER) cc_final: 0.7368 (p0) REVERT: C 936 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7349 (m-30) REVERT: C 941 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.6243 (mtp-110) outliers start: 198 outliers final: 153 residues processed: 593 average time/residue: 0.1497 time to fit residues: 143.1612 Evaluate side-chains 618 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 436 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 834 TRP Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 981 GLU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1001 HIS Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 400 ASN Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 406 TYR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 652 TRP Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 747 TRP Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 834 TRP Chi-restraints excluded: chain B residue 851 TYR Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1001 HIS Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 455 TRP Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 471 ASN Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 652 TRP Chi-restraints excluded: chain C residue 663 GLN Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 698 THR Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 778 ASP Chi-restraints excluded: chain C residue 787 PHE Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 799 SER Chi-restraints excluded: chain C residue 812 PHE Chi-restraints excluded: chain C residue 817 SER Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 834 TRP Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 911 TYR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 935 CYS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 941 ARG Chi-restraints excluded: chain C residue 1010 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 207 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 290 optimal weight: 5.9990 chunk 262 optimal weight: 0.2980 chunk 36 optimal weight: 9.9990 chunk 172 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 218 optimal weight: 8.9990 chunk 263 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.155094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.119436 restraints weight = 33687.822| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 4.89 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24025 Z= 0.177 Angle : 0.657 13.164 32656 Z= 0.340 Chirality : 0.047 0.395 3482 Planarity : 0.005 0.122 4313 Dihedral : 8.665 62.666 3432 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 7.51 % Allowed : 25.26 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.04 % 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: -2.28 (0.15), residues: 2953 helix: 0.24 (0.34), residues: 281 sheet: -0.43 (0.22), residues: 581 loop : -2.26 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.025 0.001 TYR A 856 PHE 0.022 0.002 PHE C 689 TRP 0.040 0.002 TRP B 509 HIS 0.007 0.001 HIS C 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (24025) covalent geometry : angle 0.65704 / 0.34 (32656) hydrogen bonds : bond 0.04273 / 2.87 ( 580) hydrogen bonds : angle 5.88045 / 3.97 ( 1365) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 442 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.6071 (OUTLIER) cc_final: 0.5512 (t80) REVERT: A 49 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8704 (p) REVERT: A 84 PHE cc_start: 0.7874 (m-80) cc_final: 0.7271 (m-10) REVERT: A 166 LYS cc_start: 0.8313 (mmtt) cc_final: 0.7986 (mmmt) REVERT: A 187 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.5859 (pp30) REVERT: A 205 LYS cc_start: 0.8756 (pttt) cc_final: 0.8375 (ptpp) REVERT: A 216 SER cc_start: 0.8680 (m) cc_final: 0.7879 (t) REVERT: A 217 GLN cc_start: 0.8241 (pt0) cc_final: 0.7704 (pt0) REVERT: A 219 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8130 (p0) REVERT: A 270 MET cc_start: 0.7859 (mtt) cc_final: 0.7547 (mtt) REVERT: A 322 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8349 (m-30) REVERT: A 365 ASP cc_start: 0.8360 (p0) cc_final: 0.7869 (p0) REVERT: A 370 TYR cc_start: 0.8495 (t80) cc_final: 0.7501 (t80) REVERT: A 371 LYS cc_start: 0.9324 (mttt) cc_final: 0.8449 (mmmt) REVERT: A 400 ASN cc_start: 0.8748 (m110) cc_final: 0.8303 (m110) REVERT: A 405 MET cc_start: 0.7269 (mmm) cc_final: 0.7015 (mmm) REVERT: A 422 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7347 (pp30) REVERT: A 428 ASP cc_start: 0.8432 (t0) cc_final: 0.8038 (t0) REVERT: A 475 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6218 (mt-10) REVERT: A 481 TYR cc_start: 0.8892 (m-80) cc_final: 0.8569 (m-10) REVERT: A 545 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.7864 (t0) REVERT: A 557 ASN cc_start: 0.9064 (OUTLIER) cc_final: 0.8523 (t0) REVERT: A 576 ARG cc_start: 0.8595 (mmt180) cc_final: 0.7051 (mmt180) REVERT: A 614 TYR cc_start: 0.8266 (t80) cc_final: 0.7591 (t80) REVERT: A 617 MET cc_start: 0.9078 (mtt) cc_final: 0.8395 (ttm) REVERT: A 644 LEU cc_start: 0.7888 (mt) cc_final: 0.7456 (mt) REVERT: A 668 ASN cc_start: 0.8255 (p0) cc_final: 0.7870 (p0) REVERT: A 691 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7328 (tmm) REVERT: A 702 MET cc_start: 0.7932 (ttm) cc_final: 0.7562 (ttm) REVERT: A 714 ASP cc_start: 0.8926 (t70) cc_final: 0.8688 (t0) REVERT: A 744 PHE cc_start: 0.8660 (t80) cc_final: 0.7238 (t80) REVERT: A 747 TRP cc_start: 0.7255 (m-90) cc_final: 0.6930 (m-90) REVERT: A 768 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.6510 (t80) REVERT: A 787 PHE cc_start: 0.6933 (OUTLIER) cc_final: 0.4574 (m-10) REVERT: A 793 THR cc_start: 0.7332 (OUTLIER) cc_final: 0.6908 (p) REVERT: A 833 ASP cc_start: 0.8700 (m-30) cc_final: 0.8492 (t0) REVERT: A 839 MET cc_start: 0.3505 (mmm) cc_final: 0.3086 (mmm) REVERT: A 882 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7447 (t0) REVERT: A 889 ILE cc_start: 0.8379 (mt) cc_final: 0.8035 (tp) REVERT: A 909 GLN cc_start: 0.7484 (pt0) cc_final: 0.6927 (pm20) REVERT: A 914 ASN cc_start: 0.7815 (p0) cc_final: 0.7166 (p0) REVERT: A 947 ASN cc_start: 0.9244 (p0) cc_final: 0.8989 (p0) REVERT: A 977 ASP cc_start: 0.8557 (t70) cc_final: 0.8140 (t70) REVERT: A 979 MET cc_start: 0.7306 (mtp) cc_final: 0.6681 (mtt) REVERT: A 993 ASP cc_start: 0.7826 (t70) cc_final: 0.7417 (t0) REVERT: B 18 GLN cc_start: 0.7521 (mt0) cc_final: 0.7114 (mt0) REVERT: B 65 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8229 (p) REVERT: B 66 LEU cc_start: 0.6392 (OUTLIER) cc_final: 0.6123 (tp) REVERT: B 200 GLU cc_start: 0.8168 (pm20) cc_final: 0.7901 (pm20) REVERT: B 219 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8333 (p0) REVERT: B 232 LYS cc_start: 0.6406 (OUTLIER) cc_final: 0.5588 (mtpp) REVERT: B 235 THR cc_start: 0.8773 (m) cc_final: 0.8148 (p) REVERT: B 251 ASN cc_start: 0.6737 (OUTLIER) cc_final: 0.6536 (t0) REVERT: B 365 ASP cc_start: 0.8717 (p0) cc_final: 0.8282 (p0) REVERT: B 371 LYS cc_start: 0.8980 (mmtt) cc_final: 0.8179 (mmmt) REVERT: B 382 MET cc_start: 0.8164 (tpt) cc_final: 0.7924 (tpt) REVERT: B 413 MET cc_start: 0.7049 (ttp) cc_final: 0.6645 (ttp) REVERT: B 494 TYR cc_start: 0.7578 (m-80) cc_final: 0.7313 (m-10) REVERT: B 498 LYS cc_start: 0.7765 (tppp) cc_final: 0.7102 (ttpt) REVERT: B 573 MET cc_start: 0.8330 (mmt) cc_final: 0.8005 (tpp) REVERT: B 617 MET cc_start: 0.8811 (tpp) cc_final: 0.8459 (tpp) REVERT: B 652 TRP cc_start: 0.7499 (OUTLIER) cc_final: 0.7093 (t60) REVERT: B 655 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7224 (tpp80) REVERT: B 689 PHE cc_start: 0.8755 (t80) cc_final: 0.8154 (t80) REVERT: B 691 MET cc_start: 0.7803 (ttt) cc_final: 0.7191 (ttt) REVERT: B 741 TRP cc_start: 0.8610 (m100) cc_final: 0.7397 (m100) REVERT: B 747 TRP cc_start: 0.8140 (OUTLIER) cc_final: 0.7671 (m-10) REVERT: B 834 TRP cc_start: 0.6541 (OUTLIER) cc_final: 0.6251 (m100) REVERT: B 840 LEU cc_start: 0.8188 (mt) cc_final: 0.7902 (mt) REVERT: B 860 MET cc_start: 0.7955 (ttp) cc_final: 0.7723 (ttp) REVERT: B 907 GLU cc_start: 0.7206 (pm20) cc_final: 0.6954 (pm20) REVERT: B 917 TYR cc_start: 0.6698 (m-80) cc_final: 0.6497 (m-80) REVERT: B 977 ASP cc_start: 0.8347 (t70) cc_final: 0.8050 (t70) REVERT: C 216 SER cc_start: 0.8686 (m) cc_final: 0.8086 (t) REVERT: C 232 LYS cc_start: 0.6133 (OUTLIER) cc_final: 0.5147 (mtpt) REVERT: C 235 THR cc_start: 0.8739 (m) cc_final: 0.7997 (p) REVERT: C 254 GLN cc_start: 0.7800 (mp10) cc_final: 0.7383 (mp10) REVERT: C 270 MET cc_start: 0.7672 (mtp) cc_final: 0.7266 (mtt) REVERT: C 329 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6423 (pp) REVERT: C 357 GLU cc_start: 0.8600 (pm20) cc_final: 0.8015 (pm20) REVERT: C 365 ASP cc_start: 0.8783 (p0) cc_final: 0.8355 (p0) REVERT: C 371 LYS cc_start: 0.9429 (mtpt) cc_final: 0.9117 (mtpp) REVERT: C 374 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8314 (tppt) REVERT: C 378 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7844 (m110) REVERT: C 481 TYR cc_start: 0.9041 (m-80) cc_final: 0.7845 (m-80) REVERT: C 617 MET cc_start: 0.9175 (tpp) cc_final: 0.8715 (tpt) REVERT: C 644 LEU cc_start: 0.7905 (mt) cc_final: 0.7381 (mt) REVERT: C 744 PHE cc_start: 0.8099 (t80) cc_final: 0.6339 (t80) REVERT: C 756 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8165 (mt-10) REVERT: C 839 MET cc_start: 0.5215 (mmm) cc_final: 0.4871 (mmm) REVERT: C 860 MET cc_start: 0.7945 (ttp) cc_final: 0.7599 (ttp) REVERT: C 889 ILE cc_start: 0.8476 (mt) cc_final: 0.8170 (tp) REVERT: C 905 MET cc_start: 0.7594 (ptp) cc_final: 0.7220 (ptp) REVERT: C 909 GLN cc_start: 0.6884 (pm20) cc_final: 0.6472 (pm20) REVERT: C 914 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7500 (p0) REVERT: C 936 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: C 941 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.6222 (mtp-110) outliers start: 190 outliers final: 156 residues processed: 590 average time/residue: 0.1423 time to fit residues: 135.6398 Evaluate side-chains 615 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 430 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 557 ASN Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 834 TRP Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 981 GLU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1001 HIS Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 400 ASN Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 406 TYR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 652 TRP Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 747 TRP Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 834 TRP Chi-restraints excluded: chain B residue 851 TYR Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1001 HIS Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 455 TRP Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 471 ASN Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 652 TRP Chi-restraints excluded: chain C residue 663 GLN Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 698 THR Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 778 ASP Chi-restraints excluded: chain C residue 787 PHE Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 799 SER Chi-restraints excluded: chain C residue 817 SER Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 834 TRP Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 911 TYR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 935 CYS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 941 ARG Chi-restraints excluded: chain C residue 1010 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 218 optimal weight: 9.9990 chunk 276 optimal weight: 0.0030 chunk 59 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 210 optimal weight: 0.7980 chunk 164 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 127 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 HIS ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 GLN ** C 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 959 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.146222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.110459 restraints weight = 32969.236| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 4.82 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24025 Z= 0.109 Angle : 0.618 13.327 32656 Z= 0.319 Chirality : 0.046 0.532 3482 Planarity : 0.004 0.113 4313 Dihedral : 8.267 59.932 3432 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 5.97 % Allowed : 26.88 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: -2.10 (0.15), residues: 2953 helix: 0.33 (0.34), residues: 282 sheet: -0.36 (0.22), residues: 574 loop : -2.11 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.026 0.001 TYR A 856 PHE 0.020 0.001 PHE A 483 TRP 0.032 0.002 TRP B 509 HIS 0.006 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (24025) covalent geometry : angle 0.61800 / 0.32 (32656) hydrogen bonds : bond 0.03254 / 2.22 ( 580) hydrogen bonds : angle 5.57820 / 3.77 ( 1365) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 481 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.6020 (t80) REVERT: A 63 ARG cc_start: 0.6180 (mtt180) cc_final: 0.5226 (mtp85) REVERT: A 84 PHE cc_start: 0.8117 (m-80) cc_final: 0.7441 (m-10) REVERT: A 166 LYS cc_start: 0.8556 (mmtt) cc_final: 0.8179 (mmmt) REVERT: A 187 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6307 (pp30) REVERT: A 205 LYS cc_start: 0.9021 (pttt) cc_final: 0.8672 (ptpp) REVERT: A 216 SER cc_start: 0.8812 (m) cc_final: 0.8001 (t) REVERT: A 219 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8599 (p0) REVERT: A 313 MET cc_start: 0.0861 (mtt) cc_final: 0.0390 (mpp) REVERT: A 322 ASP cc_start: 0.9102 (OUTLIER) cc_final: 0.8462 (m-30) REVERT: A 357 GLU cc_start: 0.8093 (pt0) cc_final: 0.6703 (mp0) REVERT: A 365 ASP cc_start: 0.8271 (p0) cc_final: 0.7840 (p0) REVERT: A 370 TYR cc_start: 0.8579 (t80) cc_final: 0.7819 (t80) REVERT: A 371 LYS cc_start: 0.9251 (mttt) cc_final: 0.8400 (mmmt) REVERT: A 400 ASN cc_start: 0.8836 (m110) cc_final: 0.8414 (m110) REVERT: A 405 MET cc_start: 0.7353 (mmm) cc_final: 0.7132 (mmm) REVERT: A 422 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7456 (pp30) REVERT: A 428 ASP cc_start: 0.8426 (t0) cc_final: 0.8192 (t0) REVERT: A 474 THR cc_start: 0.7160 (p) cc_final: 0.6824 (p) REVERT: A 481 TYR cc_start: 0.8616 (m-80) cc_final: 0.8414 (m-10) REVERT: A 529 MET cc_start: 0.7701 (tpp) cc_final: 0.6718 (ttm) REVERT: A 545 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7744 (t0) REVERT: A 557 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8671 (t0) REVERT: A 576 ARG cc_start: 0.8693 (mmt180) cc_final: 0.7191 (mmt180) REVERT: A 614 TYR cc_start: 0.8357 (t80) cc_final: 0.7826 (t80) REVERT: A 617 MET cc_start: 0.8886 (mtt) cc_final: 0.8383 (tpt) REVERT: A 644 LEU cc_start: 0.7920 (mt) cc_final: 0.7510 (mt) REVERT: A 668 ASN cc_start: 0.8313 (p0) cc_final: 0.8085 (p0) REVERT: A 691 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7641 (tmm) REVERT: A 702 MET cc_start: 0.8224 (ttm) cc_final: 0.7909 (ttm) REVERT: A 756 GLU cc_start: 0.8464 (mt-10) cc_final: 0.7968 (mt-10) REVERT: A 768 TYR cc_start: 0.7615 (OUTLIER) cc_final: 0.6588 (t80) REVERT: A 787 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.4604 (m-10) REVERT: A 833 ASP cc_start: 0.8614 (m-30) cc_final: 0.8404 (t0) REVERT: A 839 MET cc_start: 0.4275 (mmm) cc_final: 0.4002 (mmm) REVERT: A 882 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7665 (t0) REVERT: A 909 GLN cc_start: 0.7600 (pt0) cc_final: 0.7088 (pm20) REVERT: A 914 ASN cc_start: 0.8058 (p0) cc_final: 0.7350 (p0) REVERT: A 935 CYS cc_start: 0.9165 (t) cc_final: 0.8868 (t) REVERT: A 977 ASP cc_start: 0.8626 (t70) cc_final: 0.8221 (t70) REVERT: A 979 MET cc_start: 0.7222 (mtp) cc_final: 0.6904 (mtt) REVERT: A 993 ASP cc_start: 0.7669 (t70) cc_final: 0.7413 (t0) REVERT: B 18 GLN cc_start: 0.7916 (mt0) cc_final: 0.7456 (mt0) REVERT: B 60 ARG cc_start: 0.6230 (mtt90) cc_final: 0.6016 (mtt-85) REVERT: B 66 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6458 (tp) REVERT: B 200 GLU cc_start: 0.8342 (pm20) cc_final: 0.8007 (pm20) REVERT: B 219 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8477 (p0) REVERT: B 232 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.5979 (mtpp) REVERT: B 235 THR cc_start: 0.8843 (m) cc_final: 0.8446 (t) REVERT: B 251 ASN cc_start: 0.7158 (OUTLIER) cc_final: 0.6892 (t0) REVERT: B 357 GLU cc_start: 0.8436 (pt0) cc_final: 0.7931 (pt0) REVERT: B 365 ASP cc_start: 0.8824 (p0) cc_final: 0.8481 (p0) REVERT: B 371 LYS cc_start: 0.9045 (mmtt) cc_final: 0.8264 (mmmt) REVERT: B 413 MET cc_start: 0.7223 (ttp) cc_final: 0.6940 (ttp) REVERT: B 481 TYR cc_start: 0.8573 (m-10) cc_final: 0.8265 (m-10) REVERT: B 573 MET cc_start: 0.8481 (mmt) cc_final: 0.8274 (tpp) REVERT: B 617 MET cc_start: 0.8752 (tpp) cc_final: 0.8421 (tpp) REVERT: B 652 TRP cc_start: 0.7890 (OUTLIER) cc_final: 0.7460 (t60) REVERT: B 660 MET cc_start: 0.8833 (tpp) cc_final: 0.8127 (mtp) REVERT: B 689 PHE cc_start: 0.8673 (t80) cc_final: 0.8165 (t80) REVERT: B 721 MET cc_start: 0.4945 (mmm) cc_final: 0.4568 (mtt) REVERT: B 741 TRP cc_start: 0.8710 (m100) cc_final: 0.7575 (m100) REVERT: B 840 LEU cc_start: 0.8150 (mt) cc_final: 0.7865 (mt) REVERT: B 860 MET cc_start: 0.8382 (ttp) cc_final: 0.7882 (ttp) REVERT: B 907 GLU cc_start: 0.7584 (pm20) cc_final: 0.7223 (pm20) REVERT: B 927 SER cc_start: 0.8142 (p) cc_final: 0.7803 (t) REVERT: B 936 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8156 (m-30) REVERT: B 977 ASP cc_start: 0.8622 (t70) cc_final: 0.8365 (t70) REVERT: C 216 SER cc_start: 0.8973 (m) cc_final: 0.8354 (t) REVERT: C 219 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8580 (p0) REVERT: C 232 LYS cc_start: 0.5485 (OUTLIER) cc_final: 0.4612 (mtpt) REVERT: C 235 THR cc_start: 0.8773 (m) cc_final: 0.8075 (p) REVERT: C 254 GLN cc_start: 0.8144 (mp10) cc_final: 0.7695 (mp10) REVERT: C 257 MET cc_start: 0.8246 (mmm) cc_final: 0.7931 (mmm) REVERT: C 270 MET cc_start: 0.7629 (mtp) cc_final: 0.7289 (mtt) REVERT: C 313 MET cc_start: 0.0122 (mtp) cc_final: -0.0393 (mtt) REVERT: C 329 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6239 (pp) REVERT: C 365 ASP cc_start: 0.8637 (p0) cc_final: 0.8341 (p0) REVERT: C 371 LYS cc_start: 0.9272 (mtpt) cc_final: 0.9002 (mtpp) REVERT: C 378 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7539 (m-40) REVERT: C 386 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8068 (mm-40) REVERT: C 481 TYR cc_start: 0.8904 (m-80) cc_final: 0.7624 (m-80) REVERT: C 573 MET cc_start: 0.8140 (mmt) cc_final: 0.7833 (tpp) REVERT: C 601 VAL cc_start: 0.8792 (t) cc_final: 0.8569 (p) REVERT: C 607 HIS cc_start: 0.8057 (t-90) cc_final: 0.7529 (t-170) REVERT: C 617 MET cc_start: 0.9033 (tpp) cc_final: 0.8509 (tpt) REVERT: C 644 LEU cc_start: 0.7810 (mt) cc_final: 0.7244 (mt) REVERT: C 702 MET cc_start: 0.8350 (ttm) cc_final: 0.7782 (tmm) REVERT: C 720 ASN cc_start: 0.6550 (m110) cc_final: 0.6162 (m110) REVERT: C 744 PHE cc_start: 0.8201 (t80) cc_final: 0.6748 (t80) REVERT: C 756 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8411 (mt-10) REVERT: C 786 THR cc_start: 0.8807 (p) cc_final: 0.8577 (t) REVERT: C 839 MET cc_start: 0.5738 (mmm) cc_final: 0.5390 (mmm) REVERT: C 860 MET cc_start: 0.8214 (ttp) cc_final: 0.7694 (tmm) REVERT: C 889 ILE cc_start: 0.8692 (mt) cc_final: 0.8430 (tp) REVERT: C 905 MET cc_start: 0.7350 (ptp) cc_final: 0.7079 (ptp) REVERT: C 909 GLN cc_start: 0.7118 (pm20) cc_final: 0.6692 (pm20) REVERT: C 927 SER cc_start: 0.7874 (p) cc_final: 0.7494 (t) REVERT: C 936 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: C 941 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6328 (mtp-110) outliers start: 151 outliers final: 116 residues processed: 597 average time/residue: 0.1472 time to fit residues: 141.4564 Evaluate side-chains 600 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 461 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 557 ASN Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 834 TRP Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 981 GLU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1001 HIS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 406 TYR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 652 TRP Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 851 TYR Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1001 HIS Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 455 TRP Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 471 ASN Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 652 TRP Chi-restraints excluded: chain C residue 657 ASP Chi-restraints excluded: chain C residue 663 GLN Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 787 PHE Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 799 SER Chi-restraints excluded: chain C residue 817 SER Chi-restraints excluded: chain C residue 834 TRP Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 911 TYR Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 935 CYS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 941 ARG Chi-restraints excluded: chain C residue 1010 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 147 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 245 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 chunk 97 optimal weight: 0.2980 chunk 21 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 236 optimal weight: 9.9990 chunk 288 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.145533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.109898 restraints weight = 33010.063| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.75 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24025 Z= 0.111 Angle : 0.617 12.621 32656 Z= 0.317 Chirality : 0.045 0.407 3482 Planarity : 0.004 0.120 4313 Dihedral : 7.871 59.450 3416 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 5.53 % Allowed : 27.47 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: -1.96 (0.15), residues: 2953 helix: 0.40 (0.34), residues: 284 sheet: -0.27 (0.22), residues: 582 loop : -2.00 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.026 0.001 TYR A 856 PHE 0.021 0.001 PHE C 689 TRP 0.026 0.002 TRP B 509 HIS 0.006 0.001 HIS C 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (24025) covalent geometry : angle 0.61690 / 0.32 (32656) hydrogen bonds : bond 0.03260 / 2.22 ( 580) hydrogen bonds : angle 5.45269 / 3.68 ( 1365) =============================================================================== Job complete usr+sys time: 5320.84 seconds wall clock time: 92 minutes 14.46 seconds (5534.46 seconds total)