Starting phenix.real_space_refine on Sat Mar 7 06:06:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zgu_14713/03_2026/7zgu_14713.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zgu_14713/03_2026/7zgu_14713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zgu_14713/03_2026/7zgu_14713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zgu_14713/03_2026/7zgu_14713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zgu_14713/03_2026/7zgu_14713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zgu_14713/03_2026/7zgu_14713.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 330 5.16 5 C 24810 2.51 5 N 6618 2.21 5 O 7170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38940 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6463 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 22, 'TRANS': 786} Chain breaks: 5 Chain: "B" Number of atoms: 6463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6463 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 22, 'TRANS': 786} Chain breaks: 5 Chain: "C" Number of atoms: 6463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6463 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 22, 'TRANS': 786} Chain breaks: 5 Chain: "D" Number of atoms: 6463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6463 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 22, 'TRANS': 786} Chain breaks: 5 Chain: "E" Number of atoms: 6463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6463 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 22, 'TRANS': 786} Chain breaks: 5 Chain: "F" Number of atoms: 6463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6463 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 22, 'TRANS': 786} Chain breaks: 5 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.80, per 1000 atoms: 0.23 Number of scatterers: 38940 At special positions: 0 Unit cell: (157.08, 165.24, 140.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 330 16.00 P 12 15.00 O 7170 8.00 N 6618 7.00 C 24810 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: 3.18 Conformation dependent library (CDL) restraints added in 1.7 seconds 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9192 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 18 sheets defined 54.9% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 134 through 148 removed outlier: 3.551A pdb=" N LYS A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.520A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.628A pdb=" N ALA A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 280 removed outlier: 3.503A pdb=" N SER A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 327 through 338 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.531A pdb=" N LEU A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 Processing helix chain 'A' and resid 388 through 402 removed outlier: 3.576A pdb=" N ARG A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 removed outlier: 3.819A pdb=" N THR A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 425 Processing helix chain 'A' and resid 438 through 452 Processing helix chain 'A' and resid 462 through 479 removed outlier: 3.622A pdb=" N LEU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 493 Processing helix chain 'A' and resid 495 through 505 removed outlier: 4.031A pdb=" N MET A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 537 removed outlier: 3.728A pdb=" N TYR A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 564 removed outlier: 4.710A pdb=" N THR A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL A 560 " --> pdb=" O ARG A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.623A pdb=" N LYS A 570 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.596A pdb=" N ARG A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.632A pdb=" N LEU A 592 " --> pdb=" O THR A 589 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU A 593 " --> pdb=" O SER A 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 589 through 593' Processing helix chain 'A' and resid 597 through 618 removed outlier: 3.526A pdb=" N SER A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 636 Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 659 through 671 removed outlier: 3.547A pdb=" N CYS A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 739 removed outlier: 3.615A pdb=" N ARG A 731 " --> pdb=" O SER A 727 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLY A 732 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 733 " --> pdb=" O PHE A 729 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 736 " --> pdb=" O GLY A 732 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 737 " --> pdb=" O LEU A 733 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 738 " --> pdb=" O PHE A 734 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 739 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 766 Processing helix chain 'A' and resid 783 through 785 No H-bonds generated for 'chain 'A' and resid 783 through 785' Processing helix chain 'A' and resid 786 through 797 removed outlier: 3.564A pdb=" N LEU A 792 " --> pdb=" O PHE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 824 removed outlier: 3.721A pdb=" N VAL A 820 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 854 removed outlier: 3.997A pdb=" N CYS A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP A 846 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER A 849 " --> pdb=" O GLN A 845 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 850 " --> pdb=" O ASP A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 880 removed outlier: 3.704A pdb=" N LYS A 878 " --> pdb=" O ILE A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 912 removed outlier: 4.193A pdb=" N SER A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 937 removed outlier: 3.790A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 956 No H-bonds generated for 'chain 'A' and resid 954 through 956' Processing helix chain 'A' and resid 957 through 968 removed outlier: 3.905A pdb=" N LEU A 961 " --> pdb=" O CYS A 957 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 962 " --> pdb=" O CYS A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.702A pdb=" N VAL A 986 " --> pdb=" O GLY A 982 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU A 991 " --> pdb=" O MET A 987 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 992 " --> pdb=" O MET A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1025 removed outlier: 3.549A pdb=" N SER A1016 " --> pdb=" O TYR A1012 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA A1017 " --> pdb=" O GLU A1013 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU A1023 " --> pdb=" O GLU A1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.505A pdb=" N ARG B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 removed outlier: 3.520A pdb=" N TYR B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.628A pdb=" N ALA B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 removed outlier: 3.503A pdb=" N SER B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS B 280 " --> pdb=" O ILE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 327 through 338 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 354 through 362 removed outlier: 3.531A pdb=" N LEU B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 361 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 386 Processing helix chain 'B' and resid 388 through 402 removed outlier: 3.576A pdb=" N ARG B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.819A pdb=" N THR B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 425 Processing helix chain 'B' and resid 438 through 452 Processing helix chain 'B' and resid 462 through 479 removed outlier: 3.621A pdb=" N LEU B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 493 Processing helix chain 'B' and resid 495 through 505 removed outlier: 4.031A pdb=" N MET B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 537 removed outlier: 3.728A pdb=" N TYR B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 564 removed outlier: 4.711A pdb=" N THR B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL B 560 " --> pdb=" O ARG B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 571 removed outlier: 3.622A pdb=" N LYS B 570 " --> pdb=" O LYS B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.596A pdb=" N ARG B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 584 " --> pdb=" O LEU B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 593 removed outlier: 3.632A pdb=" N LEU B 592 " --> pdb=" O THR B 589 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 593 " --> pdb=" O SER B 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 589 through 593' Processing helix chain 'B' and resid 597 through 618 removed outlier: 3.526A pdb=" N SER B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 636 Processing helix chain 'B' and resid 639 through 648 Processing helix chain 'B' and resid 659 through 671 removed outlier: 3.549A pdb=" N CYS B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 739 removed outlier: 3.615A pdb=" N ARG B 731 " --> pdb=" O SER B 727 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLY B 732 " --> pdb=" O SER B 728 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 733 " --> pdb=" O PHE B 729 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 736 " --> pdb=" O GLY B 732 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 738 " --> pdb=" O PHE B 734 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 766 Processing helix chain 'B' and resid 783 through 785 No H-bonds generated for 'chain 'B' and resid 783 through 785' Processing helix chain 'B' and resid 786 through 797 removed outlier: 3.565A pdb=" N LEU B 792 " --> pdb=" O PHE B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 824 removed outlier: 3.722A pdb=" N VAL B 820 " --> pdb=" O ARG B 816 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 821 " --> pdb=" O LEU B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 854 removed outlier: 3.996A pdb=" N CYS B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN B 845 " --> pdb=" O SER B 841 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP B 846 " --> pdb=" O ALA B 842 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER B 849 " --> pdb=" O GLN B 845 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B 850 " --> pdb=" O ASP B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 880 removed outlier: 3.704A pdb=" N LYS B 878 " --> pdb=" O ILE B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 912 removed outlier: 4.193A pdb=" N SER B 902 " --> pdb=" O SER B 898 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B 903 " --> pdb=" O VAL B 899 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN B 912 " --> pdb=" O LEU B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 937 removed outlier: 3.790A pdb=" N GLY B 935 " --> pdb=" O LEU B 931 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 936 " --> pdb=" O LEU B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 956 No H-bonds generated for 'chain 'B' and resid 954 through 956' Processing helix chain 'B' and resid 957 through 968 removed outlier: 3.905A pdb=" N LEU B 961 " --> pdb=" O CYS B 957 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 962 " --> pdb=" O CYS B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 995 removed outlier: 3.701A pdb=" N VAL B 986 " --> pdb=" O GLY B 982 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 991 " --> pdb=" O MET B 987 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B 992 " --> pdb=" O MET B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1025 removed outlier: 3.549A pdb=" N SER B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA B1017 " --> pdb=" O GLU B1013 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B1018 " --> pdb=" O THR B1014 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B1019 " --> pdb=" O LYS B1015 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B1021 " --> pdb=" O ALA B1017 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU B1023 " --> pdb=" O GLU B1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 148 removed outlier: 3.505A pdb=" N ARG C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 168 removed outlier: 3.520A pdb=" N TYR C 168 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.629A pdb=" N ALA C 236 " --> pdb=" O LYS C 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 280 removed outlier: 3.503A pdb=" N SER C 278 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS C 280 " --> pdb=" O ILE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 327 through 338 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 354 through 362 removed outlier: 3.532A pdb=" N LEU C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 361 " --> pdb=" O LYS C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 386 Processing helix chain 'C' and resid 388 through 402 removed outlier: 3.576A pdb=" N ARG C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA C 394 " --> pdb=" O ALA C 390 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN C 402 " --> pdb=" O LEU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 3.819A pdb=" N THR C 407 " --> pdb=" O GLU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 438 through 452 Processing helix chain 'C' and resid 462 through 479 removed outlier: 3.621A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 493 Processing helix chain 'C' and resid 495 through 505 removed outlier: 4.031A pdb=" N MET C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 537 removed outlier: 3.728A pdb=" N TYR C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 535 " --> pdb=" O ALA C 531 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU C 537 " --> pdb=" O TYR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 564 removed outlier: 4.710A pdb=" N THR C 559 " --> pdb=" O SER C 555 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL C 560 " --> pdb=" O ARG C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 571 removed outlier: 3.622A pdb=" N LYS C 570 " --> pdb=" O LYS C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 584 removed outlier: 3.597A pdb=" N ARG C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 584 " --> pdb=" O LEU C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 593 removed outlier: 3.632A pdb=" N LEU C 592 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU C 593 " --> pdb=" O SER C 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 589 through 593' Processing helix chain 'C' and resid 597 through 618 removed outlier: 3.526A pdb=" N SER C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 636 Processing helix chain 'C' and resid 639 through 648 Processing helix chain 'C' and resid 659 through 671 removed outlier: 3.548A pdb=" N CYS C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 739 removed outlier: 3.615A pdb=" N ARG C 731 " --> pdb=" O SER C 727 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLY C 732 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU C 733 " --> pdb=" O PHE C 729 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 736 " --> pdb=" O GLY C 732 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 737 " --> pdb=" O LEU C 733 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 738 " --> pdb=" O PHE C 734 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 739 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 766 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 786 through 797 removed outlier: 3.564A pdb=" N LEU C 792 " --> pdb=" O PHE C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 824 removed outlier: 3.721A pdb=" N VAL C 820 " --> pdb=" O ARG C 816 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY C 821 " --> pdb=" O LEU C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 854 removed outlier: 3.996A pdb=" N CYS C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN C 845 " --> pdb=" O SER C 841 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP C 846 " --> pdb=" O ALA C 842 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER C 849 " --> pdb=" O GLN C 845 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 850 " --> pdb=" O ASP C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 880 removed outlier: 3.704A pdb=" N LYS C 878 " --> pdb=" O ILE C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 912 removed outlier: 4.194A pdb=" N SER C 902 " --> pdb=" O SER C 898 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA C 903 " --> pdb=" O VAL C 899 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN C 912 " --> pdb=" O LEU C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 937 removed outlier: 3.789A pdb=" N GLY C 935 " --> pdb=" O LEU C 931 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 936 " --> pdb=" O LEU C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 956 No H-bonds generated for 'chain 'C' and resid 954 through 956' Processing helix chain 'C' and resid 957 through 968 removed outlier: 3.905A pdb=" N LEU C 961 " --> pdb=" O CYS C 957 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C 962 " --> pdb=" O CYS C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 995 removed outlier: 3.702A pdb=" N VAL C 986 " --> pdb=" O GLY C 982 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 991 " --> pdb=" O MET C 987 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 992 " --> pdb=" O MET C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1011 through 1025 removed outlier: 3.549A pdb=" N SER C1016 " --> pdb=" O TYR C1012 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA C1017 " --> pdb=" O GLU C1013 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C1018 " --> pdb=" O THR C1014 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU C1019 " --> pdb=" O LYS C1015 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C1021 " --> pdb=" O ALA C1017 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU C1023 " --> pdb=" O GLU C1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 148 removed outlier: 3.505A pdb=" N ARG D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 146 " --> pdb=" O LYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 removed outlier: 3.520A pdb=" N TYR D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.629A pdb=" N ALA D 236 " --> pdb=" O LYS D 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 280 removed outlier: 3.502A pdb=" N SER D 278 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS D 279 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS D 280 " --> pdb=" O ILE D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 293 through 295 No H-bonds generated for 'chain 'D' and resid 293 through 295' Processing helix chain 'D' and resid 303 through 307 Processing helix chain 'D' and resid 327 through 338 Processing helix chain 'D' and resid 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 354 through 362 removed outlier: 3.532A pdb=" N LEU D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU D 361 " --> pdb=" O LYS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 386 Processing helix chain 'D' and resid 388 through 402 removed outlier: 3.576A pdb=" N ARG D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA D 394 " --> pdb=" O ALA D 390 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN D 402 " --> pdb=" O LEU D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 409 removed outlier: 3.819A pdb=" N THR D 407 " --> pdb=" O GLU D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 425 Processing helix chain 'D' and resid 438 through 452 Processing helix chain 'D' and resid 462 through 479 removed outlier: 3.621A pdb=" N LEU D 472 " --> pdb=" O GLY D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 493 Processing helix chain 'D' and resid 495 through 505 removed outlier: 4.031A pdb=" N MET D 505 " --> pdb=" O ALA D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 537 removed outlier: 3.729A pdb=" N TYR D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU D 537 " --> pdb=" O TYR D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 564 removed outlier: 4.711A pdb=" N THR D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL D 560 " --> pdb=" O ARG D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 571 removed outlier: 3.623A pdb=" N LYS D 570 " --> pdb=" O LYS D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.597A pdb=" N ARG D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 584 " --> pdb=" O LEU D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 593 removed outlier: 3.632A pdb=" N LEU D 592 " --> pdb=" O THR D 589 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU D 593 " --> pdb=" O SER D 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 589 through 593' Processing helix chain 'D' and resid 597 through 618 removed outlier: 3.526A pdb=" N SER D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 636 Processing helix chain 'D' and resid 639 through 648 Processing helix chain 'D' and resid 659 through 671 removed outlier: 3.548A pdb=" N CYS D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 739 removed outlier: 3.615A pdb=" N ARG D 731 " --> pdb=" O SER D 727 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLY D 732 " --> pdb=" O SER D 728 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU D 733 " --> pdb=" O PHE D 729 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 737 " --> pdb=" O LEU D 733 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER D 738 " --> pdb=" O PHE D 734 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 739 " --> pdb=" O SER D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 754 through 766 Processing helix chain 'D' and resid 783 through 785 No H-bonds generated for 'chain 'D' and resid 783 through 785' Processing helix chain 'D' and resid 786 through 797 removed outlier: 3.564A pdb=" N LEU D 792 " --> pdb=" O PHE D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 824 removed outlier: 3.721A pdb=" N VAL D 820 " --> pdb=" O ARG D 816 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY D 821 " --> pdb=" O LEU D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 854 removed outlier: 3.996A pdb=" N CYS D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN D 845 " --> pdb=" O SER D 841 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP D 846 " --> pdb=" O ALA D 842 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER D 849 " --> pdb=" O GLN D 845 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL D 850 " --> pdb=" O ASP D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 880 removed outlier: 3.704A pdb=" N LYS D 878 " --> pdb=" O ILE D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 898 through 912 removed outlier: 4.194A pdb=" N SER D 902 " --> pdb=" O SER D 898 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA D 903 " --> pdb=" O VAL D 899 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN D 912 " --> pdb=" O LEU D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 927 through 937 removed outlier: 3.789A pdb=" N GLY D 935 " --> pdb=" O LEU D 931 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 936 " --> pdb=" O LEU D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 956 No H-bonds generated for 'chain 'D' and resid 954 through 956' Processing helix chain 'D' and resid 957 through 968 removed outlier: 3.905A pdb=" N LEU D 961 " --> pdb=" O CYS D 957 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 962 " --> pdb=" O CYS D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 995 removed outlier: 3.702A pdb=" N VAL D 986 " --> pdb=" O GLY D 982 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU D 991 " --> pdb=" O MET D 987 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL D 992 " --> pdb=" O MET D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1011 through 1025 removed outlier: 3.548A pdb=" N SER D1016 " --> pdb=" O TYR D1012 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA D1017 " --> pdb=" O GLU D1013 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D1018 " --> pdb=" O THR D1014 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU D1019 " --> pdb=" O LYS D1015 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU D1021 " --> pdb=" O ALA D1017 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU D1023 " --> pdb=" O GLU D1019 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 148 removed outlier: 3.505A pdb=" N ARG E 145 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER E 146 " --> pdb=" O LYS E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 168 removed outlier: 3.520A pdb=" N TYR E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 245 removed outlier: 3.629A pdb=" N ALA E 236 " --> pdb=" O LYS E 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 280 removed outlier: 3.503A pdb=" N SER E 278 " --> pdb=" O ASP E 274 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS E 280 " --> pdb=" O ILE E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 290 Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 327 through 338 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 354 through 362 removed outlier: 3.531A pdb=" N LEU E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS E 360 " --> pdb=" O GLU E 356 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU E 361 " --> pdb=" O LYS E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 386 Processing helix chain 'E' and resid 388 through 402 removed outlier: 3.576A pdb=" N ARG E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA E 394 " --> pdb=" O ALA E 390 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN E 402 " --> pdb=" O LEU E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 409 removed outlier: 3.819A pdb=" N THR E 407 " --> pdb=" O GLU E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 425 Processing helix chain 'E' and resid 438 through 452 Processing helix chain 'E' and resid 462 through 479 removed outlier: 3.621A pdb=" N LEU E 472 " --> pdb=" O GLY E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 493 Processing helix chain 'E' and resid 495 through 505 removed outlier: 4.031A pdb=" N MET E 505 " --> pdb=" O ALA E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 537 removed outlier: 3.728A pdb=" N TYR E 534 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU E 535 " --> pdb=" O ALA E 531 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU E 537 " --> pdb=" O TYR E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 564 removed outlier: 4.710A pdb=" N THR E 559 " --> pdb=" O SER E 555 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL E 560 " --> pdb=" O ARG E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 571 removed outlier: 3.623A pdb=" N LYS E 570 " --> pdb=" O LYS E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 584 removed outlier: 3.597A pdb=" N ARG E 578 " --> pdb=" O ILE E 574 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL E 584 " --> pdb=" O LEU E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 593 removed outlier: 3.633A pdb=" N LEU E 592 " --> pdb=" O THR E 589 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU E 593 " --> pdb=" O SER E 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 589 through 593' Processing helix chain 'E' and resid 597 through 618 removed outlier: 3.526A pdb=" N SER E 601 " --> pdb=" O SER E 597 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 636 Processing helix chain 'E' and resid 639 through 648 Processing helix chain 'E' and resid 659 through 671 removed outlier: 3.549A pdb=" N CYS E 669 " --> pdb=" O VAL E 665 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 739 removed outlier: 3.615A pdb=" N ARG E 731 " --> pdb=" O SER E 727 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLY E 732 " --> pdb=" O SER E 728 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU E 733 " --> pdb=" O PHE E 729 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL E 736 " --> pdb=" O GLY E 732 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU E 737 " --> pdb=" O LEU E 733 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER E 738 " --> pdb=" O PHE E 734 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR E 739 " --> pdb=" O SER E 735 " (cutoff:3.500A) Processing helix chain 'E' and resid 754 through 766 Processing helix chain 'E' and resid 783 through 785 No H-bonds generated for 'chain 'E' and resid 783 through 785' Processing helix chain 'E' and resid 786 through 797 removed outlier: 3.564A pdb=" N LEU E 792 " --> pdb=" O PHE E 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 811 through 824 removed outlier: 3.721A pdb=" N VAL E 820 " --> pdb=" O ARG E 816 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY E 821 " --> pdb=" O LEU E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 840 through 854 removed outlier: 3.995A pdb=" N CYS E 844 " --> pdb=" O THR E 840 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN E 845 " --> pdb=" O SER E 841 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP E 846 " --> pdb=" O ALA E 842 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER E 849 " --> pdb=" O GLN E 845 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL E 850 " --> pdb=" O ASP E 846 " (cutoff:3.500A) Processing helix chain 'E' and resid 868 through 880 removed outlier: 3.704A pdb=" N LYS E 878 " --> pdb=" O ILE E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 898 through 912 removed outlier: 4.194A pdb=" N SER E 902 " --> pdb=" O SER E 898 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA E 903 " --> pdb=" O VAL E 899 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN E 912 " --> pdb=" O LEU E 908 " (cutoff:3.500A) Processing helix chain 'E' and resid 927 through 937 removed outlier: 3.790A pdb=" N GLY E 935 " --> pdb=" O LEU E 931 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 936 " --> pdb=" O LEU E 932 " (cutoff:3.500A) Processing helix chain 'E' and resid 954 through 956 No H-bonds generated for 'chain 'E' and resid 954 through 956' Processing helix chain 'E' and resid 957 through 968 removed outlier: 3.905A pdb=" N LEU E 961 " --> pdb=" O CYS E 957 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER E 962 " --> pdb=" O CYS E 958 " (cutoff:3.500A) Processing helix chain 'E' and resid 982 through 995 removed outlier: 3.702A pdb=" N VAL E 986 " --> pdb=" O GLY E 982 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU E 991 " --> pdb=" O MET E 987 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL E 992 " --> pdb=" O MET E 988 " (cutoff:3.500A) Processing helix chain 'E' and resid 1011 through 1025 removed outlier: 3.549A pdb=" N SER E1016 " --> pdb=" O TYR E1012 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA E1017 " --> pdb=" O GLU E1013 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU E1018 " --> pdb=" O THR E1014 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU E1019 " --> pdb=" O LYS E1015 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU E1021 " --> pdb=" O ALA E1017 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU E1023 " --> pdb=" O GLU E1019 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 148 removed outlier: 3.505A pdb=" N ARG F 145 " --> pdb=" O ARG F 141 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER F 146 " --> pdb=" O LYS F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 168 removed outlier: 3.519A pdb=" N TYR F 168 " --> pdb=" O LEU F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 245 removed outlier: 3.629A pdb=" N ALA F 236 " --> pdb=" O LYS F 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG F 237 " --> pdb=" O THR F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 280 removed outlier: 3.503A pdb=" N SER F 278 " --> pdb=" O ASP F 274 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS F 279 " --> pdb=" O LEU F 275 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS F 280 " --> pdb=" O ILE F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 290 Processing helix chain 'F' and resid 293 through 295 No H-bonds generated for 'chain 'F' and resid 293 through 295' Processing helix chain 'F' and resid 303 through 307 Processing helix chain 'F' and resid 327 through 338 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 354 through 362 removed outlier: 3.531A pdb=" N LEU F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU F 361 " --> pdb=" O LYS F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 386 Processing helix chain 'F' and resid 388 through 402 removed outlier: 3.576A pdb=" N ARG F 393 " --> pdb=" O GLU F 389 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN F 402 " --> pdb=" O LEU F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 409 removed outlier: 3.819A pdb=" N THR F 407 " --> pdb=" O GLU F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 425 Processing helix chain 'F' and resid 438 through 452 Processing helix chain 'F' and resid 462 through 479 removed outlier: 3.622A pdb=" N LEU F 472 " --> pdb=" O GLY F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 493 Processing helix chain 'F' and resid 495 through 505 removed outlier: 4.031A pdb=" N MET F 505 " --> pdb=" O ALA F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 537 removed outlier: 3.728A pdb=" N TYR F 534 " --> pdb=" O ALA F 530 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 535 " --> pdb=" O ALA F 531 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU F 537 " --> pdb=" O TYR F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 564 removed outlier: 4.711A pdb=" N THR F 559 " --> pdb=" O SER F 555 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL F 560 " --> pdb=" O ARG F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 567 through 571 removed outlier: 3.623A pdb=" N LYS F 570 " --> pdb=" O LYS F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 584 removed outlier: 3.597A pdb=" N ARG F 578 " --> pdb=" O ILE F 574 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL F 584 " --> pdb=" O LEU F 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 589 through 593 removed outlier: 3.633A pdb=" N LEU F 592 " --> pdb=" O THR F 589 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU F 593 " --> pdb=" O SER F 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 589 through 593' Processing helix chain 'F' and resid 597 through 618 removed outlier: 3.526A pdb=" N SER F 601 " --> pdb=" O SER F 597 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 636 Processing helix chain 'F' and resid 639 through 648 Processing helix chain 'F' and resid 659 through 671 removed outlier: 3.548A pdb=" N CYS F 669 " --> pdb=" O VAL F 665 " (cutoff:3.500A) Processing helix chain 'F' and resid 726 through 739 removed outlier: 3.616A pdb=" N ARG F 731 " --> pdb=" O SER F 727 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N GLY F 732 " --> pdb=" O SER F 728 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU F 733 " --> pdb=" O PHE F 729 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 736 " --> pdb=" O GLY F 732 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 737 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER F 738 " --> pdb=" O PHE F 734 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR F 739 " --> pdb=" O SER F 735 " (cutoff:3.500A) Processing helix chain 'F' and resid 754 through 766 Processing helix chain 'F' and resid 783 through 785 No H-bonds generated for 'chain 'F' and resid 783 through 785' Processing helix chain 'F' and resid 786 through 797 removed outlier: 3.563A pdb=" N LEU F 792 " --> pdb=" O PHE F 788 " (cutoff:3.500A) Processing helix chain 'F' and resid 811 through 824 removed outlier: 3.721A pdb=" N VAL F 820 " --> pdb=" O ARG F 816 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY F 821 " --> pdb=" O LEU F 817 " (cutoff:3.500A) Processing helix chain 'F' and resid 840 through 854 removed outlier: 3.996A pdb=" N CYS F 844 " --> pdb=" O THR F 840 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN F 845 " --> pdb=" O SER F 841 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP F 846 " --> pdb=" O ALA F 842 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER F 849 " --> pdb=" O GLN F 845 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL F 850 " --> pdb=" O ASP F 846 " (cutoff:3.500A) Processing helix chain 'F' and resid 868 through 880 removed outlier: 3.703A pdb=" N LYS F 878 " --> pdb=" O ILE F 874 " (cutoff:3.500A) Processing helix chain 'F' and resid 898 through 912 removed outlier: 4.193A pdb=" N SER F 902 " --> pdb=" O SER F 898 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA F 903 " --> pdb=" O VAL F 899 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN F 912 " --> pdb=" O LEU F 908 " (cutoff:3.500A) Processing helix chain 'F' and resid 927 through 937 removed outlier: 3.789A pdb=" N GLY F 935 " --> pdb=" O LEU F 931 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 936 " --> pdb=" O LEU F 932 " (cutoff:3.500A) Processing helix chain 'F' and resid 954 through 956 No H-bonds generated for 'chain 'F' and resid 954 through 956' Processing helix chain 'F' and resid 957 through 968 removed outlier: 3.904A pdb=" N LEU F 961 " --> pdb=" O CYS F 957 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER F 962 " --> pdb=" O CYS F 958 " (cutoff:3.500A) Processing helix chain 'F' and resid 982 through 995 removed outlier: 3.702A pdb=" N VAL F 986 " --> pdb=" O GLY F 982 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU F 991 " --> pdb=" O MET F 987 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL F 992 " --> pdb=" O MET F 988 " (cutoff:3.500A) Processing helix chain 'F' and resid 1011 through 1025 removed outlier: 3.548A pdb=" N SER F1016 " --> pdb=" O TYR F1012 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA F1017 " --> pdb=" O GLU F1013 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU F1018 " --> pdb=" O THR F1014 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU F1019 " --> pdb=" O LYS F1015 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU F1021 " --> pdb=" O ALA F1017 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU F1023 " --> pdb=" O GLU F1019 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 175 removed outlier: 6.805A pdb=" N VAL A 222 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR A 350 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N PHE A 224 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE A 297 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N LEU A 347 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE A 299 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR A 349 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N MET A 301 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N TYR A 255 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU A 300 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE A 257 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP A 302 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE A 259 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 652 through 654 removed outlier: 7.055A pdb=" N LEU A 679 " --> pdb=" O ASP A 747 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU A 803 " --> pdb=" O TRP A 833 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 916 through 920 removed outlier: 3.509A pdb=" N GLU A 947 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 949 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A1003 " --> pdb=" O THR A1029 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 175 removed outlier: 6.806A pdb=" N VAL B 222 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N THR B 350 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N PHE B 224 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE B 297 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N LEU B 347 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE B 299 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR B 349 " --> pdb=" O PHE B 299 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N MET B 301 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N TYR B 255 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU B 300 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE B 257 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP B 302 " --> pdb=" O PHE B 257 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE B 259 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 652 through 654 removed outlier: 7.054A pdb=" N LEU B 679 " --> pdb=" O ASP B 747 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU B 803 " --> pdb=" O TRP B 833 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 916 through 920 removed outlier: 3.509A pdb=" N GLU B 947 " --> pdb=" O LEU B 917 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B 949 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B1003 " --> pdb=" O THR B1029 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 173 through 175 removed outlier: 6.805A pdb=" N VAL C 222 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR C 350 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N PHE C 224 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE C 297 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N LEU C 347 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE C 299 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR C 349 " --> pdb=" O PHE C 299 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N MET C 301 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N TYR C 255 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU C 300 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE C 257 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP C 302 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE C 259 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 652 through 654 removed outlier: 7.054A pdb=" N LEU C 679 " --> pdb=" O ASP C 747 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU C 803 " --> pdb=" O TRP C 833 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 916 through 920 removed outlier: 3.508A pdb=" N GLU C 947 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP C 949 " --> pdb=" O LEU C 919 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C1003 " --> pdb=" O THR C1029 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 173 through 175 removed outlier: 6.805A pdb=" N VAL D 222 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR D 350 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N PHE D 224 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE D 297 " --> pdb=" O SER D 345 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N LEU D 347 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE D 299 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR D 349 " --> pdb=" O PHE D 299 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N MET D 301 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU D 298 " --> pdb=" O TYR D 255 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 652 through 654 removed outlier: 7.055A pdb=" N LEU D 679 " --> pdb=" O ASP D 747 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU D 803 " --> pdb=" O TRP D 833 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 916 through 920 removed outlier: 3.509A pdb=" N GLU D 947 " --> pdb=" O LEU D 917 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP D 949 " --> pdb=" O LEU D 919 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D1003 " --> pdb=" O THR D1029 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 173 through 175 removed outlier: 6.805A pdb=" N VAL E 222 " --> pdb=" O ILE E 348 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR E 350 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N PHE E 224 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE E 297 " --> pdb=" O SER E 345 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N LEU E 347 " --> pdb=" O ILE E 297 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE E 299 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR E 349 " --> pdb=" O PHE E 299 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N MET E 301 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU E 298 " --> pdb=" O TYR E 255 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 652 through 654 removed outlier: 7.054A pdb=" N LEU E 679 " --> pdb=" O ASP E 747 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU E 803 " --> pdb=" O TRP E 833 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 916 through 920 removed outlier: 3.509A pdb=" N GLU E 947 " --> pdb=" O LEU E 917 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP E 949 " --> pdb=" O LEU E 919 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU E1003 " --> pdb=" O THR E1029 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 173 through 175 removed outlier: 6.805A pdb=" N VAL F 222 " --> pdb=" O ILE F 348 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR F 350 " --> pdb=" O VAL F 222 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N PHE F 224 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE F 297 " --> pdb=" O SER F 345 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N LEU F 347 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE F 299 " --> pdb=" O LEU F 347 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR F 349 " --> pdb=" O PHE F 299 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N MET F 301 " --> pdb=" O THR F 349 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N TYR F 255 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU F 300 " --> pdb=" O TYR F 255 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE F 257 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP F 302 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE F 259 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 652 through 654 removed outlier: 7.055A pdb=" N LEU F 679 " --> pdb=" O ASP F 747 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU F 803 " --> pdb=" O TRP F 833 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 916 through 920 removed outlier: 3.509A pdb=" N GLU F 947 " --> pdb=" O LEU F 917 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP F 949 " --> pdb=" O LEU F 919 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU F1003 " --> pdb=" O THR F1029 " (cutoff:3.500A) 1520 hydrogen bonds defined for protein. 4488 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.11 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 12552 1.35 - 1.47: 9144 1.47 - 1.59: 17544 1.59 - 1.71: 18 1.71 - 1.83: 432 Bond restraints: 39690 Sorted by residual: bond pdb=" CB GLU D1013 " pdb=" CG GLU D1013 " ideal model delta sigma weight residual 1.520 1.583 -0.063 3.00e-02 1.11e+03 4.45e+00 bond pdb=" CB GLU F1013 " pdb=" CG GLU F1013 " ideal model delta sigma weight residual 1.520 1.583 -0.063 3.00e-02 1.11e+03 4.37e+00 bond pdb=" CB GLU A1013 " pdb=" CG GLU A1013 " ideal model delta sigma weight residual 1.520 1.583 -0.063 3.00e-02 1.11e+03 4.36e+00 bond pdb=" CB GLU B1013 " pdb=" CG GLU B1013 " ideal model delta sigma weight residual 1.520 1.582 -0.062 3.00e-02 1.11e+03 4.33e+00 bond pdb=" CB GLU C1013 " pdb=" CG GLU C1013 " ideal model delta sigma weight residual 1.520 1.582 -0.062 3.00e-02 1.11e+03 4.33e+00 ... (remaining 39685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 52841 2.50 - 5.00: 544 5.00 - 7.50: 147 7.50 - 10.00: 6 10.00 - 12.50: 6 Bond angle restraints: 53544 Sorted by residual: angle pdb=" CA GLU D1013 " pdb=" CB GLU D1013 " pdb=" CG GLU D1013 " ideal model delta sigma weight residual 114.10 126.60 -12.50 2.00e+00 2.50e-01 3.91e+01 angle pdb=" CA GLU A1013 " pdb=" CB GLU A1013 " pdb=" CG GLU A1013 " ideal model delta sigma weight residual 114.10 126.58 -12.48 2.00e+00 2.50e-01 3.90e+01 angle pdb=" CA GLU B1013 " pdb=" CB GLU B1013 " pdb=" CG GLU B1013 " ideal model delta sigma weight residual 114.10 126.57 -12.47 2.00e+00 2.50e-01 3.89e+01 angle pdb=" CA GLU F1013 " pdb=" CB GLU F1013 " pdb=" CG GLU F1013 " ideal model delta sigma weight residual 114.10 126.57 -12.47 2.00e+00 2.50e-01 3.89e+01 angle pdb=" CA GLU E1013 " pdb=" CB GLU E1013 " pdb=" CG GLU E1013 " ideal model delta sigma weight residual 114.10 126.55 -12.45 2.00e+00 2.50e-01 3.87e+01 ... (remaining 53539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.23: 22953 29.23 - 58.46: 930 58.46 - 87.69: 78 87.69 - 116.92: 0 116.92 - 146.16: 9 Dihedral angle restraints: 23970 sinusoidal: 9822 harmonic: 14148 Sorted by residual: dihedral pdb=" C5' ADP C1101 " pdb=" O5' ADP C1101 " pdb=" PA ADP C1101 " pdb=" O2A ADP C1101 " ideal model delta sinusoidal sigma weight residual -60.00 86.16 -146.16 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C5' ADP B1101 " pdb=" O5' ADP B1101 " pdb=" PA ADP B1101 " pdb=" O2A ADP B1101 " ideal model delta sinusoidal sigma weight residual -60.00 86.15 -146.15 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C5' ADP A1101 " pdb=" O5' ADP A1101 " pdb=" PA ADP A1101 " pdb=" O2A ADP A1101 " ideal model delta sinusoidal sigma weight residual -60.00 86.13 -146.13 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 23967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3997 0.033 - 0.067: 1527 0.067 - 0.100: 370 0.100 - 0.133: 159 0.133 - 0.166: 25 Chirality restraints: 6078 Sorted by residual: chirality pdb=" CB ILE C 276 " pdb=" CA ILE C 276 " pdb=" CG1 ILE C 276 " pdb=" CG2 ILE C 276 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CB ILE D 276 " pdb=" CA ILE D 276 " pdb=" CG1 ILE D 276 " pdb=" CG2 ILE D 276 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CB ILE A 276 " pdb=" CA ILE A 276 " pdb=" CG1 ILE A 276 " pdb=" CG2 ILE A 276 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 6075 not shown) Planarity restraints: 6714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 284 " 0.045 5.00e-02 4.00e+02 6.71e-02 7.21e+00 pdb=" N PRO B 285 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 285 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 285 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 284 " -0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO F 285 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO F 285 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 285 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 284 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO D 285 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 285 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 285 " 0.037 5.00e-02 4.00e+02 ... (remaining 6711 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3003 2.74 - 3.28: 41224 3.28 - 3.82: 64403 3.82 - 4.36: 77784 4.36 - 4.90: 129605 Nonbonded interactions: 316019 Sorted by model distance: nonbonded pdb=" OH TYR B 632 " pdb=" OD1 ASP B 662 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR F 632 " pdb=" OD1 ASP F 662 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR A 632 " pdb=" OD1 ASP A 662 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR C 632 " pdb=" OD1 ASP C 662 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR D 632 " pdb=" OD1 ASP D 662 " model vdw 2.202 3.040 ... (remaining 316014 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 7.070 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: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 35.480 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 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 : 0.003 0.063 39690 Z= 0.122 Angle : 0.678 12.501 53544 Z= 0.348 Chirality : 0.040 0.166 6078 Planarity : 0.004 0.067 6714 Dihedral : 14.945 146.155 14778 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.55 % Allowed : 0.52 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 4782 helix: 0.25 (0.12), residues: 2052 sheet: -0.77 (0.25), residues: 438 loop : -1.33 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 252 TYR 0.013 0.001 TYR B 249 PHE 0.012 0.001 PHE E 299 TRP 0.022 0.001 TRP C 243 HIS 0.004 0.001 HIS E 522 Details of bonding type rmsd covalent geometry : bond 0.00271 (39690) covalent geometry : angle 0.67847 (53544) hydrogen bonds : bond 0.28921 ( 1520) hydrogen bonds : angle 7.95683 ( 4488) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1133 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 1109 time to evaluate : 1.465 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: A 230 ILE cc_start: 0.8091 (tp) cc_final: 0.7881 (tp) REVERT: A 239 MET cc_start: 0.6788 (ttp) cc_final: 0.6528 (ttp) REVERT: A 276 ILE cc_start: 0.5810 (OUTLIER) cc_final: 0.5587 (mp) REVERT: A 282 ASP cc_start: 0.5810 (p0) cc_final: 0.5595 (p0) REVERT: A 301 MET cc_start: 0.6952 (ttm) cc_final: 0.6602 (ttm) REVERT: A 322 TRP cc_start: 0.7313 (t60) cc_final: 0.6390 (t60) REVERT: A 329 ASP cc_start: 0.7600 (m-30) cc_final: 0.7310 (m-30) REVERT: A 353 VAL cc_start: 0.8778 (p) cc_final: 0.8501 (t) REVERT: A 369 GLU cc_start: 0.6914 (tt0) cc_final: 0.6710 (tt0) REVERT: A 563 GLU cc_start: 0.6575 (pp20) cc_final: 0.6117 (tm-30) REVERT: A 603 GLN cc_start: 0.7920 (tp40) cc_final: 0.7169 (tm-30) REVERT: A 607 GLU cc_start: 0.7609 (tp30) cc_final: 0.7408 (tp30) REVERT: A 611 TRP cc_start: 0.7188 (t60) cc_final: 0.6554 (t60) REVERT: A 631 PHE cc_start: 0.7510 (m-10) cc_final: 0.7234 (m-80) REVERT: A 637 MET cc_start: 0.6915 (tpp) cc_final: 0.6555 (tpp) REVERT: A 645 ARG cc_start: 0.7104 (mtm110) cc_final: 0.6369 (mtm110) REVERT: A 648 ASP cc_start: 0.7533 (m-30) cc_final: 0.7223 (t0) REVERT: A 649 TYR cc_start: 0.7430 (m-80) cc_final: 0.7166 (m-10) REVERT: A 759 ARG cc_start: 0.7864 (ttt180) cc_final: 0.7650 (ttt180) REVERT: A 815 ILE cc_start: 0.8210 (mm) cc_final: 0.7873 (mm) REVERT: A 922 ASN cc_start: 0.5723 (m110) cc_final: 0.5104 (m110) REVERT: A 990 CYS cc_start: 0.7550 (m) cc_final: 0.6781 (m) REVERT: A 1006 SER cc_start: 0.8304 (m) cc_final: 0.7777 (t) REVERT: A 1022 GLN cc_start: 0.7782 (tm-30) cc_final: 0.7581 (tm-30) REVERT: B 174 ILE cc_start: 0.7363 (mt) cc_final: 0.7071 (mt) REVERT: B 239 MET cc_start: 0.6488 (ttp) cc_final: 0.6273 (ttp) REVERT: B 240 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.6199 (ttp) REVERT: B 250 GLN cc_start: 0.6804 (tp40) cc_final: 0.6585 (mm-40) REVERT: B 276 ILE cc_start: 0.6051 (OUTLIER) cc_final: 0.5672 (mp) REVERT: B 282 ASP cc_start: 0.6123 (p0) cc_final: 0.5922 (p0) REVERT: B 288 HIS cc_start: 0.7627 (m90) cc_final: 0.7328 (m90) REVERT: B 367 HIS cc_start: 0.6850 (m-70) cc_final: 0.6612 (m-70) REVERT: B 488 ASP cc_start: 0.7482 (m-30) cc_final: 0.7269 (m-30) REVERT: B 563 GLU cc_start: 0.6705 (pp20) cc_final: 0.5484 (tm-30) REVERT: B 603 GLN cc_start: 0.7768 (tp40) cc_final: 0.7055 (tm-30) REVERT: B 613 GLU cc_start: 0.7477 (tt0) cc_final: 0.7247 (tt0) REVERT: B 629 GLU cc_start: 0.6628 (mm-30) cc_final: 0.6226 (mm-30) REVERT: B 644 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7447 (mm-40) REVERT: B 649 TYR cc_start: 0.7330 (m-80) cc_final: 0.6380 (m-80) REVERT: B 652 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7886 (ttmm) REVERT: B 800 LEU cc_start: 0.8261 (mm) cc_final: 0.7997 (mt) REVERT: B 802 GLU cc_start: 0.6509 (mt-10) cc_final: 0.6241 (mt-10) REVERT: B 815 ILE cc_start: 0.8353 (mm) cc_final: 0.7527 (mm) REVERT: B 816 ARG cc_start: 0.7695 (ttt180) cc_final: 0.7329 (ttt90) REVERT: B 831 LYS cc_start: 0.7920 (mttt) cc_final: 0.7042 (mttm) REVERT: B 934 GLU cc_start: 0.6481 (tm-30) cc_final: 0.5998 (tm-30) REVERT: B 973 LYS cc_start: 0.8165 (ptmt) cc_final: 0.7713 (ptpt) REVERT: B 988 MET cc_start: 0.7536 (mmm) cc_final: 0.7068 (mmm) REVERT: B 989 PHE cc_start: 0.7755 (m-10) cc_final: 0.7413 (m-80) REVERT: B 1006 SER cc_start: 0.8165 (m) cc_final: 0.7702 (p) REVERT: B 1008 MET cc_start: 0.6391 (mmm) cc_final: 0.6067 (ttt) REVERT: B 1025 LYS cc_start: 0.6958 (mmtt) cc_final: 0.6696 (mptt) REVERT: C 239 MET cc_start: 0.6532 (ttp) cc_final: 0.6323 (ttp) REVERT: C 269 GLN cc_start: 0.4153 (mp10) cc_final: 0.3892 (mp10) REVERT: C 276 ILE cc_start: 0.5948 (OUTLIER) cc_final: 0.5656 (mt) REVERT: C 282 ASP cc_start: 0.6116 (p0) cc_final: 0.5813 (p0) REVERT: C 301 MET cc_start: 0.7028 (ttm) cc_final: 0.6791 (ttt) REVERT: C 322 TRP cc_start: 0.7525 (t60) cc_final: 0.7206 (t60) REVERT: C 367 HIS cc_start: 0.6847 (m-70) cc_final: 0.6287 (m-70) REVERT: C 419 CYS cc_start: 0.7753 (m) cc_final: 0.7201 (m) REVERT: C 488 ASP cc_start: 0.7643 (m-30) cc_final: 0.7223 (m-30) REVERT: C 603 GLN cc_start: 0.7934 (tp40) cc_final: 0.7308 (tm-30) REVERT: C 606 LEU cc_start: 0.7612 (mm) cc_final: 0.7298 (mp) REVERT: C 613 GLU cc_start: 0.7183 (tt0) cc_final: 0.6953 (tt0) REVERT: C 638 GLN cc_start: 0.7297 (mm-40) cc_final: 0.7049 (tp40) REVERT: C 649 TYR cc_start: 0.7255 (m-80) cc_final: 0.6997 (m-80) REVERT: C 743 LEU cc_start: 0.7732 (tp) cc_final: 0.7492 (tp) REVERT: C 774 ARG cc_start: 0.7250 (mtm110) cc_final: 0.6677 (mtm110) REVERT: C 853 THR cc_start: 0.8321 (t) cc_final: 0.8015 (p) REVERT: C 859 ARG cc_start: 0.7221 (mtt-85) cc_final: 0.7006 (mtt-85) REVERT: C 912 GLN cc_start: 0.7418 (tt0) cc_final: 0.7146 (tt0) REVERT: C 991 GLU cc_start: 0.7073 (pm20) cc_final: 0.6778 (pm20) REVERT: C 1022 GLN cc_start: 0.8283 (tm-30) cc_final: 0.8029 (tm-30) REVERT: D 142 LYS cc_start: 0.7238 (tttm) cc_final: 0.7031 (tmtt) REVERT: D 171 LEU cc_start: 0.8064 (mt) cc_final: 0.7855 (mp) REVERT: D 238 LYS cc_start: 0.7455 (tptt) cc_final: 0.6978 (tptp) REVERT: D 239 MET cc_start: 0.6640 (ttp) cc_final: 0.6337 (ttp) REVERT: D 240 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.6371 (mtm) REVERT: D 250 GLN cc_start: 0.7245 (tp40) cc_final: 0.6928 (tp40) REVERT: D 258 TYR cc_start: 0.7437 (t80) cc_final: 0.7121 (t80) REVERT: D 271 SER cc_start: 0.6948 (p) cc_final: 0.6738 (t) REVERT: D 322 TRP cc_start: 0.7506 (t60) cc_final: 0.6873 (t60) REVERT: D 329 ASP cc_start: 0.7021 (m-30) cc_final: 0.6751 (t70) REVERT: D 348 ILE cc_start: 0.7391 (pt) cc_final: 0.6904 (mt) REVERT: D 367 HIS cc_start: 0.6879 (m-70) cc_final: 0.6489 (m-70) REVERT: D 533 TYR cc_start: 0.6540 (t80) cc_final: 0.6241 (t80) REVERT: D 563 GLU cc_start: 0.6149 (pp20) cc_final: 0.5295 (tm-30) REVERT: D 607 GLU cc_start: 0.7290 (tp30) cc_final: 0.7022 (tp30) REVERT: D 611 TRP cc_start: 0.6985 (t60) cc_final: 0.6338 (t60) REVERT: D 627 GLN cc_start: 0.7437 (mt0) cc_final: 0.7046 (mt0) REVERT: D 637 MET cc_start: 0.7014 (tpp) cc_final: 0.6797 (tpt) REVERT: D 640 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6435 (mm-30) REVERT: D 641 ASP cc_start: 0.7064 (p0) cc_final: 0.6491 (t0) REVERT: D 644 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7492 (mm-40) REVERT: D 645 ARG cc_start: 0.7121 (mtm110) cc_final: 0.6240 (mtm180) REVERT: D 748 LEU cc_start: 0.7745 (mt) cc_final: 0.7528 (mt) REVERT: D 767 HIS cc_start: 0.7231 (t-90) cc_final: 0.6946 (t-90) REVERT: D 787 CYS cc_start: 0.7368 (m) cc_final: 0.7127 (m) REVERT: D 806 SER cc_start: 0.7619 (p) cc_final: 0.7399 (m) REVERT: D 853 THR cc_start: 0.8287 (t) cc_final: 0.8043 (p) REVERT: D 859 ARG cc_start: 0.7228 (mtt-85) cc_final: 0.7013 (mtt-85) REVERT: D 933 CYS cc_start: 0.6831 (m) cc_final: 0.6545 (m) REVERT: D 973 LYS cc_start: 0.8232 (ptmt) cc_final: 0.7820 (ptpp) REVERT: D 990 CYS cc_start: 0.7714 (m) cc_final: 0.7098 (m) REVERT: D 1019 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7586 (tp30) REVERT: D 1022 GLN cc_start: 0.7829 (tm-30) cc_final: 0.7469 (tm-30) REVERT: D 1030 VAL cc_start: 0.7758 (p) cc_final: 0.7495 (t) REVERT: E 172 ARG cc_start: 0.6796 (mtt90) cc_final: 0.6530 (mtt90) REVERT: E 175 LYS cc_start: 0.7980 (tttt) cc_final: 0.7673 (tttt) REVERT: E 238 LYS cc_start: 0.7604 (tptt) cc_final: 0.7364 (tptt) REVERT: E 282 ASP cc_start: 0.5908 (p0) cc_final: 0.5703 (p0) REVERT: E 289 LYS cc_start: 0.7596 (pttt) cc_final: 0.7392 (pttp) REVERT: E 311 PHE cc_start: 0.7409 (t80) cc_final: 0.7070 (t80) REVERT: E 322 TRP cc_start: 0.6792 (t60) cc_final: 0.6530 (t60) REVERT: E 367 HIS cc_start: 0.6620 (m-70) cc_final: 0.6388 (m-70) REVERT: E 375 GLU cc_start: 0.7077 (tt0) cc_final: 0.6800 (tt0) REVERT: E 384 LYS cc_start: 0.7819 (mttt) cc_final: 0.7583 (mtmm) REVERT: E 404 VAL cc_start: 0.7796 (t) cc_final: 0.7413 (p) REVERT: E 409 CYS cc_start: 0.7404 (m) cc_final: 0.6905 (t) REVERT: E 413 LEU cc_start: 0.8166 (tp) cc_final: 0.7932 (tt) REVERT: E 415 CYS cc_start: 0.6342 (m) cc_final: 0.4397 (m) REVERT: E 419 CYS cc_start: 0.7603 (m) cc_final: 0.7067 (m) REVERT: E 563 GLU cc_start: 0.6018 (pp20) cc_final: 0.5178 (tm-30) REVERT: E 629 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6846 (tp30) REVERT: E 631 PHE cc_start: 0.7619 (m-10) cc_final: 0.7325 (m-80) REVERT: E 637 MET cc_start: 0.7010 (tpp) cc_final: 0.6771 (tpp) REVERT: E 645 ARG cc_start: 0.7048 (mtm110) cc_final: 0.6639 (mtm110) REVERT: E 648 ASP cc_start: 0.7501 (m-30) cc_final: 0.6993 (t0) REVERT: E 649 TYR cc_start: 0.7296 (m-80) cc_final: 0.7083 (m-80) REVERT: E 741 GLN cc_start: 0.7412 (mm110) cc_final: 0.7099 (mp10) REVERT: E 844 CYS cc_start: 0.7089 (m) cc_final: 0.6885 (m) REVERT: E 853 THR cc_start: 0.8406 (t) cc_final: 0.8037 (p) REVERT: E 859 ARG cc_start: 0.7360 (mtt-85) cc_final: 0.7084 (mtt-85) REVERT: E 878 LYS cc_start: 0.8296 (mmtt) cc_final: 0.8094 (tppt) REVERT: E 880 LYS cc_start: 0.7597 (pttp) cc_final: 0.7392 (ptmt) REVERT: E 933 CYS cc_start: 0.7184 (m) cc_final: 0.6880 (m) REVERT: E 973 LYS cc_start: 0.8298 (ptmt) cc_final: 0.7789 (ptpp) REVERT: E 1006 SER cc_start: 0.7930 (m) cc_final: 0.7348 (t) REVERT: E 1019 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7368 (tp30) REVERT: E 1022 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7005 (tm-30) REVERT: F 144 VAL cc_start: 0.7247 (t) cc_final: 0.7006 (m) REVERT: F 234 ILE cc_start: 0.7392 (pt) cc_final: 0.7181 (pt) REVERT: F 238 LYS cc_start: 0.7456 (tptt) cc_final: 0.7198 (tptp) REVERT: F 239 MET cc_start: 0.6541 (ttp) cc_final: 0.6331 (ttp) REVERT: F 258 TYR cc_start: 0.7497 (t80) cc_final: 0.7240 (t80) REVERT: F 301 MET cc_start: 0.7265 (ttm) cc_final: 0.6809 (ttm) REVERT: F 342 PRO cc_start: 0.7758 (Cg_exo) cc_final: 0.7510 (Cg_endo) REVERT: F 370 ILE cc_start: 0.7444 (mm) cc_final: 0.7218 (tp) REVERT: F 526 GLN cc_start: 0.7001 (tt0) cc_final: 0.6764 (tt0) REVERT: F 533 TYR cc_start: 0.6862 (t80) cc_final: 0.6560 (t80) REVERT: F 563 GLU cc_start: 0.6070 (pp20) cc_final: 0.5115 (tm-30) REVERT: F 569 GLU cc_start: 0.6696 (tp30) cc_final: 0.6048 (tp30) REVERT: F 607 GLU cc_start: 0.7158 (tp30) cc_final: 0.6819 (tp30) REVERT: F 611 TRP cc_start: 0.7011 (t60) cc_final: 0.6498 (t60) REVERT: F 613 GLU cc_start: 0.7200 (tt0) cc_final: 0.6980 (tt0) REVERT: F 644 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7418 (mm-40) REVERT: F 645 ARG cc_start: 0.6963 (mtm110) cc_final: 0.6252 (mpp80) REVERT: F 649 TYR cc_start: 0.7106 (m-80) cc_final: 0.6762 (m-80) REVERT: F 806 SER cc_start: 0.7827 (p) cc_final: 0.7539 (m) REVERT: F 831 LYS cc_start: 0.7850 (mttt) cc_final: 0.7390 (mttt) REVERT: F 853 THR cc_start: 0.8073 (t) cc_final: 0.7718 (p) REVERT: F 876 CYS cc_start: 0.7400 (m) cc_final: 0.6955 (m) REVERT: F 927 LYS cc_start: 0.7804 (ptmt) cc_final: 0.7530 (ptmm) REVERT: F 929 ILE cc_start: 0.8477 (mt) cc_final: 0.8053 (mp) REVERT: F 933 CYS cc_start: 0.7033 (m) cc_final: 0.6774 (m) REVERT: F 1019 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7606 (mm-30) REVERT: F 1022 GLN cc_start: 0.7466 (tm-30) cc_final: 0.7176 (tm-30) REVERT: F 1023 GLU cc_start: 0.6897 (mp0) cc_final: 0.6515 (mp0) REVERT: F 1029 THR cc_start: 0.8025 (m) cc_final: 0.7700 (t) outliers start: 24 outliers final: 11 residues processed: 1121 average time/residue: 0.2469 time to fit residues: 445.7226 Evaluate side-chains 916 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 900 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 1013 GLU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 1013 GLU Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 1013 GLU Chi-restraints excluded: chain E residue 240 MET Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 1013 GLU Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 1013 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 470 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 ASN A 911 ASN ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN B 225 GLN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 ASN B 952 ASN C 674 HIS ** C 824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 911 ASN ** D 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 ASN D 824 HIS D 893 ASN D 911 ASN D 952 ASN E 824 HIS E 893 ASN E 911 ASN ** E 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1002 ASN ** F 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 911 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.181552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.148300 restraints weight = 62806.889| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.27 r_work: 0.3716 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 39690 Z= 0.184 Angle : 0.729 11.581 53544 Z= 0.367 Chirality : 0.045 0.211 6078 Planarity : 0.005 0.064 6714 Dihedral : 7.875 155.868 5298 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.00 % Allowed : 11.76 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.12), residues: 4782 helix: -0.13 (0.10), residues: 2232 sheet: -1.85 (0.20), residues: 600 loop : -1.59 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG E 660 TYR 0.024 0.002 TYR C 632 PHE 0.026 0.002 PHE B 568 TRP 0.020 0.002 TRP C 322 HIS 0.012 0.001 HIS E 938 Details of bonding type rmsd covalent geometry : bond 0.00398 (39690) covalent geometry : angle 0.72853 (53544) hydrogen bonds : bond 0.05800 ( 1520) hydrogen bonds : angle 5.78829 ( 4488) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 953 time to evaluate : 1.036 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 143 TYR cc_start: 0.7381 (t80) cc_final: 0.7085 (t80) REVERT: A 239 MET cc_start: 0.7490 (ttp) cc_final: 0.7219 (ttp) REVERT: A 272 LEU cc_start: 0.8288 (tp) cc_final: 0.7768 (tt) REVERT: A 276 ILE cc_start: 0.6489 (OUTLIER) cc_final: 0.6270 (mt) REVERT: A 329 ASP cc_start: 0.7919 (m-30) cc_final: 0.7499 (p0) REVERT: A 349 THR cc_start: 0.8108 (p) cc_final: 0.7776 (p) REVERT: A 353 VAL cc_start: 0.8866 (p) cc_final: 0.8643 (t) REVERT: A 369 GLU cc_start: 0.7727 (tt0) cc_final: 0.7491 (tt0) REVERT: A 384 LYS cc_start: 0.7779 (mtpt) cc_final: 0.7565 (ttpt) REVERT: A 419 CYS cc_start: 0.7871 (m) cc_final: 0.7451 (m) REVERT: A 563 GLU cc_start: 0.6727 (pp20) cc_final: 0.6506 (tm-30) REVERT: A 603 GLN cc_start: 0.7517 (tp40) cc_final: 0.6796 (tm-30) REVERT: A 607 GLU cc_start: 0.7764 (tp30) cc_final: 0.7548 (tp30) REVERT: A 613 GLU cc_start: 0.7815 (tt0) cc_final: 0.7275 (tt0) REVERT: A 637 MET cc_start: 0.7368 (tpp) cc_final: 0.7065 (tpp) REVERT: A 652 LYS cc_start: 0.8409 (ttmt) cc_final: 0.8147 (ttmm) REVERT: A 662 ASP cc_start: 0.7983 (m-30) cc_final: 0.7417 (m-30) REVERT: A 669 CYS cc_start: 0.7673 (m) cc_final: 0.7242 (m) REVERT: A 785 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7845 (pt0) REVERT: A 789 ASP cc_start: 0.7486 (m-30) cc_final: 0.7252 (m-30) REVERT: A 839 LEU cc_start: 0.8193 (mp) cc_final: 0.7843 (mt) REVERT: A 880 LYS cc_start: 0.8082 (ptmt) cc_final: 0.7607 (ptmm) REVERT: A 973 LYS cc_start: 0.8213 (ptmt) cc_final: 0.7587 (ptpp) REVERT: A 990 CYS cc_start: 0.7129 (m) cc_final: 0.6396 (m) REVERT: A 1006 SER cc_start: 0.8382 (m) cc_final: 0.7867 (t) REVERT: A 1022 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7707 (tm-30) REVERT: B 168 TYR cc_start: 0.7347 (t80) cc_final: 0.6967 (t80) REVERT: B 172 ARG cc_start: 0.6925 (mtt90) cc_final: 0.6624 (mtt90) REVERT: B 238 LYS cc_start: 0.7352 (tptt) cc_final: 0.6984 (tptp) REVERT: B 239 MET cc_start: 0.7264 (ttp) cc_final: 0.7051 (ttp) REVERT: B 306 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6173 (mm-30) REVERT: B 322 TRP cc_start: 0.7566 (t60) cc_final: 0.7333 (t60) REVERT: B 367 HIS cc_start: 0.7274 (m-70) cc_final: 0.6887 (m-70) REVERT: B 369 GLU cc_start: 0.7278 (tt0) cc_final: 0.6983 (tt0) REVERT: B 384 LYS cc_start: 0.7422 (mtpp) cc_final: 0.7214 (ttpt) REVERT: B 385 TYR cc_start: 0.7953 (t80) cc_final: 0.7572 (t80) REVERT: B 488 ASP cc_start: 0.7557 (m-30) cc_final: 0.7337 (m-30) REVERT: B 502 PHE cc_start: 0.7586 (m-10) cc_final: 0.7375 (m-10) REVERT: B 523 MET cc_start: 0.7512 (tpt) cc_final: 0.6315 (tpt) REVERT: B 563 GLU cc_start: 0.6812 (pp20) cc_final: 0.6102 (tm-30) REVERT: B 636 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7296 (tp30) REVERT: B 644 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7701 (mm-40) REVERT: B 647 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8201 (mtm) REVERT: B 758 MET cc_start: 0.7599 (tpt) cc_final: 0.7184 (tpt) REVERT: B 785 GLU cc_start: 0.8294 (pt0) cc_final: 0.7921 (pt0) REVERT: B 800 LEU cc_start: 0.8451 (mm) cc_final: 0.8049 (mt) REVERT: B 845 GLN cc_start: 0.7965 (tp-100) cc_final: 0.7745 (tp-100) REVERT: B 861 TYR cc_start: 0.8415 (m-80) cc_final: 0.8062 (m-80) REVERT: B 864 GLU cc_start: 0.7770 (tp30) cc_final: 0.7533 (tp30) REVERT: B 929 ILE cc_start: 0.8392 (mp) cc_final: 0.8042 (mt) REVERT: B 934 GLU cc_start: 0.6950 (tm-30) cc_final: 0.6271 (tm-30) REVERT: B 988 MET cc_start: 0.7838 (mmm) cc_final: 0.7399 (tmm) REVERT: B 1006 SER cc_start: 0.8187 (m) cc_final: 0.7857 (p) REVERT: B 1008 MET cc_start: 0.6643 (mmm) cc_final: 0.6231 (ttt) REVERT: B 1013 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7426 (tm-30) REVERT: B 1022 GLN cc_start: 0.8287 (tm-30) cc_final: 0.8015 (tm-30) REVERT: B 1023 GLU cc_start: 0.7408 (mp0) cc_final: 0.6981 (mp0) REVERT: B 1025 LYS cc_start: 0.6749 (mmtt) cc_final: 0.6398 (mptt) REVERT: C 282 ASP cc_start: 0.6237 (p0) cc_final: 0.6027 (p0) REVERT: C 311 PHE cc_start: 0.7546 (t80) cc_final: 0.7232 (t80) REVERT: C 337 ARG cc_start: 0.7649 (mtt180) cc_final: 0.7427 (mtm180) REVERT: C 338 LYS cc_start: 0.7992 (mtpp) cc_final: 0.7692 (mtpp) REVERT: C 367 HIS cc_start: 0.7250 (m-70) cc_final: 0.6664 (m-70) REVERT: C 369 GLU cc_start: 0.7483 (tt0) cc_final: 0.7149 (tt0) REVERT: C 385 TYR cc_start: 0.8087 (t80) cc_final: 0.7675 (t80) REVERT: C 419 CYS cc_start: 0.8199 (m) cc_final: 0.7556 (m) REVERT: C 488 ASP cc_start: 0.7777 (m-30) cc_final: 0.7384 (m-30) REVERT: C 603 GLN cc_start: 0.7665 (tp40) cc_final: 0.7117 (tm-30) REVERT: C 637 MET cc_start: 0.7585 (tpp) cc_final: 0.7332 (tpp) REVERT: C 645 ARG cc_start: 0.7661 (mtm110) cc_final: 0.7404 (mtm110) REVERT: C 649 TYR cc_start: 0.7848 (m-80) cc_final: 0.7632 (m-80) REVERT: C 731 ARG cc_start: 0.7035 (ttm170) cc_final: 0.6709 (mtp-110) REVERT: C 853 THR cc_start: 0.8283 (t) cc_final: 0.7830 (p) REVERT: C 933 CYS cc_start: 0.8092 (p) cc_final: 0.7885 (p) REVERT: C 938 HIS cc_start: 0.7828 (t-90) cc_final: 0.7418 (t-170) REVERT: C 991 GLU cc_start: 0.7061 (pm20) cc_final: 0.6696 (pm20) REVERT: C 1009 TYR cc_start: 0.6993 (m-80) cc_final: 0.6556 (m-80) REVERT: D 142 LYS cc_start: 0.7291 (tttm) cc_final: 0.7026 (tmtt) REVERT: D 238 LYS cc_start: 0.7524 (tptt) cc_final: 0.7038 (tptp) REVERT: D 239 MET cc_start: 0.7525 (ttp) cc_final: 0.7247 (ttp) REVERT: D 250 GLN cc_start: 0.7174 (tp40) cc_final: 0.6802 (tp40) REVERT: D 329 ASP cc_start: 0.7477 (m-30) cc_final: 0.7057 (t70) REVERT: D 348 ILE cc_start: 0.7714 (pt) cc_final: 0.7330 (mt) REVERT: D 351 ARG cc_start: 0.7830 (mtm180) cc_final: 0.7540 (mtm180) REVERT: D 367 HIS cc_start: 0.7219 (m-70) cc_final: 0.6702 (m-70) REVERT: D 370 ILE cc_start: 0.7588 (mm) cc_final: 0.7300 (tp) REVERT: D 389 GLU cc_start: 0.7496 (mp0) cc_final: 0.7278 (mp0) REVERT: D 505 MET cc_start: 0.5255 (ppp) cc_final: 0.5013 (ppp) REVERT: D 603 GLN cc_start: 0.7558 (tp40) cc_final: 0.7239 (tp40) REVERT: D 637 MET cc_start: 0.7550 (tpp) cc_final: 0.7101 (tpp) REVERT: D 640 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6751 (mm-30) REVERT: D 641 ASP cc_start: 0.7630 (p0) cc_final: 0.7141 (t0) REVERT: D 677 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7283 (mm-30) REVERT: D 741 GLN cc_start: 0.7798 (mm110) cc_final: 0.7426 (mm110) REVERT: D 806 SER cc_start: 0.8312 (p) cc_final: 0.8076 (m) REVERT: D 853 THR cc_start: 0.8334 (t) cc_final: 0.7827 (p) REVERT: D 864 GLU cc_start: 0.7634 (tp30) cc_final: 0.7401 (tp30) REVERT: D 880 LYS cc_start: 0.7632 (pttt) cc_final: 0.7295 (ptpt) REVERT: D 883 GLN cc_start: 0.6242 (pm20) cc_final: 0.5974 (pm20) REVERT: D 893 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7582 (t0) REVERT: D 929 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7840 (mp) REVERT: D 933 CYS cc_start: 0.7719 (m) cc_final: 0.7371 (m) REVERT: D 938 HIS cc_start: 0.7579 (t-90) cc_final: 0.7140 (t-170) REVERT: D 970 SER cc_start: 0.6947 (m) cc_final: 0.6743 (m) REVERT: D 990 CYS cc_start: 0.7435 (m) cc_final: 0.6672 (m) REVERT: D 1005 LEU cc_start: 0.6778 (mp) cc_final: 0.6378 (mt) REVERT: D 1006 SER cc_start: 0.7912 (m) cc_final: 0.7531 (t) REVERT: D 1022 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7806 (tm-30) REVERT: D 1023 GLU cc_start: 0.6360 (mp0) cc_final: 0.5922 (mp0) REVERT: E 138 LYS cc_start: 0.7370 (tmmt) cc_final: 0.7031 (tmmt) REVERT: E 172 ARG cc_start: 0.7401 (mtt90) cc_final: 0.7047 (mtt90) REVERT: E 175 LYS cc_start: 0.8085 (tttt) cc_final: 0.7814 (tttt) REVERT: E 367 HIS cc_start: 0.7057 (m-70) cc_final: 0.6596 (m-70) REVERT: E 369 GLU cc_start: 0.7812 (tt0) cc_final: 0.7596 (tt0) REVERT: E 375 GLU cc_start: 0.7659 (tt0) cc_final: 0.7278 (tt0) REVERT: E 383 PHE cc_start: 0.7842 (m-10) cc_final: 0.7546 (m-10) REVERT: E 404 VAL cc_start: 0.7944 (t) cc_final: 0.7557 (p) REVERT: E 409 CYS cc_start: 0.8070 (m) cc_final: 0.7179 (t) REVERT: E 415 CYS cc_start: 0.7183 (m) cc_final: 0.5931 (m) REVERT: E 419 CYS cc_start: 0.7712 (m) cc_final: 0.7298 (m) REVERT: E 563 GLU cc_start: 0.6312 (pp20) cc_final: 0.5911 (tm-30) REVERT: E 603 GLN cc_start: 0.7210 (tp40) cc_final: 0.6500 (tm-30) REVERT: E 611 TRP cc_start: 0.7665 (t60) cc_final: 0.6926 (t60) REVERT: E 613 GLU cc_start: 0.7875 (tt0) cc_final: 0.7478 (tt0) REVERT: E 631 PHE cc_start: 0.7973 (m-10) cc_final: 0.7701 (m-80) REVERT: E 647 MET cc_start: 0.8059 (ttp) cc_final: 0.7717 (mtm) REVERT: E 648 ASP cc_start: 0.8029 (m-30) cc_final: 0.7600 (t0) REVERT: E 649 TYR cc_start: 0.7703 (m-80) cc_final: 0.6934 (m-80) REVERT: E 652 LYS cc_start: 0.8457 (ttmt) cc_final: 0.8177 (ttmm) REVERT: E 731 ARG cc_start: 0.7140 (ttm170) cc_final: 0.6578 (ttm110) REVERT: E 741 GLN cc_start: 0.7828 (mm110) cc_final: 0.7387 (mp10) REVERT: E 785 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: E 831 LYS cc_start: 0.8754 (mttt) cc_final: 0.8553 (mttp) REVERT: E 853 THR cc_start: 0.8415 (t) cc_final: 0.7943 (p) REVERT: E 859 ARG cc_start: 0.8334 (mtt-85) cc_final: 0.8113 (mtt-85) REVERT: E 878 LYS cc_start: 0.8446 (mmtt) cc_final: 0.8245 (tppt) REVERT: E 893 ASN cc_start: 0.8426 (t160) cc_final: 0.8194 (t0) REVERT: E 933 CYS cc_start: 0.8348 (m) cc_final: 0.8057 (m) REVERT: E 973 LYS cc_start: 0.8204 (ptmt) cc_final: 0.7610 (ptpp) REVERT: E 987 MET cc_start: 0.6116 (mmt) cc_final: 0.5385 (mmm) REVERT: E 1006 SER cc_start: 0.8041 (m) cc_final: 0.7510 (t) REVERT: E 1019 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7149 (tp30) REVERT: E 1022 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7371 (tm-30) REVERT: E 1023 GLU cc_start: 0.6435 (mp0) cc_final: 0.5257 (mp0) REVERT: F 172 ARG cc_start: 0.6940 (mtt90) cc_final: 0.6064 (mtt90) REVERT: F 239 MET cc_start: 0.7397 (ttp) cc_final: 0.7191 (ttp) REVERT: F 301 MET cc_start: 0.7617 (ttm) cc_final: 0.7155 (ttm) REVERT: F 338 LYS cc_start: 0.8071 (mtmm) cc_final: 0.7437 (mtmm) REVERT: F 342 PRO cc_start: 0.7833 (Cg_exo) cc_final: 0.7604 (Cg_endo) REVERT: F 523 MET cc_start: 0.7538 (tpp) cc_final: 0.7289 (mmm) REVERT: F 526 GLN cc_start: 0.7430 (tt0) cc_final: 0.6965 (tm-30) REVERT: F 569 GLU cc_start: 0.7086 (tp30) cc_final: 0.6490 (tp30) REVERT: F 607 GLU cc_start: 0.7334 (tp30) cc_final: 0.6994 (tp30) REVERT: F 611 TRP cc_start: 0.7418 (t60) cc_final: 0.6684 (t60) REVERT: F 613 GLU cc_start: 0.7693 (tt0) cc_final: 0.7427 (tt0) REVERT: F 644 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7414 (mm-40) REVERT: F 648 ASP cc_start: 0.8062 (t70) cc_final: 0.7861 (t0) REVERT: F 649 TYR cc_start: 0.7676 (m-80) cc_final: 0.7144 (m-80) REVERT: F 672 ASN cc_start: 0.8262 (p0) cc_final: 0.8020 (p0) REVERT: F 731 ARG cc_start: 0.7476 (ttm170) cc_final: 0.7039 (ttm110) REVERT: F 741 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7573 (mm-40) REVERT: F 806 SER cc_start: 0.8430 (p) cc_final: 0.8186 (m) REVERT: F 853 THR cc_start: 0.8214 (t) cc_final: 0.7608 (p) REVERT: F 876 CYS cc_start: 0.8253 (m) cc_final: 0.7718 (m) REVERT: F 938 HIS cc_start: 0.7670 (t-90) cc_final: 0.7337 (t-170) REVERT: F 1019 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7735 (mm-30) REVERT: F 1029 THR cc_start: 0.8344 (m) cc_final: 0.7920 (t) outliers start: 88 outliers final: 53 residues processed: 987 average time/residue: 0.2360 time to fit residues: 377.7619 Evaluate side-chains 923 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 863 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 647 MET Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 897 THR Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 771 ASN Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 849 SER Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 893 ASN Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 874 ILE Chi-restraints excluded: chain E residue 899 VAL Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 970 SER Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 522 HIS Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 841 SER Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 948 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 59 optimal weight: 2.9990 chunk 375 optimal weight: 2.9990 chunk 354 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 460 optimal weight: 0.6980 chunk 371 optimal weight: 0.0870 chunk 413 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 174 optimal weight: 20.0000 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS A 674 HIS A 767 HIS A 912 GLN ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 260 HIS B 627 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 638 GLN E 741 GLN E 893 ASN ** E 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 952 ASN F 952 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.177991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.144966 restraints weight = 62381.716| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.20 r_work: 0.3697 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 39690 Z= 0.161 Angle : 0.671 11.486 53544 Z= 0.334 Chirality : 0.043 0.174 6078 Planarity : 0.005 0.074 6714 Dihedral : 7.556 155.164 5258 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.59 % Allowed : 15.48 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.12), residues: 4782 helix: -0.11 (0.10), residues: 2238 sheet: -1.87 (0.20), residues: 600 loop : -1.60 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 773 TYR 0.021 0.002 TYR B 635 PHE 0.030 0.002 PHE E 304 TRP 0.014 0.001 TRP A 243 HIS 0.011 0.001 HIS F 522 Details of bonding type rmsd covalent geometry : bond 0.00349 (39690) covalent geometry : angle 0.67112 (53544) hydrogen bonds : bond 0.05143 ( 1520) hydrogen bonds : angle 5.30659 ( 4488) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 897 time to evaluate : 1.384 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 143 TYR cc_start: 0.7335 (t80) cc_final: 0.6968 (t80) REVERT: A 145 ARG cc_start: 0.7971 (ttm110) cc_final: 0.7745 (ttm110) REVERT: A 239 MET cc_start: 0.7498 (ttp) cc_final: 0.7231 (ttp) REVERT: A 301 MET cc_start: 0.7580 (ttt) cc_final: 0.7271 (ttt) REVERT: A 326 GLU cc_start: 0.7168 (tp30) cc_final: 0.6939 (tp30) REVERT: A 348 ILE cc_start: 0.7902 (pt) cc_final: 0.7611 (mt) REVERT: A 349 THR cc_start: 0.8132 (p) cc_final: 0.7781 (p) REVERT: A 353 VAL cc_start: 0.8857 (p) cc_final: 0.8630 (t) REVERT: A 384 LYS cc_start: 0.7783 (mtpt) cc_final: 0.7549 (ttpt) REVERT: A 419 CYS cc_start: 0.7974 (m) cc_final: 0.7625 (m) REVERT: A 563 GLU cc_start: 0.6807 (pp20) cc_final: 0.6433 (tm-30) REVERT: A 603 GLN cc_start: 0.7461 (tp40) cc_final: 0.6737 (tm-30) REVERT: A 607 GLU cc_start: 0.7782 (tp30) cc_final: 0.7558 (tp30) REVERT: A 613 GLU cc_start: 0.7732 (tt0) cc_final: 0.7215 (tt0) REVERT: A 631 PHE cc_start: 0.7902 (m-80) cc_final: 0.7595 (m-80) REVERT: A 647 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.8000 (ttp) REVERT: A 652 LYS cc_start: 0.8413 (ttmt) cc_final: 0.8119 (ttmm) REVERT: A 660 ARG cc_start: 0.7545 (tpp80) cc_final: 0.7301 (ttm-80) REVERT: A 661 MET cc_start: 0.8360 (tpt) cc_final: 0.8147 (tpt) REVERT: A 669 CYS cc_start: 0.7629 (m) cc_final: 0.6997 (m) REVERT: A 741 GLN cc_start: 0.7762 (mp10) cc_final: 0.7535 (mp10) REVERT: A 747 ASP cc_start: 0.7291 (t0) cc_final: 0.7088 (t70) REVERT: A 785 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7679 (pt0) REVERT: A 973 LYS cc_start: 0.8253 (ptmt) cc_final: 0.7926 (ptmm) REVERT: A 978 ASN cc_start: 0.7413 (p0) cc_final: 0.7183 (p0) REVERT: A 991 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6488 (pm20) REVERT: A 1006 SER cc_start: 0.8447 (m) cc_final: 0.8007 (t) REVERT: A 1019 GLU cc_start: 0.8256 (tp30) cc_final: 0.7797 (mt-10) REVERT: B 168 TYR cc_start: 0.7435 (t80) cc_final: 0.7226 (t80) REVERT: B 172 ARG cc_start: 0.7008 (mtt90) cc_final: 0.6723 (mtt90) REVERT: B 238 LYS cc_start: 0.7539 (tptt) cc_final: 0.7103 (tptp) REVERT: B 259 ILE cc_start: 0.7789 (mp) cc_final: 0.7270 (pt) REVERT: B 269 GLN cc_start: 0.6237 (mm-40) cc_final: 0.5972 (mm-40) REVERT: B 306 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6247 (mm-30) REVERT: B 323 GLN cc_start: 0.8295 (mm110) cc_final: 0.8043 (mm110) REVERT: B 337 ARG cc_start: 0.7318 (mtt180) cc_final: 0.7082 (mpp80) REVERT: B 367 HIS cc_start: 0.7305 (m-70) cc_final: 0.6969 (m-70) REVERT: B 385 TYR cc_start: 0.8034 (t80) cc_final: 0.7563 (t80) REVERT: B 480 GLN cc_start: 0.6947 (mp10) cc_final: 0.6632 (mp10) REVERT: B 488 ASP cc_start: 0.7551 (m-30) cc_final: 0.7329 (m-30) REVERT: B 523 MET cc_start: 0.7722 (tpt) cc_final: 0.6772 (tpt) REVERT: B 636 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7057 (tp30) REVERT: B 644 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7625 (mm-40) REVERT: B 730 CYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6646 (t) REVERT: B 745 GLU cc_start: 0.7415 (tt0) cc_final: 0.7204 (tt0) REVERT: B 758 MET cc_start: 0.7487 (tpt) cc_final: 0.7086 (tpt) REVERT: B 785 GLU cc_start: 0.8275 (pt0) cc_final: 0.7824 (pt0) REVERT: B 826 LEU cc_start: 0.7826 (tp) cc_final: 0.7469 (tp) REVERT: B 845 GLN cc_start: 0.7980 (tp-100) cc_final: 0.7710 (tp-100) REVERT: B 934 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6294 (tm-30) REVERT: B 1008 MET cc_start: 0.6606 (mmm) cc_final: 0.6166 (ttt) REVERT: B 1009 TYR cc_start: 0.6737 (m-80) cc_final: 0.6496 (m-80) REVERT: B 1013 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7407 (tm-30) REVERT: B 1022 GLN cc_start: 0.8315 (tm-30) cc_final: 0.8045 (tm-30) REVERT: B 1023 GLU cc_start: 0.7282 (mp0) cc_final: 0.6769 (mp0) REVERT: C 170 ARG cc_start: 0.7997 (tpp80) cc_final: 0.7745 (tpm170) REVERT: C 337 ARG cc_start: 0.7544 (mtt180) cc_final: 0.7321 (mtm180) REVERT: C 338 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7714 (mtpp) REVERT: C 367 HIS cc_start: 0.7260 (m-70) cc_final: 0.6656 (m-70) REVERT: C 419 CYS cc_start: 0.8266 (m) cc_final: 0.7769 (m) REVERT: C 488 ASP cc_start: 0.7746 (m-30) cc_final: 0.7350 (m-30) REVERT: C 523 MET cc_start: 0.7928 (tpp) cc_final: 0.7646 (tpt) REVERT: C 534 TYR cc_start: 0.7796 (m-10) cc_final: 0.7463 (m-80) REVERT: C 563 GLU cc_start: 0.6925 (pp20) cc_final: 0.6662 (tm-30) REVERT: C 603 GLN cc_start: 0.7560 (tp40) cc_final: 0.6966 (tm-30) REVERT: C 637 MET cc_start: 0.7364 (tpp) cc_final: 0.7032 (tpp) REVERT: C 645 ARG cc_start: 0.7734 (mtm110) cc_final: 0.7440 (mtm110) REVERT: C 731 ARG cc_start: 0.7154 (ttm170) cc_final: 0.6807 (mtp-110) REVERT: C 880 LYS cc_start: 0.7965 (ptmt) cc_final: 0.7703 (ptmm) REVERT: C 912 GLN cc_start: 0.7715 (tt0) cc_final: 0.7425 (tt0) REVERT: C 933 CYS cc_start: 0.8120 (p) cc_final: 0.7869 (p) REVERT: C 991 GLU cc_start: 0.6930 (pm20) cc_final: 0.6528 (pm20) REVERT: C 1006 SER cc_start: 0.8330 (m) cc_final: 0.7865 (t) REVERT: C 1009 TYR cc_start: 0.6967 (m-80) cc_final: 0.6540 (m-80) REVERT: D 142 LYS cc_start: 0.7241 (tttm) cc_final: 0.6949 (tmtt) REVERT: D 238 LYS cc_start: 0.7630 (tptt) cc_final: 0.7142 (tptp) REVERT: D 239 MET cc_start: 0.7581 (ttp) cc_final: 0.7290 (ttp) REVERT: D 240 MET cc_start: 0.7008 (mtp) cc_final: 0.6694 (mtm) REVERT: D 250 GLN cc_start: 0.7161 (tp40) cc_final: 0.6829 (tp40) REVERT: D 311 PHE cc_start: 0.7674 (t80) cc_final: 0.7360 (t80) REVERT: D 323 GLN cc_start: 0.8269 (mm110) cc_final: 0.7997 (mm-40) REVERT: D 329 ASP cc_start: 0.7514 (m-30) cc_final: 0.6978 (t70) REVERT: D 348 ILE cc_start: 0.7890 (pt) cc_final: 0.7520 (mt) REVERT: D 351 ARG cc_start: 0.7941 (mtm180) cc_final: 0.7647 (mtm180) REVERT: D 367 HIS cc_start: 0.7325 (m-70) cc_final: 0.6846 (m-70) REVERT: D 369 GLU cc_start: 0.7388 (tt0) cc_final: 0.6855 (tt0) REVERT: D 370 ILE cc_start: 0.7682 (mm) cc_final: 0.7320 (tp) REVERT: D 378 ARG cc_start: 0.6803 (mtt180) cc_final: 0.6525 (mtm180) REVERT: D 389 GLU cc_start: 0.7492 (mp0) cc_final: 0.7282 (mp0) REVERT: D 426 MET cc_start: 0.7263 (tpt) cc_final: 0.6939 (tpp) REVERT: D 563 GLU cc_start: 0.6454 (pp20) cc_final: 0.6252 (tm-30) REVERT: D 637 MET cc_start: 0.7472 (tpp) cc_final: 0.7122 (tpt) REVERT: D 640 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6748 (mm-30) REVERT: D 641 ASP cc_start: 0.7580 (p0) cc_final: 0.7014 (t0) REVERT: D 645 ARG cc_start: 0.7748 (mtm110) cc_final: 0.6927 (mtm110) REVERT: D 741 GLN cc_start: 0.7637 (mm110) cc_final: 0.7297 (mm110) REVERT: D 792 LEU cc_start: 0.8316 (mm) cc_final: 0.8048 (mt) REVERT: D 853 THR cc_start: 0.8418 (t) cc_final: 0.7943 (p) REVERT: D 861 TYR cc_start: 0.8461 (m-80) cc_final: 0.8250 (m-80) REVERT: D 880 LYS cc_start: 0.7754 (pttt) cc_final: 0.7291 (ptmt) REVERT: D 929 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7859 (mp) REVERT: D 933 CYS cc_start: 0.7813 (m) cc_final: 0.7449 (m) REVERT: D 938 HIS cc_start: 0.7481 (t-90) cc_final: 0.7054 (t-90) REVERT: D 973 LYS cc_start: 0.8205 (ptmt) cc_final: 0.7718 (ptpp) REVERT: D 988 MET cc_start: 0.7373 (mmm) cc_final: 0.7024 (mmm) REVERT: D 990 CYS cc_start: 0.7443 (m) cc_final: 0.6697 (m) REVERT: D 991 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6330 (pm20) REVERT: D 1006 SER cc_start: 0.7946 (m) cc_final: 0.7566 (t) REVERT: D 1022 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7760 (tm-30) REVERT: D 1023 GLU cc_start: 0.6357 (mp0) cc_final: 0.5716 (mp0) REVERT: E 172 ARG cc_start: 0.7346 (mtt90) cc_final: 0.6902 (mtt90) REVERT: E 175 LYS cc_start: 0.8072 (tttt) cc_final: 0.7815 (tttt) REVERT: E 210 ASP cc_start: 0.8109 (p0) cc_final: 0.7880 (p0) REVERT: E 277 MET cc_start: 0.6615 (ptm) cc_final: 0.6309 (ptm) REVERT: E 326 GLU cc_start: 0.7023 (tp30) cc_final: 0.6732 (mp0) REVERT: E 375 GLU cc_start: 0.7729 (tt0) cc_final: 0.7353 (tt0) REVERT: E 404 VAL cc_start: 0.7998 (t) cc_final: 0.7561 (p) REVERT: E 409 CYS cc_start: 0.8148 (m) cc_final: 0.7275 (t) REVERT: E 415 CYS cc_start: 0.7206 (m) cc_final: 0.6005 (m) REVERT: E 419 CYS cc_start: 0.7784 (m) cc_final: 0.7398 (m) REVERT: E 505 MET cc_start: 0.5236 (ppp) cc_final: 0.4400 (ppp) REVERT: E 603 GLN cc_start: 0.7166 (tp40) cc_final: 0.6393 (tm-30) REVERT: E 610 LYS cc_start: 0.8554 (mppt) cc_final: 0.8257 (ttmm) REVERT: E 611 TRP cc_start: 0.7707 (t60) cc_final: 0.6996 (t60) REVERT: E 613 GLU cc_start: 0.7759 (tt0) cc_final: 0.7448 (tt0) REVERT: E 631 PHE cc_start: 0.7991 (m-10) cc_final: 0.7777 (m-80) REVERT: E 645 ARG cc_start: 0.8160 (mmm160) cc_final: 0.7658 (mmm160) REVERT: E 647 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7759 (mtm) REVERT: E 648 ASP cc_start: 0.8056 (m-30) cc_final: 0.7620 (t0) REVERT: E 649 TYR cc_start: 0.7618 (m-80) cc_final: 0.6959 (m-80) REVERT: E 731 ARG cc_start: 0.7223 (ttm170) cc_final: 0.6673 (ttm110) REVERT: E 741 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7438 (mm-40) REVERT: E 785 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: E 796 SER cc_start: 0.7514 (t) cc_final: 0.7229 (p) REVERT: E 853 THR cc_start: 0.8524 (t) cc_final: 0.8046 (p) REVERT: E 893 ASN cc_start: 0.8450 (t0) cc_final: 0.8214 (t0) REVERT: E 933 CYS cc_start: 0.8363 (m) cc_final: 0.7826 (p) REVERT: E 973 LYS cc_start: 0.8259 (ptmt) cc_final: 0.7768 (ptpp) REVERT: E 987 MET cc_start: 0.6329 (mmt) cc_final: 0.5907 (mmt) REVERT: E 991 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6670 (pm20) REVERT: E 1006 SER cc_start: 0.8084 (m) cc_final: 0.7649 (t) REVERT: E 1009 TYR cc_start: 0.6682 (m-80) cc_final: 0.6235 (m-80) REVERT: E 1019 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7381 (tp30) REVERT: E 1022 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7555 (tm-30) REVERT: F 234 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6868 (pt) REVERT: F 301 MET cc_start: 0.7631 (ttm) cc_final: 0.6784 (ttp) REVERT: F 338 LYS cc_start: 0.8015 (mtmm) cc_final: 0.7405 (mtmm) REVERT: F 369 GLU cc_start: 0.7355 (tt0) cc_final: 0.7075 (tt0) REVERT: F 526 GLN cc_start: 0.7339 (tt0) cc_final: 0.6975 (tm-30) REVERT: F 569 GLU cc_start: 0.7040 (tp30) cc_final: 0.6459 (tp30) REVERT: F 607 GLU cc_start: 0.7364 (tp30) cc_final: 0.7099 (tp30) REVERT: F 613 GLU cc_start: 0.7688 (tt0) cc_final: 0.7378 (tt0) REVERT: F 637 MET cc_start: 0.7819 (tpt) cc_final: 0.7317 (tpt) REVERT: F 644 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7322 (mm-40) REVERT: F 647 MET cc_start: 0.8212 (ttp) cc_final: 0.7868 (ttm) REVERT: F 649 TYR cc_start: 0.7580 (m-80) cc_final: 0.7194 (m-80) REVERT: F 652 LYS cc_start: 0.8349 (ttmt) cc_final: 0.8021 (ttmt) REVERT: F 731 ARG cc_start: 0.7574 (ttm170) cc_final: 0.7223 (ttm110) REVERT: F 741 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7496 (mm-40) REVERT: F 758 MET cc_start: 0.7795 (tpt) cc_final: 0.7379 (tpt) REVERT: F 806 SER cc_start: 0.8453 (p) cc_final: 0.8241 (m) REVERT: F 853 THR cc_start: 0.8219 (t) cc_final: 0.7590 (p) REVERT: F 876 CYS cc_start: 0.8333 (m) cc_final: 0.7818 (m) REVERT: F 991 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6757 (pm20) REVERT: F 1006 SER cc_start: 0.7927 (m) cc_final: 0.7607 (t) REVERT: F 1019 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7648 (mm-30) REVERT: F 1022 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7499 (tm-30) REVERT: F 1029 THR cc_start: 0.8349 (m) cc_final: 0.7821 (p) outliers start: 114 outliers final: 72 residues processed: 947 average time/residue: 0.2404 time to fit residues: 371.9314 Evaluate side-chains 928 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 844 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 806 SER Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 897 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 849 SER Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 991 GLU Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 522 HIS Chi-restraints excluded: chain E residue 573 LEU Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 793 VAL Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 899 VAL Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain E residue 970 SER Chi-restraints excluded: chain E residue 991 GLU Chi-restraints excluded: chain E residue 1028 LEU Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 522 HIS Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 793 VAL Chi-restraints excluded: chain F residue 841 SER Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 927 LYS Chi-restraints excluded: chain F residue 929 ILE Chi-restraints excluded: chain F residue 948 LEU Chi-restraints excluded: chain F residue 991 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 381 optimal weight: 2.9990 chunk 343 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 353 optimal weight: 5.9990 chunk 11 optimal weight: 0.0970 chunk 168 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 293 optimal weight: 0.7980 chunk 376 optimal weight: 0.6980 chunk 430 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 HIS A 938 HIS ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 HIS ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 HIS D 644 GLN E 638 GLN E 644 GLN F 845 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.177845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.144886 restraints weight = 62162.328| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 3.19 r_work: 0.3693 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39690 Z= 0.144 Angle : 0.645 9.162 53544 Z= 0.319 Chirality : 0.042 0.205 6078 Planarity : 0.005 0.065 6714 Dihedral : 7.424 148.850 5256 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.23 % Allowed : 18.37 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.31 (0.12), residues: 4782 helix: 0.00 (0.10), residues: 2274 sheet: -1.65 (0.20), residues: 594 loop : -1.57 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 660 TYR 0.025 0.002 TYR E 143 PHE 0.032 0.002 PHE A 396 TRP 0.011 0.001 TRP A 243 HIS 0.006 0.001 HIS F 522 Details of bonding type rmsd covalent geometry : bond 0.00312 (39690) covalent geometry : angle 0.64485 (53544) hydrogen bonds : bond 0.04243 ( 1520) hydrogen bonds : angle 5.03569 ( 4488) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 905 time to evaluate : 1.325 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 143 TYR cc_start: 0.7316 (t80) cc_final: 0.6937 (t80) REVERT: A 172 ARG cc_start: 0.7134 (mtt90) cc_final: 0.6767 (mtt90) REVERT: A 239 MET cc_start: 0.7417 (ttp) cc_final: 0.7184 (ttp) REVERT: A 269 GLN cc_start: 0.5819 (mp10) cc_final: 0.5270 (mp10) REVERT: A 301 MET cc_start: 0.7627 (ttt) cc_final: 0.7342 (ttt) REVERT: A 326 GLU cc_start: 0.7182 (tp30) cc_final: 0.6580 (tm-30) REVERT: A 353 VAL cc_start: 0.8842 (p) cc_final: 0.8625 (t) REVERT: A 384 LYS cc_start: 0.7760 (mtpt) cc_final: 0.7540 (ttpt) REVERT: A 419 CYS cc_start: 0.8060 (m) cc_final: 0.7760 (m) REVERT: A 505 MET cc_start: 0.4511 (ppp) cc_final: 0.3796 (ppp) REVERT: A 563 GLU cc_start: 0.6931 (pp20) cc_final: 0.6373 (tm-30) REVERT: A 569 GLU cc_start: 0.7310 (tp30) cc_final: 0.7081 (tp30) REVERT: A 607 GLU cc_start: 0.7778 (tp30) cc_final: 0.7571 (tp30) REVERT: A 613 GLU cc_start: 0.7714 (tt0) cc_final: 0.7155 (tt0) REVERT: A 631 PHE cc_start: 0.7889 (m-10) cc_final: 0.7604 (m-80) REVERT: A 652 LYS cc_start: 0.8348 (ttmt) cc_final: 0.8073 (ttmm) REVERT: A 662 ASP cc_start: 0.7827 (m-30) cc_final: 0.7351 (m-30) REVERT: A 669 CYS cc_start: 0.7532 (m) cc_final: 0.6920 (m) REVERT: A 672 ASN cc_start: 0.7877 (p0) cc_final: 0.7411 (m-40) REVERT: A 785 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7666 (pt0) REVERT: A 792 LEU cc_start: 0.8243 (mp) cc_final: 0.8020 (mt) REVERT: A 864 GLU cc_start: 0.7754 (tp30) cc_final: 0.7319 (tp30) REVERT: A 930 LYS cc_start: 0.8176 (mttt) cc_final: 0.7725 (mttt) REVERT: A 973 LYS cc_start: 0.8245 (ptmt) cc_final: 0.7716 (ptpp) REVERT: A 974 LEU cc_start: 0.8107 (tt) cc_final: 0.7868 (tt) REVERT: A 978 ASN cc_start: 0.7245 (p0) cc_final: 0.7031 (p0) REVERT: A 991 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6473 (pm20) REVERT: A 1005 LEU cc_start: 0.7551 (mt) cc_final: 0.7239 (mm) REVERT: A 1006 SER cc_start: 0.8458 (m) cc_final: 0.8036 (t) REVERT: A 1019 GLU cc_start: 0.8187 (tp30) cc_final: 0.7685 (mt-10) REVERT: B 145 ARG cc_start: 0.7640 (ttm-80) cc_final: 0.7254 (mtp85) REVERT: B 172 ARG cc_start: 0.6983 (mtt90) cc_final: 0.6661 (mtt90) REVERT: B 238 LYS cc_start: 0.7407 (tptt) cc_final: 0.7015 (tptp) REVERT: B 259 ILE cc_start: 0.7746 (mp) cc_final: 0.7201 (pt) REVERT: B 306 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6249 (mm-30) REVERT: B 323 GLN cc_start: 0.8366 (mm110) cc_final: 0.8050 (mm110) REVERT: B 367 HIS cc_start: 0.7336 (m-70) cc_final: 0.6968 (m-70) REVERT: B 385 TYR cc_start: 0.8047 (t80) cc_final: 0.7577 (t80) REVERT: B 409 CYS cc_start: 0.8014 (m) cc_final: 0.6638 (p) REVERT: B 480 GLN cc_start: 0.6836 (mp10) cc_final: 0.6499 (mp10) REVERT: B 482 ILE cc_start: 0.6877 (mt) cc_final: 0.6472 (mt) REVERT: B 488 ASP cc_start: 0.7576 (m-30) cc_final: 0.7349 (m-30) REVERT: B 523 MET cc_start: 0.7752 (tpt) cc_final: 0.7019 (tpt) REVERT: B 526 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: B 636 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6949 (tp30) REVERT: B 745 GLU cc_start: 0.7514 (tt0) cc_final: 0.7234 (tt0) REVERT: B 758 MET cc_start: 0.7331 (tpt) cc_final: 0.6947 (tpt) REVERT: B 763 GLU cc_start: 0.8329 (tp30) cc_final: 0.7847 (tm-30) REVERT: B 826 LEU cc_start: 0.7899 (tp) cc_final: 0.7537 (tp) REVERT: B 845 GLN cc_start: 0.7996 (tp-100) cc_final: 0.7740 (tp-100) REVERT: B 864 GLU cc_start: 0.7726 (tp30) cc_final: 0.7481 (tp30) REVERT: B 874 ILE cc_start: 0.8048 (tp) cc_final: 0.7777 (tp) REVERT: B 934 GLU cc_start: 0.6920 (tm-30) cc_final: 0.6300 (tm-30) REVERT: B 1008 MET cc_start: 0.6535 (mmm) cc_final: 0.6045 (ttt) REVERT: B 1009 TYR cc_start: 0.6733 (m-80) cc_final: 0.6440 (m-80) REVERT: B 1013 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7433 (tm-30) REVERT: B 1022 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7938 (tm-30) REVERT: C 170 ARG cc_start: 0.8003 (tpp80) cc_final: 0.7664 (tpp-160) REVERT: C 259 ILE cc_start: 0.7743 (mp) cc_final: 0.7165 (pt) REVERT: C 262 ARG cc_start: 0.8194 (ttm-80) cc_final: 0.7812 (ttm-80) REVERT: C 337 ARG cc_start: 0.7541 (mtt180) cc_final: 0.7331 (mtm180) REVERT: C 338 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7741 (mtpp) REVERT: C 367 HIS cc_start: 0.7252 (m-70) cc_final: 0.6667 (m-70) REVERT: C 409 CYS cc_start: 0.7859 (m) cc_final: 0.7298 (t) REVERT: C 417 ILE cc_start: 0.7987 (mt) cc_final: 0.7758 (mm) REVERT: C 419 CYS cc_start: 0.8328 (m) cc_final: 0.7798 (m) REVERT: C 477 ILE cc_start: 0.7257 (pt) cc_final: 0.6839 (tp) REVERT: C 488 ASP cc_start: 0.7685 (m-30) cc_final: 0.7292 (m-30) REVERT: C 523 MET cc_start: 0.8148 (tpp) cc_final: 0.7728 (tpp) REVERT: C 537 GLU cc_start: 0.5614 (pm20) cc_final: 0.4695 (pm20) REVERT: C 585 ASN cc_start: 0.7858 (t0) cc_final: 0.7284 (t0) REVERT: C 603 GLN cc_start: 0.7517 (tp40) cc_final: 0.6955 (tm-30) REVERT: C 613 GLU cc_start: 0.7755 (tt0) cc_final: 0.7371 (mt-10) REVERT: C 637 MET cc_start: 0.7318 (tpp) cc_final: 0.6705 (tpp) REVERT: C 731 ARG cc_start: 0.7241 (ttm170) cc_final: 0.6891 (mtp-110) REVERT: C 741 GLN cc_start: 0.7624 (mm110) cc_final: 0.7424 (mm110) REVERT: C 880 LYS cc_start: 0.7974 (ptmt) cc_final: 0.7653 (ptmm) REVERT: C 912 GLN cc_start: 0.7745 (tt0) cc_final: 0.7505 (tt0) REVERT: C 933 CYS cc_start: 0.8098 (p) cc_final: 0.7840 (p) REVERT: C 991 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6441 (pm20) REVERT: C 1006 SER cc_start: 0.8361 (m) cc_final: 0.7921 (t) REVERT: C 1007 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7059 (mm-30) REVERT: C 1009 TYR cc_start: 0.7013 (m-80) cc_final: 0.6528 (m-80) REVERT: D 142 LYS cc_start: 0.7189 (tttm) cc_final: 0.6882 (tmtt) REVERT: D 238 LYS cc_start: 0.7675 (tptt) cc_final: 0.7204 (tptp) REVERT: D 240 MET cc_start: 0.7117 (mtp) cc_final: 0.6638 (mtm) REVERT: D 250 GLN cc_start: 0.7169 (tp40) cc_final: 0.6825 (tp40) REVERT: D 311 PHE cc_start: 0.7817 (t80) cc_final: 0.7497 (t80) REVERT: D 323 GLN cc_start: 0.8263 (mm110) cc_final: 0.8035 (mm-40) REVERT: D 329 ASP cc_start: 0.7500 (m-30) cc_final: 0.6924 (t70) REVERT: D 348 ILE cc_start: 0.7948 (pt) cc_final: 0.7619 (mt) REVERT: D 351 ARG cc_start: 0.7930 (mtm180) cc_final: 0.7618 (mtm180) REVERT: D 367 HIS cc_start: 0.7332 (m-70) cc_final: 0.6840 (m-70) REVERT: D 369 GLU cc_start: 0.7462 (tt0) cc_final: 0.6994 (tt0) REVERT: D 370 ILE cc_start: 0.7738 (mm) cc_final: 0.7348 (tp) REVERT: D 489 LEU cc_start: 0.8305 (tp) cc_final: 0.8018 (mt) REVERT: D 585 ASN cc_start: 0.7924 (t0) cc_final: 0.7664 (t0) REVERT: D 613 GLU cc_start: 0.7658 (tt0) cc_final: 0.7220 (tt0) REVERT: D 614 VAL cc_start: 0.8478 (t) cc_final: 0.8235 (p) REVERT: D 640 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6833 (mm-30) REVERT: D 736 VAL cc_start: 0.8759 (t) cc_final: 0.8558 (p) REVERT: D 792 LEU cc_start: 0.8293 (mm) cc_final: 0.8044 (mt) REVERT: D 853 THR cc_start: 0.8393 (t) cc_final: 0.7870 (p) REVERT: D 880 LYS cc_start: 0.7768 (pttt) cc_final: 0.7344 (ptmt) REVERT: D 929 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7812 (mp) REVERT: D 933 CYS cc_start: 0.7878 (m) cc_final: 0.7507 (m) REVERT: D 973 LYS cc_start: 0.8204 (ptmt) cc_final: 0.7720 (ptpp) REVERT: D 990 CYS cc_start: 0.7348 (m) cc_final: 0.6608 (m) REVERT: D 991 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.6225 (pm20) REVERT: D 1006 SER cc_start: 0.8027 (m) cc_final: 0.7620 (t) REVERT: D 1009 TYR cc_start: 0.6692 (m-80) cc_final: 0.6300 (m-80) REVERT: D 1022 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7698 (tm-30) REVERT: D 1023 GLU cc_start: 0.6340 (mp0) cc_final: 0.5643 (mp0) REVERT: E 143 TYR cc_start: 0.7043 (t80) cc_final: 0.6755 (t80) REVERT: E 172 ARG cc_start: 0.7278 (mtt90) cc_final: 0.6834 (mtt90) REVERT: E 175 LYS cc_start: 0.8083 (tttt) cc_final: 0.7814 (tttt) REVERT: E 210 ASP cc_start: 0.8115 (p0) cc_final: 0.7778 (p0) REVERT: E 213 ASP cc_start: 0.7047 (m-30) cc_final: 0.6757 (m-30) REVERT: E 267 VAL cc_start: 0.3108 (OUTLIER) cc_final: 0.2740 (p) REVERT: E 269 GLN cc_start: 0.5127 (mp10) cc_final: 0.4882 (mp10) REVERT: E 277 MET cc_start: 0.6682 (ptm) cc_final: 0.6313 (ptm) REVERT: E 338 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7793 (mtpt) REVERT: E 351 ARG cc_start: 0.7801 (mtm180) cc_final: 0.7556 (mtm180) REVERT: E 367 HIS cc_start: 0.7217 (m-70) cc_final: 0.6759 (m-70) REVERT: E 375 GLU cc_start: 0.7760 (tt0) cc_final: 0.7383 (tt0) REVERT: E 384 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8073 (ttmm) REVERT: E 404 VAL cc_start: 0.7963 (t) cc_final: 0.7513 (p) REVERT: E 409 CYS cc_start: 0.8161 (m) cc_final: 0.7286 (t) REVERT: E 415 CYS cc_start: 0.7190 (m) cc_final: 0.6101 (m) REVERT: E 505 MET cc_start: 0.5238 (ppp) cc_final: 0.4719 (ppp) REVERT: E 603 GLN cc_start: 0.7095 (tp40) cc_final: 0.6339 (tm-30) REVERT: E 610 LYS cc_start: 0.8516 (mppt) cc_final: 0.8217 (mtmm) REVERT: E 611 TRP cc_start: 0.7744 (t60) cc_final: 0.7051 (t60) REVERT: E 613 GLU cc_start: 0.7721 (tt0) cc_final: 0.7212 (tt0) REVERT: E 634 LEU cc_start: 0.8854 (mm) cc_final: 0.8460 (mm) REVERT: E 647 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7848 (mtm) REVERT: E 648 ASP cc_start: 0.8039 (m-30) cc_final: 0.7640 (t0) REVERT: E 731 ARG cc_start: 0.7279 (ttm170) cc_final: 0.6710 (ttm110) REVERT: E 741 GLN cc_start: 0.7626 (mm-40) cc_final: 0.7388 (mm-40) REVERT: E 745 GLU cc_start: 0.7395 (tt0) cc_final: 0.7100 (tt0) REVERT: E 785 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: E 789 ASP cc_start: 0.7824 (m-30) cc_final: 0.7614 (m-30) REVERT: E 826 LEU cc_start: 0.7931 (tp) cc_final: 0.7366 (tt) REVERT: E 853 THR cc_start: 0.8503 (t) cc_final: 0.8019 (p) REVERT: E 864 GLU cc_start: 0.7710 (tp30) cc_final: 0.7480 (tp30) REVERT: E 933 CYS cc_start: 0.8377 (m) cc_final: 0.7845 (p) REVERT: E 936 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7462 (tt) REVERT: E 973 LYS cc_start: 0.8197 (ptmt) cc_final: 0.7699 (ptpp) REVERT: E 983 ASP cc_start: 0.6545 (t0) cc_final: 0.6051 (t0) REVERT: E 987 MET cc_start: 0.6541 (mmt) cc_final: 0.6094 (mmt) REVERT: E 1006 SER cc_start: 0.8149 (m) cc_final: 0.7776 (t) REVERT: E 1009 TYR cc_start: 0.6736 (m-80) cc_final: 0.6258 (m-80) REVERT: E 1019 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7375 (tp30) REVERT: E 1022 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7510 (tm-30) REVERT: E 1029 THR cc_start: 0.8467 (m) cc_final: 0.7962 (p) REVERT: F 269 GLN cc_start: 0.4869 (mp10) cc_final: 0.4501 (mp10) REVERT: F 272 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7419 (tt) REVERT: F 301 MET cc_start: 0.7485 (ttm) cc_final: 0.6571 (ttp) REVERT: F 312 ASP cc_start: 0.7579 (t70) cc_final: 0.7018 (t0) REVERT: F 338 LYS cc_start: 0.8001 (mtmm) cc_final: 0.7580 (mtpp) REVERT: F 369 GLU cc_start: 0.7310 (tt0) cc_final: 0.7063 (tt0) REVERT: F 379 LYS cc_start: 0.7355 (ttmt) cc_final: 0.7153 (ttmt) REVERT: F 526 GLN cc_start: 0.7310 (tt0) cc_final: 0.6884 (tm-30) REVERT: F 563 GLU cc_start: 0.6582 (pp20) cc_final: 0.6327 (tm-30) REVERT: F 569 GLU cc_start: 0.7077 (tp30) cc_final: 0.6722 (tp30) REVERT: F 607 GLU cc_start: 0.7392 (tp30) cc_final: 0.7054 (tp30) REVERT: F 613 GLU cc_start: 0.7680 (tt0) cc_final: 0.7354 (tt0) REVERT: F 637 MET cc_start: 0.7886 (tpt) cc_final: 0.7465 (tpt) REVERT: F 644 GLN cc_start: 0.7600 (mm-40) cc_final: 0.7279 (mm-40) REVERT: F 647 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7840 (mtm) REVERT: F 649 TYR cc_start: 0.7544 (m-80) cc_final: 0.7199 (m-80) REVERT: F 669 CYS cc_start: 0.7693 (m) cc_final: 0.7431 (m) REVERT: F 741 GLN cc_start: 0.7580 (mm-40) cc_final: 0.7350 (mm-40) REVERT: F 785 GLU cc_start: 0.8200 (pt0) cc_final: 0.7631 (mt-10) REVERT: F 853 THR cc_start: 0.8205 (t) cc_final: 0.7611 (p) REVERT: F 876 CYS cc_start: 0.8372 (m) cc_final: 0.7861 (m) REVERT: F 933 CYS cc_start: 0.8146 (m) cc_final: 0.7908 (m) REVERT: F 987 MET cc_start: 0.6439 (mmt) cc_final: 0.6017 (mmm) REVERT: F 991 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6693 (pm20) REVERT: F 1006 SER cc_start: 0.7980 (m) cc_final: 0.7688 (t) REVERT: F 1009 TYR cc_start: 0.6509 (m-80) cc_final: 0.6247 (m-80) REVERT: F 1019 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7651 (mm-30) REVERT: F 1022 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7452 (tm-30) REVERT: F 1029 THR cc_start: 0.8337 (m) cc_final: 0.7809 (p) outliers start: 142 outliers final: 89 residues processed: 972 average time/residue: 0.2373 time to fit residues: 377.1731 Evaluate side-chains 960 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 856 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 522 HIS Chi-restraints excluded: chain B residue 526 GLN Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 522 HIS Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 991 GLU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 644 GLN Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 991 GLU Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 522 HIS Chi-restraints excluded: chain E residue 573 LEU Chi-restraints excluded: chain E residue 644 GLN Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 765 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 793 VAL Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 899 VAL Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 522 HIS Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 647 MET Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 793 VAL Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 841 SER Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 927 LYS Chi-restraints excluded: chain F residue 929 ILE Chi-restraints excluded: chain F residue 948 LEU Chi-restraints excluded: chain F residue 973 LYS Chi-restraints excluded: chain F residue 991 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 230 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 310 optimal weight: 8.9990 chunk 262 optimal weight: 4.9990 chunk 7 optimal weight: 0.0980 chunk 286 optimal weight: 0.9980 chunk 327 optimal weight: 0.0570 chunk 406 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 350 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 HIS A1022 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 GLN F 767 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.179388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.146472 restraints weight = 61679.858| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 3.21 r_work: 0.3702 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39690 Z= 0.121 Angle : 0.627 10.346 53544 Z= 0.309 Chirality : 0.041 0.167 6078 Planarity : 0.005 0.071 6714 Dihedral : 7.311 144.604 5256 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.25 % Allowed : 19.67 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.12), residues: 4782 helix: 0.15 (0.11), residues: 2274 sheet: -1.83 (0.19), residues: 648 loop : -1.38 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 859 TYR 0.018 0.001 TYR B 649 PHE 0.028 0.001 PHE A 396 TRP 0.012 0.001 TRP A 243 HIS 0.010 0.001 HIS F 767 Details of bonding type rmsd covalent geometry : bond 0.00266 (39690) covalent geometry : angle 0.62741 (53544) hydrogen bonds : bond 0.03951 ( 1520) hydrogen bonds : angle 4.90067 ( 4488) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 866 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 TYR cc_start: 0.7303 (t80) cc_final: 0.6924 (t80) REVERT: A 172 ARG cc_start: 0.7084 (mtt90) cc_final: 0.6687 (mtt90) REVERT: A 239 MET cc_start: 0.7428 (ttp) cc_final: 0.7187 (ttp) REVERT: A 298 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6505 (pt) REVERT: A 301 MET cc_start: 0.7637 (ttt) cc_final: 0.7354 (ttt) REVERT: A 326 GLU cc_start: 0.7198 (tp30) cc_final: 0.6969 (tp30) REVERT: A 348 ILE cc_start: 0.7902 (pt) cc_final: 0.7698 (mt) REVERT: A 353 VAL cc_start: 0.8825 (p) cc_final: 0.8609 (t) REVERT: A 419 CYS cc_start: 0.8021 (m) cc_final: 0.7712 (m) REVERT: A 563 GLU cc_start: 0.6961 (pp20) cc_final: 0.6587 (tp30) REVERT: A 569 GLU cc_start: 0.7339 (tp30) cc_final: 0.7111 (tp30) REVERT: A 607 GLU cc_start: 0.7841 (tp30) cc_final: 0.7598 (tp30) REVERT: A 613 GLU cc_start: 0.7732 (tt0) cc_final: 0.7166 (tt0) REVERT: A 631 PHE cc_start: 0.7890 (m-10) cc_final: 0.7610 (m-80) REVERT: A 637 MET cc_start: 0.7289 (tpt) cc_final: 0.7064 (tpt) REVERT: A 652 LYS cc_start: 0.8376 (ttmt) cc_final: 0.8106 (ttmm) REVERT: A 660 ARG cc_start: 0.7493 (tpp80) cc_final: 0.7169 (ttm-80) REVERT: A 662 ASP cc_start: 0.7833 (m-30) cc_final: 0.7364 (m-30) REVERT: A 669 CYS cc_start: 0.7557 (m) cc_final: 0.6940 (m) REVERT: A 672 ASN cc_start: 0.7842 (p0) cc_final: 0.7458 (m-40) REVERT: A 785 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7670 (pt0) REVERT: A 864 GLU cc_start: 0.7691 (tp30) cc_final: 0.7475 (tp30) REVERT: A 930 LYS cc_start: 0.8162 (mttt) cc_final: 0.7710 (mttt) REVERT: A 973 LYS cc_start: 0.8252 (ptmt) cc_final: 0.7733 (ptpp) REVERT: A 974 LEU cc_start: 0.8084 (tt) cc_final: 0.7852 (tt) REVERT: A 978 ASN cc_start: 0.7286 (p0) cc_final: 0.7074 (p0) REVERT: A 991 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6444 (pm20) REVERT: A 1006 SER cc_start: 0.8461 (m) cc_final: 0.8074 (t) REVERT: A 1019 GLU cc_start: 0.8157 (tp30) cc_final: 0.7718 (mt-10) REVERT: B 172 ARG cc_start: 0.6921 (mtt90) cc_final: 0.6612 (mtt90) REVERT: B 238 LYS cc_start: 0.7327 (tptt) cc_final: 0.6978 (tptp) REVERT: B 259 ILE cc_start: 0.7734 (mp) cc_final: 0.7181 (pt) REVERT: B 306 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6805 (mm-30) REVERT: B 323 GLN cc_start: 0.8398 (mm110) cc_final: 0.8059 (mm110) REVERT: B 367 HIS cc_start: 0.7320 (m-70) cc_final: 0.6931 (m-70) REVERT: B 385 TYR cc_start: 0.8049 (t80) cc_final: 0.7591 (t80) REVERT: B 409 CYS cc_start: 0.7978 (m) cc_final: 0.6613 (p) REVERT: B 480 GLN cc_start: 0.6745 (mp10) cc_final: 0.6392 (mp10) REVERT: B 488 ASP cc_start: 0.7597 (m-30) cc_final: 0.7353 (m-30) REVERT: B 532 MET cc_start: 0.8113 (mmm) cc_final: 0.7868 (tpp) REVERT: B 613 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6991 (mm-30) REVERT: B 677 GLU cc_start: 0.7579 (tp30) cc_final: 0.7192 (tp30) REVERT: B 758 MET cc_start: 0.7320 (tpt) cc_final: 0.6946 (tpt) REVERT: B 826 LEU cc_start: 0.7936 (tp) cc_final: 0.7549 (tp) REVERT: B 845 GLN cc_start: 0.7990 (tp-100) cc_final: 0.7717 (tp-100) REVERT: B 934 GLU cc_start: 0.6859 (tm-30) cc_final: 0.6234 (tm-30) REVERT: B 1008 MET cc_start: 0.6493 (mmm) cc_final: 0.6077 (ttt) REVERT: B 1009 TYR cc_start: 0.6647 (m-80) cc_final: 0.6394 (m-80) REVERT: B 1013 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7429 (tm-30) REVERT: C 170 ARG cc_start: 0.7977 (tpp80) cc_final: 0.7646 (tpp-160) REVERT: C 259 ILE cc_start: 0.7719 (mp) cc_final: 0.7118 (pt) REVERT: C 262 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7835 (ttm-80) REVERT: C 337 ARG cc_start: 0.7521 (mtt180) cc_final: 0.7318 (mtm180) REVERT: C 338 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7713 (mtpp) REVERT: C 367 HIS cc_start: 0.7279 (m-70) cc_final: 0.6693 (m-70) REVERT: C 409 CYS cc_start: 0.7867 (m) cc_final: 0.7303 (t) REVERT: C 419 CYS cc_start: 0.8330 (m) cc_final: 0.7821 (m) REVERT: C 467 TRP cc_start: 0.6483 (t-100) cc_final: 0.6087 (t-100) REVERT: C 477 ILE cc_start: 0.7296 (pt) cc_final: 0.6855 (tp) REVERT: C 585 ASN cc_start: 0.7882 (t0) cc_final: 0.7663 (t0) REVERT: C 607 GLU cc_start: 0.7729 (tp30) cc_final: 0.7518 (tp30) REVERT: C 613 GLU cc_start: 0.7738 (tt0) cc_final: 0.7345 (mt-10) REVERT: C 637 MET cc_start: 0.7351 (tpp) cc_final: 0.7056 (tpp) REVERT: C 641 ASP cc_start: 0.7614 (p0) cc_final: 0.7009 (t0) REVERT: C 731 ARG cc_start: 0.7195 (ttm170) cc_final: 0.6831 (mtp-110) REVERT: C 741 GLN cc_start: 0.7599 (mm110) cc_final: 0.7391 (mm110) REVERT: C 839 LEU cc_start: 0.8255 (mp) cc_final: 0.7981 (tp) REVERT: C 861 TYR cc_start: 0.8422 (m-80) cc_final: 0.8162 (m-80) REVERT: C 880 LYS cc_start: 0.7959 (ptmt) cc_final: 0.7654 (ptmm) REVERT: C 912 GLN cc_start: 0.7744 (tt0) cc_final: 0.7484 (tt0) REVERT: C 933 CYS cc_start: 0.8077 (p) cc_final: 0.7803 (p) REVERT: C 991 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6420 (pm20) REVERT: C 1006 SER cc_start: 0.8343 (m) cc_final: 0.7895 (t) REVERT: C 1009 TYR cc_start: 0.6962 (m-80) cc_final: 0.6597 (m-80) REVERT: D 142 LYS cc_start: 0.7194 (tttm) cc_final: 0.6871 (tmtt) REVERT: D 238 LYS cc_start: 0.7668 (tptt) cc_final: 0.7204 (tptp) REVERT: D 250 GLN cc_start: 0.7159 (tp40) cc_final: 0.6813 (tp40) REVERT: D 329 ASP cc_start: 0.7475 (m-30) cc_final: 0.7017 (t0) REVERT: D 351 ARG cc_start: 0.7913 (mtm180) cc_final: 0.7617 (mtm180) REVERT: D 367 HIS cc_start: 0.7304 (m-70) cc_final: 0.6793 (m-70) REVERT: D 369 GLU cc_start: 0.7481 (tt0) cc_final: 0.7252 (tt0) REVERT: D 585 ASN cc_start: 0.7879 (t0) cc_final: 0.7625 (t0) REVERT: D 611 TRP cc_start: 0.7628 (t60) cc_final: 0.7014 (t60) REVERT: D 613 GLU cc_start: 0.7601 (tt0) cc_final: 0.7028 (tt0) REVERT: D 614 VAL cc_start: 0.8494 (t) cc_final: 0.8261 (p) REVERT: D 637 MET cc_start: 0.7488 (tpt) cc_final: 0.7244 (tpp) REVERT: D 640 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6914 (mm-30) REVERT: D 736 VAL cc_start: 0.8781 (t) cc_final: 0.8566 (p) REVERT: D 792 LEU cc_start: 0.8260 (mm) cc_final: 0.8018 (mt) REVERT: D 853 THR cc_start: 0.8367 (t) cc_final: 0.7852 (p) REVERT: D 880 LYS cc_start: 0.7747 (pttt) cc_final: 0.7333 (ptmt) REVERT: D 899 VAL cc_start: 0.6407 (OUTLIER) cc_final: 0.6112 (p) REVERT: D 929 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7818 (mp) REVERT: D 933 CYS cc_start: 0.7902 (m) cc_final: 0.7539 (m) REVERT: D 973 LYS cc_start: 0.8153 (ptmt) cc_final: 0.7654 (ptpp) REVERT: D 990 CYS cc_start: 0.7395 (m) cc_final: 0.6643 (m) REVERT: D 991 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6193 (pm20) REVERT: D 1006 SER cc_start: 0.8002 (m) cc_final: 0.7637 (t) REVERT: D 1007 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6903 (mm-30) REVERT: D 1009 TYR cc_start: 0.6640 (m-80) cc_final: 0.6122 (m-80) REVERT: D 1022 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7699 (tm-30) REVERT: D 1023 GLU cc_start: 0.6354 (mp0) cc_final: 0.5661 (mp0) REVERT: E 143 TYR cc_start: 0.7062 (t80) cc_final: 0.6722 (t80) REVERT: E 172 ARG cc_start: 0.7322 (mtt90) cc_final: 0.6843 (mtt90) REVERT: E 174 ILE cc_start: 0.7919 (mt) cc_final: 0.7706 (tt) REVERT: E 175 LYS cc_start: 0.8071 (tttt) cc_final: 0.7793 (tttt) REVERT: E 210 ASP cc_start: 0.8113 (p0) cc_final: 0.7762 (p0) REVERT: E 213 ASP cc_start: 0.7079 (m-30) cc_final: 0.6790 (m-30) REVERT: E 269 GLN cc_start: 0.5048 (mp10) cc_final: 0.4807 (mp10) REVERT: E 277 MET cc_start: 0.6726 (ptm) cc_final: 0.6337 (ptm) REVERT: E 338 LYS cc_start: 0.8054 (mtpt) cc_final: 0.7796 (mtpt) REVERT: E 348 ILE cc_start: 0.8042 (pt) cc_final: 0.7809 (mp) REVERT: E 367 HIS cc_start: 0.7234 (m-70) cc_final: 0.6673 (m-70) REVERT: E 375 GLU cc_start: 0.7736 (tt0) cc_final: 0.7329 (tt0) REVERT: E 404 VAL cc_start: 0.7948 (t) cc_final: 0.7494 (p) REVERT: E 409 CYS cc_start: 0.8130 (m) cc_final: 0.7339 (t) REVERT: E 415 CYS cc_start: 0.7175 (m) cc_final: 0.6161 (m) REVERT: E 417 ILE cc_start: 0.7563 (mt) cc_final: 0.7341 (mm) REVERT: E 603 GLN cc_start: 0.7114 (tp40) cc_final: 0.6342 (tm-30) REVERT: E 611 TRP cc_start: 0.7735 (t60) cc_final: 0.7068 (t60) REVERT: E 613 GLU cc_start: 0.7633 (tt0) cc_final: 0.7317 (tt0) REVERT: E 634 LEU cc_start: 0.8837 (mm) cc_final: 0.8430 (mm) REVERT: E 648 ASP cc_start: 0.8060 (m-30) cc_final: 0.7600 (t0) REVERT: E 649 TYR cc_start: 0.7518 (m-80) cc_final: 0.6962 (m-80) REVERT: E 731 ARG cc_start: 0.7257 (ttm170) cc_final: 0.6682 (ttm110) REVERT: E 741 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7323 (mm-40) REVERT: E 745 GLU cc_start: 0.7387 (tt0) cc_final: 0.7083 (tt0) REVERT: E 785 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: E 826 LEU cc_start: 0.7946 (tp) cc_final: 0.7395 (tt) REVERT: E 853 THR cc_start: 0.8478 (t) cc_final: 0.8009 (p) REVERT: E 864 GLU cc_start: 0.7709 (tp30) cc_final: 0.7490 (tp30) REVERT: E 933 CYS cc_start: 0.8338 (m) cc_final: 0.8038 (m) REVERT: E 936 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7440 (tt) REVERT: E 973 LYS cc_start: 0.8170 (ptmt) cc_final: 0.7675 (ptpp) REVERT: E 983 ASP cc_start: 0.6634 (OUTLIER) cc_final: 0.6050 (t0) REVERT: E 987 MET cc_start: 0.6457 (mmt) cc_final: 0.6032 (mmt) REVERT: E 991 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6535 (pm20) REVERT: E 1006 SER cc_start: 0.8115 (m) cc_final: 0.7776 (t) REVERT: E 1009 TYR cc_start: 0.6724 (m-80) cc_final: 0.6296 (m-80) REVERT: E 1019 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7385 (tp30) REVERT: E 1022 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7524 (tm-30) REVERT: E 1029 THR cc_start: 0.8436 (m) cc_final: 0.7949 (p) REVERT: F 269 GLN cc_start: 0.4838 (mp10) cc_final: 0.4475 (mp10) REVERT: F 272 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7381 (tt) REVERT: F 301 MET cc_start: 0.7411 (ttm) cc_final: 0.6489 (ttp) REVERT: F 312 ASP cc_start: 0.7607 (t70) cc_final: 0.7055 (t0) REVERT: F 338 LYS cc_start: 0.7984 (mtmm) cc_final: 0.7558 (mtpp) REVERT: F 369 GLU cc_start: 0.7322 (tt0) cc_final: 0.7067 (tt0) REVERT: F 379 LYS cc_start: 0.7332 (ttmt) cc_final: 0.7127 (ttmt) REVERT: F 526 GLN cc_start: 0.7279 (tt0) cc_final: 0.6884 (tm-30) REVERT: F 563 GLU cc_start: 0.6640 (pp20) cc_final: 0.6408 (tm-30) REVERT: F 569 GLU cc_start: 0.7071 (tp30) cc_final: 0.6730 (tp30) REVERT: F 607 GLU cc_start: 0.7427 (tp30) cc_final: 0.7050 (tp30) REVERT: F 611 TRP cc_start: 0.7586 (t60) cc_final: 0.6811 (t60) REVERT: F 613 GLU cc_start: 0.7651 (tt0) cc_final: 0.7342 (tt0) REVERT: F 637 MET cc_start: 0.7882 (tpt) cc_final: 0.7453 (tpt) REVERT: F 641 ASP cc_start: 0.7299 (t0) cc_final: 0.6954 (t0) REVERT: F 644 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7255 (mm-40) REVERT: F 645 ARG cc_start: 0.7359 (mtm110) cc_final: 0.7032 (mtm110) REVERT: F 647 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7805 (mtm) REVERT: F 649 TYR cc_start: 0.7566 (m-80) cc_final: 0.7224 (m-80) REVERT: F 652 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8152 (ttmt) REVERT: F 669 CYS cc_start: 0.7708 (m) cc_final: 0.7454 (m) REVERT: F 741 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7320 (mm-40) REVERT: F 745 GLU cc_start: 0.7548 (tt0) cc_final: 0.7183 (tt0) REVERT: F 785 GLU cc_start: 0.8192 (pt0) cc_final: 0.7653 (mt-10) REVERT: F 796 SER cc_start: 0.7127 (t) cc_final: 0.6697 (p) REVERT: F 853 THR cc_start: 0.8158 (t) cc_final: 0.7569 (p) REVERT: F 864 GLU cc_start: 0.7776 (tp30) cc_final: 0.7440 (tp30) REVERT: F 876 CYS cc_start: 0.8384 (m) cc_final: 0.7857 (m) REVERT: F 933 CYS cc_start: 0.8138 (m) cc_final: 0.7902 (m) REVERT: F 987 MET cc_start: 0.6495 (mmt) cc_final: 0.5934 (mmm) REVERT: F 991 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6684 (pm20) REVERT: F 1006 SER cc_start: 0.7948 (m) cc_final: 0.7667 (t) REVERT: F 1009 TYR cc_start: 0.6520 (m-80) cc_final: 0.6261 (m-80) REVERT: F 1019 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7694 (mm-30) REVERT: F 1022 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7547 (tm-30) REVERT: F 1029 THR cc_start: 0.8316 (m) cc_final: 0.7814 (p) outliers start: 143 outliers final: 90 residues processed: 935 average time/residue: 0.2333 time to fit residues: 357.4817 Evaluate side-chains 933 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 828 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 522 HIS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 522 HIS Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 897 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 991 GLU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 991 GLU Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 522 HIS Chi-restraints excluded: chain E residue 573 LEU Chi-restraints excluded: chain E residue 644 GLN Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 765 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 793 VAL Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 825 LEU Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain E residue 983 ASP Chi-restraints excluded: chain E residue 991 GLU Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 417 ILE Chi-restraints excluded: chain F residue 522 HIS Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 647 MET Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 793 VAL Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 927 LYS Chi-restraints excluded: chain F residue 929 ILE Chi-restraints excluded: chain F residue 948 LEU Chi-restraints excluded: chain F residue 991 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 12 optimal weight: 5.9990 chunk 393 optimal weight: 6.9990 chunk 391 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 chunk 425 optimal weight: 9.9990 chunk 401 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 308 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 HIS A 767 HIS A1001 GLN B 269 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1001 GLN ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN D 771 ASN D 916 HIS D1001 GLN E 225 GLN ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.176715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.143821 restraints weight = 62023.752| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 3.22 r_work: 0.3660 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 39690 Z= 0.184 Angle : 0.696 10.914 53544 Z= 0.346 Chirality : 0.044 0.178 6078 Planarity : 0.005 0.070 6714 Dihedral : 7.508 149.098 5256 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.73 % Allowed : 20.33 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.12), residues: 4782 helix: 0.10 (0.11), residues: 2232 sheet: -1.77 (0.19), residues: 612 loop : -1.65 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 351 TYR 0.022 0.002 TYR E 168 PHE 0.029 0.002 PHE B 508 TRP 0.012 0.001 TRP D 416 HIS 0.007 0.001 HIS A 767 Details of bonding type rmsd covalent geometry : bond 0.00400 (39690) covalent geometry : angle 0.69627 (53544) hydrogen bonds : bond 0.04645 ( 1520) hydrogen bonds : angle 5.06211 ( 4488) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 882 time to evaluate : 1.446 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 143 TYR cc_start: 0.7363 (t80) cc_final: 0.7042 (t80) REVERT: A 172 ARG cc_start: 0.7064 (mtt90) cc_final: 0.6625 (mtt90) REVERT: A 239 MET cc_start: 0.7449 (ttp) cc_final: 0.7188 (ttp) REVERT: A 256 LEU cc_start: 0.7674 (mp) cc_final: 0.7446 (mp) REVERT: A 298 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6573 (pt) REVERT: A 301 MET cc_start: 0.7689 (ttt) cc_final: 0.7100 (ttp) REVERT: A 329 ASP cc_start: 0.7914 (m-30) cc_final: 0.7273 (p0) REVERT: A 353 VAL cc_start: 0.8813 (p) cc_final: 0.8606 (t) REVERT: A 419 CYS cc_start: 0.7949 (m) cc_final: 0.7672 (m) REVERT: A 505 MET cc_start: 0.4486 (ppp) cc_final: 0.3736 (ppp) REVERT: A 523 MET cc_start: 0.7657 (mmm) cc_final: 0.7333 (tpp) REVERT: A 563 GLU cc_start: 0.7250 (pp20) cc_final: 0.7042 (tp30) REVERT: A 569 GLU cc_start: 0.7430 (tp30) cc_final: 0.7201 (tp30) REVERT: A 607 GLU cc_start: 0.7817 (tp30) cc_final: 0.7568 (tp30) REVERT: A 631 PHE cc_start: 0.7928 (m-10) cc_final: 0.7630 (m-80) REVERT: A 649 TYR cc_start: 0.7693 (m-80) cc_final: 0.7141 (m-80) REVERT: A 652 LYS cc_start: 0.8353 (ttmt) cc_final: 0.8083 (ttmm) REVERT: A 662 ASP cc_start: 0.7866 (m-30) cc_final: 0.7406 (m-30) REVERT: A 669 CYS cc_start: 0.7571 (m) cc_final: 0.6998 (m) REVERT: A 745 GLU cc_start: 0.7488 (tt0) cc_final: 0.7280 (mt-10) REVERT: A 785 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7699 (pt0) REVERT: A 864 GLU cc_start: 0.7821 (tp30) cc_final: 0.7481 (tp30) REVERT: A 897 THR cc_start: 0.8098 (m) cc_final: 0.7792 (m) REVERT: A 930 LYS cc_start: 0.8154 (mttt) cc_final: 0.7698 (mttt) REVERT: A 973 LYS cc_start: 0.8227 (ptmt) cc_final: 0.7691 (ptpp) REVERT: A 974 LEU cc_start: 0.8079 (tt) cc_final: 0.7834 (tt) REVERT: A 978 ASN cc_start: 0.7244 (p0) cc_final: 0.6979 (p0) REVERT: A 988 MET cc_start: 0.7427 (mmm) cc_final: 0.6371 (tmm) REVERT: A 991 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6404 (pm20) REVERT: A 1006 SER cc_start: 0.8389 (m) cc_final: 0.8040 (t) REVERT: A 1013 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7347 (tm-30) REVERT: A 1019 GLU cc_start: 0.8117 (tp30) cc_final: 0.7607 (mt-10) REVERT: B 172 ARG cc_start: 0.6951 (mtt90) cc_final: 0.6618 (mtt90) REVERT: B 238 LYS cc_start: 0.7455 (tptt) cc_final: 0.7166 (tptp) REVERT: B 367 HIS cc_start: 0.7354 (m-70) cc_final: 0.6870 (m-70) REVERT: B 385 TYR cc_start: 0.8108 (t80) cc_final: 0.7590 (t80) REVERT: B 480 GLN cc_start: 0.6867 (mp10) cc_final: 0.6506 (mp10) REVERT: B 488 ASP cc_start: 0.7588 (m-30) cc_final: 0.7352 (m-30) REVERT: B 526 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: B 613 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7047 (mm-30) REVERT: B 677 GLU cc_start: 0.7648 (tp30) cc_final: 0.7208 (tp30) REVERT: B 758 MET cc_start: 0.7373 (tpt) cc_final: 0.7030 (tpt) REVERT: B 823 LYS cc_start: 0.8050 (mmtp) cc_final: 0.7709 (mttp) REVERT: B 826 LEU cc_start: 0.7951 (tp) cc_final: 0.7547 (tt) REVERT: B 845 GLN cc_start: 0.8003 (tp-100) cc_final: 0.7701 (tp-100) REVERT: B 864 GLU cc_start: 0.7847 (tp30) cc_final: 0.7638 (tp30) REVERT: B 1008 MET cc_start: 0.6503 (mmm) cc_final: 0.6186 (ttt) REVERT: B 1009 TYR cc_start: 0.6594 (m-80) cc_final: 0.6383 (m-80) REVERT: B 1013 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7454 (tm-30) REVERT: C 145 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7592 (ttm110) REVERT: C 172 ARG cc_start: 0.7349 (mtt90) cc_final: 0.7017 (mtp85) REVERT: C 262 ARG cc_start: 0.8186 (ttm-80) cc_final: 0.7719 (ttm-80) REVERT: C 337 ARG cc_start: 0.7503 (mtt180) cc_final: 0.7294 (mtm180) REVERT: C 367 HIS cc_start: 0.7388 (m-70) cc_final: 0.6834 (m-70) REVERT: C 400 GLN cc_start: 0.7552 (tt0) cc_final: 0.7307 (tt0) REVERT: C 409 CYS cc_start: 0.7890 (m) cc_final: 0.7246 (t) REVERT: C 417 ILE cc_start: 0.8100 (mt) cc_final: 0.7662 (tt) REVERT: C 419 CYS cc_start: 0.8317 (m) cc_final: 0.7862 (m) REVERT: C 442 VAL cc_start: 0.7796 (p) cc_final: 0.7542 (m) REVERT: C 477 ILE cc_start: 0.7439 (pt) cc_final: 0.7045 (tp) REVERT: C 482 ILE cc_start: 0.6998 (mt) cc_final: 0.6025 (tt) REVERT: C 488 ASP cc_start: 0.7585 (m-30) cc_final: 0.7234 (m-30) REVERT: C 523 MET cc_start: 0.8068 (mmm) cc_final: 0.7759 (tpp) REVERT: C 585 ASN cc_start: 0.7888 (t0) cc_final: 0.7419 (t0) REVERT: C 607 GLU cc_start: 0.7749 (tp30) cc_final: 0.7534 (tp30) REVERT: C 613 GLU cc_start: 0.7808 (tt0) cc_final: 0.7444 (mt-10) REVERT: C 637 MET cc_start: 0.7424 (tpp) cc_final: 0.6829 (tpp) REVERT: C 645 ARG cc_start: 0.7732 (mtm110) cc_final: 0.7526 (mtm110) REVERT: C 731 ARG cc_start: 0.7284 (ttm170) cc_final: 0.6913 (mtp-110) REVERT: C 864 GLU cc_start: 0.7512 (tp30) cc_final: 0.7308 (tp30) REVERT: C 880 LYS cc_start: 0.8024 (ptmt) cc_final: 0.7706 (ptmm) REVERT: C 912 GLN cc_start: 0.7716 (tt0) cc_final: 0.7472 (tt0) REVERT: C 933 CYS cc_start: 0.8166 (p) cc_final: 0.7873 (p) REVERT: C 991 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6451 (pm20) REVERT: C 1006 SER cc_start: 0.8312 (m) cc_final: 0.7911 (t) REVERT: C 1009 TYR cc_start: 0.6968 (m-80) cc_final: 0.6661 (m-80) REVERT: D 142 LYS cc_start: 0.7250 (tttm) cc_final: 0.7010 (tmtt) REVERT: D 238 LYS cc_start: 0.7731 (tptt) cc_final: 0.7306 (tptp) REVERT: D 250 GLN cc_start: 0.7135 (tp40) cc_final: 0.6755 (tp40) REVERT: D 275 LEU cc_start: 0.7490 (mt) cc_final: 0.7093 (mt) REVERT: D 329 ASP cc_start: 0.7436 (m-30) cc_final: 0.7046 (t70) REVERT: D 337 ARG cc_start: 0.7263 (mtm180) cc_final: 0.7044 (mtt180) REVERT: D 400 GLN cc_start: 0.7741 (tt0) cc_final: 0.7437 (tt0) REVERT: D 415 CYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6771 (t) REVERT: D 585 ASN cc_start: 0.7911 (t0) cc_final: 0.7641 (t0) REVERT: D 613 GLU cc_start: 0.7670 (tt0) cc_final: 0.7084 (tt0) REVERT: D 614 VAL cc_start: 0.8529 (t) cc_final: 0.8317 (p) REVERT: D 637 MET cc_start: 0.7610 (tpt) cc_final: 0.7367 (tpp) REVERT: D 640 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6990 (mm-30) REVERT: D 792 LEU cc_start: 0.8291 (mm) cc_final: 0.8037 (mt) REVERT: D 853 THR cc_start: 0.8418 (t) cc_final: 0.7911 (p) REVERT: D 877 GLU cc_start: 0.7581 (pp20) cc_final: 0.7269 (pp20) REVERT: D 880 LYS cc_start: 0.7798 (pttt) cc_final: 0.7307 (ptmt) REVERT: D 899 VAL cc_start: 0.6605 (OUTLIER) cc_final: 0.6348 (p) REVERT: D 929 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8056 (mp) REVERT: D 970 SER cc_start: 0.7248 (t) cc_final: 0.6734 (p) REVERT: D 973 LYS cc_start: 0.8212 (ptmt) cc_final: 0.7685 (ptpp) REVERT: D 990 CYS cc_start: 0.7443 (m) cc_final: 0.6682 (m) REVERT: D 991 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6250 (pm20) REVERT: D 1006 SER cc_start: 0.8027 (m) cc_final: 0.7651 (t) REVERT: D 1009 TYR cc_start: 0.6651 (m-80) cc_final: 0.6405 (m-80) REVERT: D 1022 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7706 (tm-30) REVERT: D 1023 GLU cc_start: 0.6366 (mp0) cc_final: 0.5615 (mp0) REVERT: D 1029 THR cc_start: 0.8359 (m) cc_final: 0.7780 (p) REVERT: E 143 TYR cc_start: 0.7122 (t80) cc_final: 0.6779 (t80) REVERT: E 145 ARG cc_start: 0.7855 (ttp-110) cc_final: 0.7493 (ttm110) REVERT: E 172 ARG cc_start: 0.7400 (mtt90) cc_final: 0.6955 (mtt90) REVERT: E 174 ILE cc_start: 0.7998 (mt) cc_final: 0.7794 (tt) REVERT: E 175 LYS cc_start: 0.8118 (tttt) cc_final: 0.7845 (tttt) REVERT: E 277 MET cc_start: 0.6607 (ptm) cc_final: 0.6217 (ptm) REVERT: E 338 LYS cc_start: 0.8074 (mtpt) cc_final: 0.7837 (mttt) REVERT: E 348 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7879 (mp) REVERT: E 367 HIS cc_start: 0.7295 (m-70) cc_final: 0.6752 (m-70) REVERT: E 369 GLU cc_start: 0.7721 (tt0) cc_final: 0.7457 (tt0) REVERT: E 375 GLU cc_start: 0.7843 (tt0) cc_final: 0.7451 (tt0) REVERT: E 404 VAL cc_start: 0.8027 (t) cc_final: 0.7569 (p) REVERT: E 409 CYS cc_start: 0.8244 (m) cc_final: 0.7378 (t) REVERT: E 415 CYS cc_start: 0.7115 (m) cc_final: 0.6050 (m) REVERT: E 585 ASN cc_start: 0.7735 (t0) cc_final: 0.7526 (t0) REVERT: E 603 GLN cc_start: 0.7181 (tp40) cc_final: 0.6394 (tm-30) REVERT: E 648 ASP cc_start: 0.8094 (m-30) cc_final: 0.7755 (t0) REVERT: E 663 HIS cc_start: 0.7797 (m90) cc_final: 0.7511 (m-70) REVERT: E 731 ARG cc_start: 0.7292 (ttm170) cc_final: 0.6737 (ttm110) REVERT: E 745 GLU cc_start: 0.7432 (tt0) cc_final: 0.7149 (tt0) REVERT: E 777 LEU cc_start: 0.8398 (mp) cc_final: 0.7954 (mm) REVERT: E 785 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: E 853 THR cc_start: 0.8490 (t) cc_final: 0.8013 (p) REVERT: E 869 ASP cc_start: 0.7408 (t0) cc_final: 0.7196 (m-30) REVERT: E 933 CYS cc_start: 0.8379 (m) cc_final: 0.8065 (m) REVERT: E 938 HIS cc_start: 0.7949 (t-90) cc_final: 0.7727 (t-90) REVERT: E 973 LYS cc_start: 0.8164 (ptmt) cc_final: 0.7687 (ptpp) REVERT: E 983 ASP cc_start: 0.6758 (OUTLIER) cc_final: 0.6099 (t0) REVERT: E 987 MET cc_start: 0.6873 (mmt) cc_final: 0.6451 (mmt) REVERT: E 991 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6615 (pm20) REVERT: E 1006 SER cc_start: 0.8141 (m) cc_final: 0.7817 (t) REVERT: E 1009 TYR cc_start: 0.6780 (m-80) cc_final: 0.6295 (m-80) REVERT: E 1019 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7376 (tp30) REVERT: E 1022 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7580 (tm-30) REVERT: E 1029 THR cc_start: 0.8428 (m) cc_final: 0.7933 (p) REVERT: F 269 GLN cc_start: 0.5189 (mp10) cc_final: 0.4748 (mp10) REVERT: F 301 MET cc_start: 0.7526 (ttm) cc_final: 0.6814 (ttp) REVERT: F 312 ASP cc_start: 0.7721 (t70) cc_final: 0.7190 (t0) REVERT: F 338 LYS cc_start: 0.8008 (mtmm) cc_final: 0.7563 (mtpp) REVERT: F 369 GLU cc_start: 0.7516 (tt0) cc_final: 0.7216 (tt0) REVERT: F 379 LYS cc_start: 0.7340 (ttmt) cc_final: 0.7134 (ttmt) REVERT: F 563 GLU cc_start: 0.6905 (pp20) cc_final: 0.6512 (tm-30) REVERT: F 569 GLU cc_start: 0.7135 (tp30) cc_final: 0.6798 (tp30) REVERT: F 607 GLU cc_start: 0.7433 (tp30) cc_final: 0.7110 (tp30) REVERT: F 613 GLU cc_start: 0.7657 (tt0) cc_final: 0.7325 (tt0) REVERT: F 637 MET cc_start: 0.7865 (tpt) cc_final: 0.7483 (tpt) REVERT: F 644 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7361 (mm-40) REVERT: F 647 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7665 (mtm) REVERT: F 649 TYR cc_start: 0.7537 (m-80) cc_final: 0.7183 (m-80) REVERT: F 652 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8170 (ttmt) REVERT: F 669 CYS cc_start: 0.7741 (m) cc_final: 0.7458 (m) REVERT: F 745 GLU cc_start: 0.7537 (tt0) cc_final: 0.7171 (tt0) REVERT: F 785 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: F 796 SER cc_start: 0.7171 (t) cc_final: 0.6731 (p) REVERT: F 806 SER cc_start: 0.8497 (p) cc_final: 0.8290 (m) REVERT: F 853 THR cc_start: 0.8207 (t) cc_final: 0.7748 (p) REVERT: F 876 CYS cc_start: 0.8457 (m) cc_final: 0.8017 (m) REVERT: F 933 CYS cc_start: 0.8185 (m) cc_final: 0.7927 (m) REVERT: F 973 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7997 (mtmt) REVERT: F 987 MET cc_start: 0.6886 (mmt) cc_final: 0.6335 (mmm) REVERT: F 991 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6726 (pm20) REVERT: F 1006 SER cc_start: 0.7967 (m) cc_final: 0.7704 (t) REVERT: F 1009 TYR cc_start: 0.6619 (m-80) cc_final: 0.6325 (m-80) REVERT: F 1019 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7725 (mm-30) REVERT: F 1022 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7596 (tm-30) REVERT: F 1029 THR cc_start: 0.8280 (m) cc_final: 0.7971 (p) outliers start: 164 outliers final: 106 residues processed: 964 average time/residue: 0.2408 time to fit residues: 381.0372 Evaluate side-chains 970 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 846 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 522 HIS Chi-restraints excluded: chain B residue 526 GLN Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 632 TYR Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 632 TYR Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 991 GLU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 415 CYS Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 644 GLN Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 849 SER Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 991 GLU Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 288 HIS Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 522 HIS Chi-restraints excluded: chain E residue 573 LEU Chi-restraints excluded: chain E residue 624 GLN Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 765 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 793 VAL Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 929 ILE Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain E residue 983 ASP Chi-restraints excluded: chain E residue 991 GLU Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 522 HIS Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 647 MET Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 785 GLU Chi-restraints excluded: chain F residue 793 VAL Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 825 LEU Chi-restraints excluded: chain F residue 841 SER Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 927 LYS Chi-restraints excluded: chain F residue 929 ILE Chi-restraints excluded: chain F residue 948 LEU Chi-restraints excluded: chain F residue 973 LYS Chi-restraints excluded: chain F residue 991 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 329 optimal weight: 0.3980 chunk 453 optimal weight: 0.4980 chunk 360 optimal weight: 1.9990 chunk 365 optimal weight: 0.6980 chunk 342 optimal weight: 0.4980 chunk 362 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 363 optimal weight: 6.9990 chunk 468 optimal weight: 6.9990 chunk 214 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 HIS ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 HIS ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 865 ASN ** C 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.179201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.146368 restraints weight = 61947.387| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.27 r_work: 0.3688 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39690 Z= 0.124 Angle : 0.645 9.473 53544 Z= 0.319 Chirality : 0.041 0.184 6078 Planarity : 0.005 0.073 6714 Dihedral : 7.330 144.504 5256 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.64 % Allowed : 21.17 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.12), residues: 4782 helix: 0.30 (0.11), residues: 2232 sheet: -1.72 (0.19), residues: 588 loop : -1.59 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 645 TYR 0.034 0.001 TYR E 649 PHE 0.028 0.001 PHE A 528 TRP 0.012 0.001 TRP A 243 HIS 0.005 0.001 HIS A 916 Details of bonding type rmsd covalent geometry : bond 0.00272 (39690) covalent geometry : angle 0.64457 (53544) hydrogen bonds : bond 0.03819 ( 1520) hydrogen bonds : angle 4.86601 ( 4488) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 847 time to evaluate : 1.446 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 143 TYR cc_start: 0.7278 (t80) cc_final: 0.7001 (t80) REVERT: A 172 ARG cc_start: 0.7083 (mtt90) cc_final: 0.6591 (mtt90) REVERT: A 239 MET cc_start: 0.7415 (ttp) cc_final: 0.7171 (ttp) REVERT: A 298 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6607 (pt) REVERT: A 329 ASP cc_start: 0.7867 (m-30) cc_final: 0.7272 (p0) REVERT: A 353 VAL cc_start: 0.8852 (p) cc_final: 0.8636 (t) REVERT: A 419 CYS cc_start: 0.7969 (m) cc_final: 0.7677 (m) REVERT: A 505 MET cc_start: 0.4517 (ppp) cc_final: 0.4300 (ppp) REVERT: A 523 MET cc_start: 0.7586 (mmm) cc_final: 0.7271 (tpp) REVERT: A 563 GLU cc_start: 0.7262 (pp20) cc_final: 0.7043 (tp30) REVERT: A 569 GLU cc_start: 0.7419 (tp30) cc_final: 0.7200 (tp30) REVERT: A 607 GLU cc_start: 0.7825 (tp30) cc_final: 0.7557 (tp30) REVERT: A 631 PHE cc_start: 0.7922 (m-10) cc_final: 0.7627 (m-80) REVERT: A 649 TYR cc_start: 0.7550 (m-80) cc_final: 0.7165 (m-80) REVERT: A 652 LYS cc_start: 0.8344 (ttmt) cc_final: 0.8073 (ttmm) REVERT: A 662 ASP cc_start: 0.7851 (m-30) cc_final: 0.7393 (m-30) REVERT: A 669 CYS cc_start: 0.7536 (m) cc_final: 0.6950 (m) REVERT: A 785 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: A 930 LYS cc_start: 0.8172 (mttt) cc_final: 0.7702 (mttt) REVERT: A 973 LYS cc_start: 0.8198 (ptmt) cc_final: 0.7670 (ptpp) REVERT: A 974 LEU cc_start: 0.8090 (tt) cc_final: 0.7864 (tt) REVERT: A 978 ASN cc_start: 0.7255 (p0) cc_final: 0.7002 (p0) REVERT: A 988 MET cc_start: 0.7408 (mmm) cc_final: 0.6325 (tmm) REVERT: A 991 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6373 (pm20) REVERT: A 1006 SER cc_start: 0.8382 (m) cc_final: 0.8043 (t) REVERT: A 1013 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7447 (tm-30) REVERT: A 1019 GLU cc_start: 0.8106 (tp30) cc_final: 0.7819 (mt-10) REVERT: B 145 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7437 (mtp85) REVERT: B 172 ARG cc_start: 0.6979 (mtt90) cc_final: 0.6607 (mtt90) REVERT: B 259 ILE cc_start: 0.7732 (mp) cc_final: 0.7164 (pt) REVERT: B 267 VAL cc_start: 0.4496 (OUTLIER) cc_final: 0.4293 (p) REVERT: B 301 MET cc_start: 0.6882 (ttm) cc_final: 0.6610 (ttm) REVERT: B 367 HIS cc_start: 0.7330 (m-70) cc_final: 0.6757 (m-70) REVERT: B 385 TYR cc_start: 0.8093 (t80) cc_final: 0.7582 (t80) REVERT: B 480 GLN cc_start: 0.6697 (mp10) cc_final: 0.6339 (mp10) REVERT: B 488 ASP cc_start: 0.7552 (m-30) cc_final: 0.7317 (m-30) REVERT: B 526 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: B 610 LYS cc_start: 0.8752 (mmmm) cc_final: 0.8537 (mppt) REVERT: B 613 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7025 (mm-30) REVERT: B 649 TYR cc_start: 0.7408 (m-80) cc_final: 0.5508 (m-80) REVERT: B 652 LYS cc_start: 0.8354 (ttmt) cc_final: 0.8093 (ttmm) REVERT: B 758 MET cc_start: 0.7283 (tpt) cc_final: 0.6946 (tpt) REVERT: B 826 LEU cc_start: 0.7962 (tp) cc_final: 0.7550 (tt) REVERT: B 845 GLN cc_start: 0.7942 (tp-100) cc_final: 0.7651 (tp-100) REVERT: B 864 GLU cc_start: 0.7731 (tp30) cc_final: 0.7462 (tp30) REVERT: B 1008 MET cc_start: 0.6472 (mmm) cc_final: 0.6179 (ttt) REVERT: B 1009 TYR cc_start: 0.6621 (m-80) cc_final: 0.6398 (m-80) REVERT: B 1013 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7439 (tm-30) REVERT: B 1029 THR cc_start: 0.8438 (m) cc_final: 0.8015 (p) REVERT: C 145 ARG cc_start: 0.7880 (ttp-110) cc_final: 0.7537 (ttm110) REVERT: C 259 ILE cc_start: 0.7710 (mp) cc_final: 0.7127 (pt) REVERT: C 262 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7626 (ttm-80) REVERT: C 301 MET cc_start: 0.7694 (ttm) cc_final: 0.7018 (ttp) REVERT: C 367 HIS cc_start: 0.7355 (m-70) cc_final: 0.6794 (m-70) REVERT: C 409 CYS cc_start: 0.7882 (m) cc_final: 0.7310 (t) REVERT: C 419 CYS cc_start: 0.8323 (m) cc_final: 0.7852 (m) REVERT: C 477 ILE cc_start: 0.7375 (pt) cc_final: 0.6948 (tp) REVERT: C 482 ILE cc_start: 0.6912 (mt) cc_final: 0.6528 (tt) REVERT: C 523 MET cc_start: 0.8028 (mmm) cc_final: 0.7696 (tpp) REVERT: C 585 ASN cc_start: 0.7865 (t0) cc_final: 0.7548 (t0) REVERT: C 607 GLU cc_start: 0.7761 (tp30) cc_final: 0.7541 (tp30) REVERT: C 613 GLU cc_start: 0.7784 (tt0) cc_final: 0.7428 (mt-10) REVERT: C 641 ASP cc_start: 0.7526 (p0) cc_final: 0.7051 (t0) REVERT: C 731 ARG cc_start: 0.7289 (ttm170) cc_final: 0.6857 (mtp85) REVERT: C 758 MET cc_start: 0.7685 (tpt) cc_final: 0.7206 (tpt) REVERT: C 785 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: C 861 TYR cc_start: 0.8427 (m-80) cc_final: 0.8218 (m-80) REVERT: C 864 GLU cc_start: 0.7454 (tp30) cc_final: 0.7110 (tp30) REVERT: C 880 LYS cc_start: 0.7973 (ptmt) cc_final: 0.7685 (ptmm) REVERT: C 912 GLN cc_start: 0.7705 (tt0) cc_final: 0.7477 (tt0) REVERT: C 933 CYS cc_start: 0.8184 (p) cc_final: 0.7906 (p) REVERT: C 988 MET cc_start: 0.7372 (mmm) cc_final: 0.7053 (tpp) REVERT: C 1006 SER cc_start: 0.8289 (m) cc_final: 0.7864 (t) REVERT: C 1009 TYR cc_start: 0.6949 (m-80) cc_final: 0.6599 (m-80) REVERT: D 142 LYS cc_start: 0.7226 (tttm) cc_final: 0.6950 (tmtt) REVERT: D 234 ILE cc_start: 0.6054 (OUTLIER) cc_final: 0.5717 (pt) REVERT: D 238 LYS cc_start: 0.7649 (tptt) cc_final: 0.7267 (tptp) REVERT: D 240 MET cc_start: 0.6455 (mtp) cc_final: 0.6068 (mtm) REVERT: D 250 GLN cc_start: 0.7099 (tp40) cc_final: 0.6736 (tp40) REVERT: D 329 ASP cc_start: 0.7412 (m-30) cc_final: 0.6991 (t70) REVERT: D 369 GLU cc_start: 0.7563 (tt0) cc_final: 0.7281 (tt0) REVERT: D 400 GLN cc_start: 0.7720 (tt0) cc_final: 0.7409 (tt0) REVERT: D 415 CYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6820 (t) REVERT: D 585 ASN cc_start: 0.7893 (t0) cc_final: 0.7621 (t0) REVERT: D 611 TRP cc_start: 0.7687 (t60) cc_final: 0.7073 (t60) REVERT: D 614 VAL cc_start: 0.8512 (t) cc_final: 0.8295 (p) REVERT: D 640 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7055 (mm-30) REVERT: D 792 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7991 (mt) REVERT: D 851 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6890 (tp) REVERT: D 853 THR cc_start: 0.8367 (t) cc_final: 0.7864 (p) REVERT: D 877 GLU cc_start: 0.7578 (pp20) cc_final: 0.7247 (pp20) REVERT: D 880 LYS cc_start: 0.7779 (pttt) cc_final: 0.7268 (ptmt) REVERT: D 929 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.8019 (mp) REVERT: D 938 HIS cc_start: 0.7274 (t-90) cc_final: 0.6935 (t-170) REVERT: D 970 SER cc_start: 0.7176 (t) cc_final: 0.6673 (p) REVERT: D 973 LYS cc_start: 0.8123 (ptmt) cc_final: 0.7595 (ptpp) REVERT: D 983 ASP cc_start: 0.6123 (t0) cc_final: 0.5869 (t0) REVERT: D 987 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.6250 (mmm) REVERT: D 990 CYS cc_start: 0.7422 (m) cc_final: 0.6717 (m) REVERT: D 991 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.6181 (pm20) REVERT: D 1006 SER cc_start: 0.8025 (m) cc_final: 0.7623 (t) REVERT: D 1007 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6270 (tp30) REVERT: D 1009 TYR cc_start: 0.6633 (m-80) cc_final: 0.6087 (m-80) REVERT: D 1022 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7686 (tm-30) REVERT: D 1023 GLU cc_start: 0.6324 (mp0) cc_final: 0.5571 (mp0) REVERT: D 1029 THR cc_start: 0.8369 (m) cc_final: 0.7815 (p) REVERT: E 143 TYR cc_start: 0.7044 (t80) cc_final: 0.6725 (t80) REVERT: E 145 ARG cc_start: 0.7814 (ttp-110) cc_final: 0.7341 (ttm110) REVERT: E 172 ARG cc_start: 0.7374 (mtt90) cc_final: 0.6901 (mtt90) REVERT: E 175 LYS cc_start: 0.8109 (tttt) cc_final: 0.7833 (tttt) REVERT: E 272 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7585 (tt) REVERT: E 275 LEU cc_start: 0.7458 (mp) cc_final: 0.7223 (mt) REVERT: E 277 MET cc_start: 0.6582 (ptm) cc_final: 0.6260 (ptm) REVERT: E 338 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7826 (mttt) REVERT: E 348 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7831 (mp) REVERT: E 367 HIS cc_start: 0.7290 (m-70) cc_final: 0.6868 (m90) REVERT: E 369 GLU cc_start: 0.7722 (tt0) cc_final: 0.7423 (tt0) REVERT: E 375 GLU cc_start: 0.7764 (tt0) cc_final: 0.7365 (tt0) REVERT: E 404 VAL cc_start: 0.7992 (t) cc_final: 0.7532 (p) REVERT: E 409 CYS cc_start: 0.8135 (m) cc_final: 0.7406 (t) REVERT: E 415 CYS cc_start: 0.7054 (m) cc_final: 0.6106 (m) REVERT: E 603 GLN cc_start: 0.7100 (tp40) cc_final: 0.6330 (tm-30) REVERT: E 611 TRP cc_start: 0.7779 (t60) cc_final: 0.7088 (t60) REVERT: E 613 GLU cc_start: 0.7730 (tt0) cc_final: 0.7299 (tt0) REVERT: E 637 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6974 (ttm) REVERT: E 648 ASP cc_start: 0.8033 (m-30) cc_final: 0.7695 (t0) REVERT: E 663 HIS cc_start: 0.7770 (m90) cc_final: 0.7479 (m-70) REVERT: E 731 ARG cc_start: 0.7285 (ttm170) cc_final: 0.6723 (ttm110) REVERT: E 745 GLU cc_start: 0.7422 (tt0) cc_final: 0.7152 (tt0) REVERT: E 777 LEU cc_start: 0.8303 (mp) cc_final: 0.7930 (mm) REVERT: E 785 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7857 (pt0) REVERT: E 853 THR cc_start: 0.8458 (t) cc_final: 0.7982 (p) REVERT: E 864 GLU cc_start: 0.7652 (tp30) cc_final: 0.7380 (tp30) REVERT: E 869 ASP cc_start: 0.7381 (t0) cc_final: 0.7174 (m-30) REVERT: E 933 CYS cc_start: 0.8354 (m) cc_final: 0.8039 (m) REVERT: E 973 LYS cc_start: 0.8126 (ptmt) cc_final: 0.7642 (ptpp) REVERT: E 991 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6573 (pm20) REVERT: E 1006 SER cc_start: 0.8099 (m) cc_final: 0.7743 (t) REVERT: E 1009 TYR cc_start: 0.6699 (m-80) cc_final: 0.6257 (m-80) REVERT: E 1019 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7269 (tp30) REVERT: E 1022 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7563 (tm-30) REVERT: E 1029 THR cc_start: 0.8428 (m) cc_final: 0.7945 (p) REVERT: F 272 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7520 (tt) REVERT: F 301 MET cc_start: 0.7460 (ttm) cc_final: 0.6720 (ttp) REVERT: F 304 PHE cc_start: 0.7820 (t80) cc_final: 0.7573 (t80) REVERT: F 312 ASP cc_start: 0.7719 (t70) cc_final: 0.7200 (t0) REVERT: F 338 LYS cc_start: 0.7998 (mtmm) cc_final: 0.7282 (mtmm) REVERT: F 369 GLU cc_start: 0.7526 (tt0) cc_final: 0.6993 (tt0) REVERT: F 370 ILE cc_start: 0.7992 (mm) cc_final: 0.7661 (tp) REVERT: F 371 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7396 (mm) REVERT: F 379 LYS cc_start: 0.7306 (ttmt) cc_final: 0.7099 (ttmt) REVERT: F 563 GLU cc_start: 0.6853 (pp20) cc_final: 0.6630 (tm-30) REVERT: F 607 GLU cc_start: 0.7447 (tp30) cc_final: 0.7113 (tp30) REVERT: F 611 TRP cc_start: 0.7636 (t60) cc_final: 0.6839 (t60) REVERT: F 613 GLU cc_start: 0.7647 (tt0) cc_final: 0.7314 (tt0) REVERT: F 637 MET cc_start: 0.7885 (tpt) cc_final: 0.7559 (tpt) REVERT: F 644 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7341 (mm-40) REVERT: F 645 ARG cc_start: 0.7399 (mtm110) cc_final: 0.7093 (mtm180) REVERT: F 647 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7662 (mtm) REVERT: F 649 TYR cc_start: 0.7550 (m-80) cc_final: 0.7226 (m-80) REVERT: F 652 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8143 (ttmt) REVERT: F 745 GLU cc_start: 0.7549 (tt0) cc_final: 0.7171 (tt0) REVERT: F 785 GLU cc_start: 0.8192 (pt0) cc_final: 0.7682 (mp0) REVERT: F 796 SER cc_start: 0.7133 (t) cc_final: 0.6679 (p) REVERT: F 853 THR cc_start: 0.8121 (t) cc_final: 0.7433 (p) REVERT: F 876 CYS cc_start: 0.8406 (m) cc_final: 0.7874 (m) REVERT: F 933 CYS cc_start: 0.8151 (m) cc_final: 0.7919 (m) REVERT: F 973 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7913 (mtmt) REVERT: F 987 MET cc_start: 0.6822 (mmt) cc_final: 0.6425 (mmt) REVERT: F 991 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6653 (pm20) REVERT: F 1006 SER cc_start: 0.7985 (m) cc_final: 0.7700 (t) REVERT: F 1009 TYR cc_start: 0.6578 (m-80) cc_final: 0.6314 (m-80) REVERT: F 1019 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7679 (mm-30) REVERT: F 1022 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7523 (tm-30) REVERT: F 1029 THR cc_start: 0.8325 (m) cc_final: 0.7942 (p) outliers start: 160 outliers final: 96 residues processed: 936 average time/residue: 0.2425 time to fit residues: 371.0025 Evaluate side-chains 946 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 826 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 522 HIS Chi-restraints excluded: chain B residue 526 GLN Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 785 GLU Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 840 THR Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 415 CYS Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 644 GLN Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 849 SER Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 851 LEU Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain D residue 991 GLU Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 288 HIS Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 522 HIS Chi-restraints excluded: chain E residue 573 LEU Chi-restraints excluded: chain E residue 637 MET Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 765 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 793 VAL Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 929 ILE Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain E residue 991 GLU Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 522 HIS Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 600 ILE Chi-restraints excluded: chain F residue 647 MET Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 793 VAL Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 841 SER Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 929 ILE Chi-restraints excluded: chain F residue 948 LEU Chi-restraints excluded: chain F residue 973 LYS Chi-restraints excluded: chain F residue 991 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 359 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 chunk 349 optimal weight: 1.9990 chunk 468 optimal weight: 6.9990 chunk 409 optimal weight: 4.9990 chunk 209 optimal weight: 0.2980 chunk 421 optimal weight: 3.9990 chunk 368 optimal weight: 1.9990 chunk 440 optimal weight: 0.6980 chunk 331 optimal weight: 0.0370 chunk 261 optimal weight: 6.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 674 HIS ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN D 767 HIS ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 767 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.177118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.144551 restraints weight = 61797.024| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 3.19 r_work: 0.3683 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39690 Z= 0.137 Angle : 0.657 10.827 53544 Z= 0.324 Chirality : 0.042 0.185 6078 Planarity : 0.005 0.068 6714 Dihedral : 7.273 139.878 5256 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.64 % Allowed : 21.21 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.12), residues: 4782 helix: 0.33 (0.11), residues: 2226 sheet: -1.94 (0.18), residues: 642 loop : -1.45 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 645 TYR 0.024 0.002 TYR E 168 PHE 0.024 0.001 PHE A 528 TRP 0.013 0.001 TRP A 243 HIS 0.009 0.001 HIS F 767 Details of bonding type rmsd covalent geometry : bond 0.00303 (39690) covalent geometry : angle 0.65704 (53544) hydrogen bonds : bond 0.03984 ( 1520) hydrogen bonds : angle 4.86788 ( 4488) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 862 time to evaluate : 1.399 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 143 TYR cc_start: 0.7240 (t80) cc_final: 0.6975 (t80) REVERT: A 172 ARG cc_start: 0.7075 (mtt90) cc_final: 0.6614 (mtt90) REVERT: A 239 MET cc_start: 0.7383 (ttp) cc_final: 0.7132 (ttp) REVERT: A 259 ILE cc_start: 0.7735 (mp) cc_final: 0.7122 (pt) REVERT: A 272 LEU cc_start: 0.8251 (tp) cc_final: 0.7861 (tt) REVERT: A 298 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6529 (pt) REVERT: A 301 MET cc_start: 0.7664 (ttt) cc_final: 0.7016 (ttp) REVERT: A 329 ASP cc_start: 0.7796 (m-30) cc_final: 0.7229 (p0) REVERT: A 353 VAL cc_start: 0.8828 (p) cc_final: 0.8620 (t) REVERT: A 371 LEU cc_start: 0.7766 (mm) cc_final: 0.7372 (mm) REVERT: A 419 CYS cc_start: 0.7922 (m) cc_final: 0.7667 (m) REVERT: A 505 MET cc_start: 0.4530 (ppp) cc_final: 0.4303 (ppp) REVERT: A 523 MET cc_start: 0.7618 (mmm) cc_final: 0.7320 (tpp) REVERT: A 569 GLU cc_start: 0.7385 (tp30) cc_final: 0.7171 (tp30) REVERT: A 607 GLU cc_start: 0.7841 (tp30) cc_final: 0.7562 (tp30) REVERT: A 631 PHE cc_start: 0.7933 (m-10) cc_final: 0.7694 (m-80) REVERT: A 649 TYR cc_start: 0.7571 (m-80) cc_final: 0.7245 (m-80) REVERT: A 652 LYS cc_start: 0.8292 (ttmt) cc_final: 0.8062 (ttmm) REVERT: A 654 GLU cc_start: 0.7388 (tp30) cc_final: 0.7019 (tp30) REVERT: A 662 ASP cc_start: 0.7857 (m-30) cc_final: 0.7425 (m-30) REVERT: A 669 CYS cc_start: 0.7575 (m) cc_final: 0.7021 (m) REVERT: A 785 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7530 (pm20) REVERT: A 930 LYS cc_start: 0.8171 (mttt) cc_final: 0.7701 (mttt) REVERT: A 973 LYS cc_start: 0.8226 (ptmt) cc_final: 0.7693 (ptpp) REVERT: A 974 LEU cc_start: 0.8089 (tt) cc_final: 0.7870 (tt) REVERT: A 978 ASN cc_start: 0.7234 (p0) cc_final: 0.6974 (p0) REVERT: A 988 MET cc_start: 0.7372 (mmm) cc_final: 0.6286 (tmm) REVERT: A 991 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6359 (pm20) REVERT: A 1006 SER cc_start: 0.8373 (m) cc_final: 0.8058 (t) REVERT: A 1013 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7448 (tm-30) REVERT: B 145 ARG cc_start: 0.7752 (ttm-80) cc_final: 0.7454 (mtp85) REVERT: B 172 ARG cc_start: 0.6915 (mtt90) cc_final: 0.6540 (mtt90) REVERT: B 259 ILE cc_start: 0.7765 (mp) cc_final: 0.7176 (pt) REVERT: B 267 VAL cc_start: 0.4578 (OUTLIER) cc_final: 0.4377 (p) REVERT: B 301 MET cc_start: 0.6877 (ttm) cc_final: 0.6624 (ttm) REVERT: B 367 HIS cc_start: 0.7309 (m-70) cc_final: 0.6766 (m-70) REVERT: B 385 TYR cc_start: 0.8075 (t80) cc_final: 0.7631 (t80) REVERT: B 480 GLN cc_start: 0.6669 (mp10) cc_final: 0.6334 (mp10) REVERT: B 526 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: B 610 LYS cc_start: 0.8785 (mmmm) cc_final: 0.8561 (mppt) REVERT: B 613 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7152 (mm-30) REVERT: B 649 TYR cc_start: 0.7331 (m-80) cc_final: 0.6770 (m-80) REVERT: B 652 LYS cc_start: 0.8332 (ttmt) cc_final: 0.8065 (ttmm) REVERT: B 662 ASP cc_start: 0.7622 (m-30) cc_final: 0.7215 (m-30) REVERT: B 677 GLU cc_start: 0.7620 (tp30) cc_final: 0.7204 (tp30) REVERT: B 758 MET cc_start: 0.7229 (tpt) cc_final: 0.6931 (tpt) REVERT: B 826 LEU cc_start: 0.7966 (tp) cc_final: 0.7538 (tt) REVERT: B 845 GLN cc_start: 0.7965 (tp-100) cc_final: 0.7666 (tp-100) REVERT: B 864 GLU cc_start: 0.7777 (tp30) cc_final: 0.7503 (tp30) REVERT: B 1008 MET cc_start: 0.6468 (mmm) cc_final: 0.6182 (ttt) REVERT: B 1009 TYR cc_start: 0.6605 (m-80) cc_final: 0.6392 (m-80) REVERT: B 1013 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7422 (tm-30) REVERT: B 1029 THR cc_start: 0.8438 (m) cc_final: 0.8029 (p) REVERT: C 145 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7543 (ttm110) REVERT: C 172 ARG cc_start: 0.7239 (mtt90) cc_final: 0.6915 (mtp85) REVERT: C 259 ILE cc_start: 0.7743 (mp) cc_final: 0.7169 (pt) REVERT: C 262 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7736 (ttm-80) REVERT: C 298 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6616 (pt) REVERT: C 367 HIS cc_start: 0.7366 (m-70) cc_final: 0.6839 (m-70) REVERT: C 409 CYS cc_start: 0.7894 (m) cc_final: 0.7318 (t) REVERT: C 419 CYS cc_start: 0.8319 (m) cc_final: 0.7855 (m) REVERT: C 477 ILE cc_start: 0.7435 (pt) cc_final: 0.7057 (tp) REVERT: C 488 ASP cc_start: 0.7519 (m-30) cc_final: 0.7216 (m-30) REVERT: C 523 MET cc_start: 0.8054 (mmm) cc_final: 0.7694 (tpp) REVERT: C 585 ASN cc_start: 0.7698 (t0) cc_final: 0.7460 (t0) REVERT: C 607 GLU cc_start: 0.7713 (tp30) cc_final: 0.7490 (tp30) REVERT: C 613 GLU cc_start: 0.7802 (tt0) cc_final: 0.7456 (mt-10) REVERT: C 637 MET cc_start: 0.7483 (tpt) cc_final: 0.7131 (tpt) REVERT: C 774 ARG cc_start: 0.8041 (mtm110) cc_final: 0.7674 (mtm110) REVERT: C 785 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: C 864 GLU cc_start: 0.7474 (tp30) cc_final: 0.7260 (tp30) REVERT: C 880 LYS cc_start: 0.8023 (ptmt) cc_final: 0.7736 (ptmm) REVERT: C 912 GLN cc_start: 0.7694 (tt0) cc_final: 0.7461 (tt0) REVERT: C 933 CYS cc_start: 0.8197 (p) cc_final: 0.7895 (p) REVERT: C 1006 SER cc_start: 0.8282 (m) cc_final: 0.7860 (t) REVERT: C 1009 TYR cc_start: 0.6956 (m-80) cc_final: 0.6608 (m-80) REVERT: D 142 LYS cc_start: 0.7234 (tttm) cc_final: 0.6976 (tmtt) REVERT: D 234 ILE cc_start: 0.6126 (OUTLIER) cc_final: 0.5782 (pt) REVERT: D 238 LYS cc_start: 0.7627 (tptt) cc_final: 0.7280 (tptp) REVERT: D 250 GLN cc_start: 0.7096 (tp40) cc_final: 0.6742 (tp40) REVERT: D 369 GLU cc_start: 0.7541 (tt0) cc_final: 0.7247 (tt0) REVERT: D 400 GLN cc_start: 0.7718 (tt0) cc_final: 0.7409 (tt0) REVERT: D 415 CYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6546 (t) REVERT: D 611 TRP cc_start: 0.7693 (t60) cc_final: 0.7085 (t60) REVERT: D 614 VAL cc_start: 0.8529 (t) cc_final: 0.8311 (p) REVERT: D 640 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6983 (mm-30) REVERT: D 649 TYR cc_start: 0.7447 (m-80) cc_final: 0.7212 (m-80) REVERT: D 669 CYS cc_start: 0.7800 (m) cc_final: 0.7427 (p) REVERT: D 792 LEU cc_start: 0.8273 (mm) cc_final: 0.8026 (mt) REVERT: D 851 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6914 (tp) REVERT: D 853 THR cc_start: 0.8366 (t) cc_final: 0.7863 (p) REVERT: D 877 GLU cc_start: 0.7586 (pp20) cc_final: 0.7254 (pp20) REVERT: D 929 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.8038 (mp) REVERT: D 938 HIS cc_start: 0.7281 (t-90) cc_final: 0.6901 (t-170) REVERT: D 942 LYS cc_start: 0.8392 (mmtp) cc_final: 0.8137 (mmtp) REVERT: D 970 SER cc_start: 0.7253 (t) cc_final: 0.6779 (p) REVERT: D 973 LYS cc_start: 0.8148 (ptmt) cc_final: 0.7619 (ptpp) REVERT: D 983 ASP cc_start: 0.6221 (t0) cc_final: 0.5458 (t0) REVERT: D 987 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.6099 (mmm) REVERT: D 988 MET cc_start: 0.7156 (mmm) cc_final: 0.6780 (mmm) REVERT: D 991 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6257 (pm20) REVERT: D 1006 SER cc_start: 0.8046 (m) cc_final: 0.7674 (t) REVERT: D 1022 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7692 (tm-30) REVERT: D 1029 THR cc_start: 0.8371 (m) cc_final: 0.7841 (p) REVERT: E 143 TYR cc_start: 0.7062 (t80) cc_final: 0.6729 (t80) REVERT: E 145 ARG cc_start: 0.7798 (ttp-110) cc_final: 0.7315 (ttm110) REVERT: E 172 ARG cc_start: 0.7327 (mtt90) cc_final: 0.6876 (mtt90) REVERT: E 175 LYS cc_start: 0.8153 (tttt) cc_final: 0.7884 (tttt) REVERT: E 269 GLN cc_start: 0.5229 (mp10) cc_final: 0.4869 (mp10) REVERT: E 275 LEU cc_start: 0.7459 (mp) cc_final: 0.7234 (mt) REVERT: E 277 MET cc_start: 0.6572 (ptm) cc_final: 0.6238 (ptm) REVERT: E 338 LYS cc_start: 0.8051 (mtpt) cc_final: 0.7646 (mtpt) REVERT: E 367 HIS cc_start: 0.7256 (m-70) cc_final: 0.6883 (m90) REVERT: E 375 GLU cc_start: 0.7781 (tt0) cc_final: 0.7383 (tt0) REVERT: E 404 VAL cc_start: 0.8030 (t) cc_final: 0.7576 (p) REVERT: E 409 CYS cc_start: 0.8111 (m) cc_final: 0.7416 (t) REVERT: E 415 CYS cc_start: 0.7083 (m) cc_final: 0.5897 (m) REVERT: E 419 CYS cc_start: 0.7839 (m) cc_final: 0.7394 (m) REVERT: E 585 ASN cc_start: 0.7538 (OUTLIER) cc_final: 0.7209 (t0) REVERT: E 603 GLN cc_start: 0.7114 (tp40) cc_final: 0.6342 (tm-30) REVERT: E 637 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.7039 (ttp) REVERT: E 648 ASP cc_start: 0.8026 (m-30) cc_final: 0.7674 (t0) REVERT: E 663 HIS cc_start: 0.7798 (m90) cc_final: 0.7516 (m-70) REVERT: E 731 ARG cc_start: 0.7259 (ttm170) cc_final: 0.6716 (ttm110) REVERT: E 745 GLU cc_start: 0.7380 (tt0) cc_final: 0.7115 (tt0) REVERT: E 777 LEU cc_start: 0.8293 (mp) cc_final: 0.7860 (mm) REVERT: E 785 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7837 (pt0) REVERT: E 853 THR cc_start: 0.8473 (t) cc_final: 0.8004 (p) REVERT: E 864 GLU cc_start: 0.7726 (tp30) cc_final: 0.7399 (tp30) REVERT: E 869 ASP cc_start: 0.7430 (t0) cc_final: 0.7203 (m-30) REVERT: E 933 CYS cc_start: 0.8357 (m) cc_final: 0.8037 (m) REVERT: E 973 LYS cc_start: 0.8131 (ptmt) cc_final: 0.7641 (ptpp) REVERT: E 991 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6571 (pm20) REVERT: E 1006 SER cc_start: 0.8126 (m) cc_final: 0.7772 (t) REVERT: E 1009 TYR cc_start: 0.6702 (m-80) cc_final: 0.6251 (m-80) REVERT: E 1019 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7335 (tp30) REVERT: E 1022 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7477 (tm-30) REVERT: E 1029 THR cc_start: 0.8429 (m) cc_final: 0.7942 (p) REVERT: F 301 MET cc_start: 0.7508 (ttm) cc_final: 0.7242 (ttp) REVERT: F 312 ASP cc_start: 0.7747 (t70) cc_final: 0.7355 (t0) REVERT: F 338 LYS cc_start: 0.7982 (mtmm) cc_final: 0.7267 (mtmm) REVERT: F 369 GLU cc_start: 0.7530 (tt0) cc_final: 0.6989 (tt0) REVERT: F 370 ILE cc_start: 0.8057 (mm) cc_final: 0.7714 (tp) REVERT: F 371 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7378 (mm) REVERT: F 379 LYS cc_start: 0.7315 (ttmt) cc_final: 0.7095 (ttmt) REVERT: F 563 GLU cc_start: 0.6856 (pp20) cc_final: 0.6504 (tm-30) REVERT: F 607 GLU cc_start: 0.7435 (tp30) cc_final: 0.7086 (tp30) REVERT: F 611 TRP cc_start: 0.7636 (t60) cc_final: 0.6878 (t60) REVERT: F 613 GLU cc_start: 0.7624 (tt0) cc_final: 0.7298 (tt0) REVERT: F 637 MET cc_start: 0.7951 (tpt) cc_final: 0.7563 (tpt) REVERT: F 644 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7326 (mm-40) REVERT: F 645 ARG cc_start: 0.7401 (mtm110) cc_final: 0.7084 (mtm110) REVERT: F 647 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7649 (mtm) REVERT: F 649 TYR cc_start: 0.7522 (m-80) cc_final: 0.7191 (m-80) REVERT: F 652 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8151 (ttmt) REVERT: F 672 ASN cc_start: 0.8035 (p0) cc_final: 0.7703 (p0) REVERT: F 745 GLU cc_start: 0.7518 (tt0) cc_final: 0.7168 (tt0) REVERT: F 758 MET cc_start: 0.7727 (tpt) cc_final: 0.7373 (tpt) REVERT: F 777 LEU cc_start: 0.8217 (mp) cc_final: 0.7929 (mt) REVERT: F 785 GLU cc_start: 0.8164 (pt0) cc_final: 0.7548 (mt-10) REVERT: F 796 SER cc_start: 0.7085 (t) cc_final: 0.6635 (p) REVERT: F 853 THR cc_start: 0.8138 (t) cc_final: 0.7657 (p) REVERT: F 876 CYS cc_start: 0.8412 (m) cc_final: 0.7871 (m) REVERT: F 933 CYS cc_start: 0.8155 (m) cc_final: 0.7932 (m) REVERT: F 973 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7932 (mtmt) REVERT: F 987 MET cc_start: 0.6880 (mmt) cc_final: 0.6480 (mmt) REVERT: F 991 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6631 (pm20) REVERT: F 1006 SER cc_start: 0.8004 (m) cc_final: 0.7722 (t) REVERT: F 1009 TYR cc_start: 0.6591 (m-80) cc_final: 0.6347 (m-80) REVERT: F 1019 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7711 (mm-30) REVERT: F 1022 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7600 (tm-30) REVERT: F 1029 THR cc_start: 0.8331 (m) cc_final: 0.7967 (p) outliers start: 160 outliers final: 107 residues processed: 945 average time/residue: 0.2412 time to fit residues: 372.2212 Evaluate side-chains 959 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 830 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 522 HIS Chi-restraints excluded: chain B residue 526 GLN Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 632 TYR Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 785 GLU Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 840 THR Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 415 CYS Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 644 GLN Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 851 LEU Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain D residue 991 GLU Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 288 HIS Chi-restraints excluded: chain E residue 522 HIS Chi-restraints excluded: chain E residue 573 LEU Chi-restraints excluded: chain E residue 585 ASN Chi-restraints excluded: chain E residue 624 GLN Chi-restraints excluded: chain E residue 637 MET Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 765 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 793 VAL Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 929 ILE Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain E residue 991 GLU Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 522 HIS Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 600 ILE Chi-restraints excluded: chain F residue 647 MET Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 793 VAL Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 825 LEU Chi-restraints excluded: chain F residue 841 SER Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 927 LYS Chi-restraints excluded: chain F residue 929 ILE Chi-restraints excluded: chain F residue 948 LEU Chi-restraints excluded: chain F residue 973 LYS Chi-restraints excluded: chain F residue 991 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 382 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 464 optimal weight: 0.3980 chunk 310 optimal weight: 2.9990 chunk 463 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 355 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 HIS ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN ** D 663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 956 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.177150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.144520 restraints weight = 61810.340| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 3.23 r_work: 0.3662 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 39690 Z= 0.168 Angle : 0.693 14.911 53544 Z= 0.341 Chirality : 0.043 0.233 6078 Planarity : 0.005 0.070 6714 Dihedral : 7.386 142.004 5256 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.64 % Allowed : 21.56 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.12), residues: 4782 helix: 0.26 (0.11), residues: 2226 sheet: -1.90 (0.19), residues: 600 loop : -1.62 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 645 TYR 0.024 0.002 TYR E 168 PHE 0.035 0.002 PHE F 396 TRP 0.012 0.001 TRP D 416 HIS 0.005 0.001 HIS E 916 Details of bonding type rmsd covalent geometry : bond 0.00368 (39690) covalent geometry : angle 0.69301 (53544) hydrogen bonds : bond 0.04248 ( 1520) hydrogen bonds : angle 4.97643 ( 4488) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 867 time to evaluate : 1.506 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: A 143 TYR cc_start: 0.7263 (t80) cc_final: 0.6958 (t80) REVERT: A 172 ARG cc_start: 0.7151 (mtt90) cc_final: 0.6631 (mtt90) REVERT: A 220 HIS cc_start: 0.6999 (m-70) cc_final: 0.6300 (m-70) REVERT: A 239 MET cc_start: 0.7428 (ttp) cc_final: 0.7192 (ttp) REVERT: A 240 MET cc_start: 0.6720 (mtp) cc_final: 0.6356 (mtm) REVERT: A 259 ILE cc_start: 0.7771 (mp) cc_final: 0.7158 (pt) REVERT: A 272 LEU cc_start: 0.8314 (tp) cc_final: 0.8093 (tp) REVERT: A 298 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6617 (pt) REVERT: A 329 ASP cc_start: 0.7881 (m-30) cc_final: 0.7256 (p0) REVERT: A 371 LEU cc_start: 0.7753 (mm) cc_final: 0.7404 (mm) REVERT: A 419 CYS cc_start: 0.7963 (m) cc_final: 0.7734 (m) REVERT: A 442 VAL cc_start: 0.7393 (p) cc_final: 0.7131 (m) REVERT: A 505 MET cc_start: 0.4591 (ppp) cc_final: 0.4296 (ppp) REVERT: A 523 MET cc_start: 0.7686 (mmm) cc_final: 0.7408 (tpp) REVERT: A 569 GLU cc_start: 0.7420 (tp30) cc_final: 0.7213 (tp30) REVERT: A 603 GLN cc_start: 0.7381 (tp40) cc_final: 0.6792 (tm-30) REVERT: A 607 GLU cc_start: 0.7860 (tp30) cc_final: 0.7580 (tp30) REVERT: A 631 PHE cc_start: 0.7952 (m-10) cc_final: 0.7691 (m-80) REVERT: A 649 TYR cc_start: 0.7536 (m-80) cc_final: 0.7241 (m-80) REVERT: A 652 LYS cc_start: 0.8253 (ttmt) cc_final: 0.8022 (ttmm) REVERT: A 654 GLU cc_start: 0.7404 (tp30) cc_final: 0.7019 (tp30) REVERT: A 662 ASP cc_start: 0.7861 (m-30) cc_final: 0.7431 (m-30) REVERT: A 669 CYS cc_start: 0.7606 (m) cc_final: 0.7129 (m) REVERT: A 785 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7507 (pm20) REVERT: A 877 GLU cc_start: 0.7681 (pp20) cc_final: 0.7232 (pp20) REVERT: A 930 LYS cc_start: 0.8187 (mttt) cc_final: 0.7711 (mttt) REVERT: A 973 LYS cc_start: 0.8234 (ptmt) cc_final: 0.7903 (ptmm) REVERT: A 974 LEU cc_start: 0.8095 (tt) cc_final: 0.7879 (tt) REVERT: A 978 ASN cc_start: 0.7199 (p0) cc_final: 0.6946 (p0) REVERT: A 983 ASP cc_start: 0.6745 (OUTLIER) cc_final: 0.6506 (t70) REVERT: A 988 MET cc_start: 0.7466 (mmm) cc_final: 0.6370 (tmm) REVERT: A 991 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6390 (pm20) REVERT: A 1006 SER cc_start: 0.8337 (m) cc_final: 0.8060 (t) REVERT: A 1013 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7462 (tm-30) REVERT: B 145 ARG cc_start: 0.7719 (ttm-80) cc_final: 0.7415 (mtp85) REVERT: B 172 ARG cc_start: 0.6935 (mtt90) cc_final: 0.6514 (mtt90) REVERT: B 259 ILE cc_start: 0.7728 (mp) cc_final: 0.7171 (pt) REVERT: B 367 HIS cc_start: 0.7315 (m-70) cc_final: 0.6774 (m-70) REVERT: B 385 TYR cc_start: 0.8109 (t80) cc_final: 0.7622 (t80) REVERT: B 442 VAL cc_start: 0.7176 (p) cc_final: 0.6902 (m) REVERT: B 480 GLN cc_start: 0.6794 (mp10) cc_final: 0.6475 (mp10) REVERT: B 505 MET cc_start: 0.5235 (ppp) cc_final: 0.4982 (ppp) REVERT: B 523 MET cc_start: 0.7690 (tpt) cc_final: 0.7461 (mmm) REVERT: B 613 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7134 (mm-30) REVERT: B 649 TYR cc_start: 0.7336 (m-80) cc_final: 0.6717 (m-80) REVERT: B 652 LYS cc_start: 0.8351 (ttmt) cc_final: 0.8073 (ttmm) REVERT: B 677 GLU cc_start: 0.7636 (tp30) cc_final: 0.7175 (tp30) REVERT: B 758 MET cc_start: 0.7262 (tpt) cc_final: 0.6957 (tpt) REVERT: B 763 GLU cc_start: 0.8354 (tp30) cc_final: 0.8152 (tm-30) REVERT: B 826 LEU cc_start: 0.7944 (tp) cc_final: 0.7525 (tt) REVERT: B 845 GLN cc_start: 0.7954 (tp-100) cc_final: 0.7636 (tp-100) REVERT: B 864 GLU cc_start: 0.7813 (tp30) cc_final: 0.7553 (tp30) REVERT: B 1009 TYR cc_start: 0.6629 (m-80) cc_final: 0.6400 (m-80) REVERT: B 1013 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7474 (tm-30) REVERT: B 1029 THR cc_start: 0.8421 (m) cc_final: 0.8022 (p) REVERT: C 145 ARG cc_start: 0.7852 (ttp-110) cc_final: 0.7640 (ttm110) REVERT: C 172 ARG cc_start: 0.7241 (mtt90) cc_final: 0.6913 (mtp85) REVERT: C 259 ILE cc_start: 0.7799 (mp) cc_final: 0.7245 (pt) REVERT: C 262 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7758 (ttm-80) REVERT: C 298 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6650 (pt) REVERT: C 367 HIS cc_start: 0.7409 (m-70) cc_final: 0.6863 (m-70) REVERT: C 371 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7526 (mm) REVERT: C 400 GLN cc_start: 0.7534 (tt0) cc_final: 0.7278 (tt0) REVERT: C 409 CYS cc_start: 0.7917 (m) cc_final: 0.7323 (t) REVERT: C 419 CYS cc_start: 0.8302 (m) cc_final: 0.7890 (m) REVERT: C 442 VAL cc_start: 0.7776 (p) cc_final: 0.7503 (m) REVERT: C 477 ILE cc_start: 0.7550 (pt) cc_final: 0.7177 (tp) REVERT: C 523 MET cc_start: 0.8094 (mmm) cc_final: 0.7810 (tpp) REVERT: C 585 ASN cc_start: 0.7689 (t0) cc_final: 0.7447 (t0) REVERT: C 607 GLU cc_start: 0.7764 (tp30) cc_final: 0.7534 (tp30) REVERT: C 613 GLU cc_start: 0.7850 (tt0) cc_final: 0.7507 (mt-10) REVERT: C 637 MET cc_start: 0.7498 (tpt) cc_final: 0.7151 (tpt) REVERT: C 641 ASP cc_start: 0.7597 (p0) cc_final: 0.7187 (t0) REVERT: C 774 ARG cc_start: 0.8058 (mtm110) cc_final: 0.7699 (mtm110) REVERT: C 785 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7860 (pt0) REVERT: C 864 GLU cc_start: 0.7519 (tp30) cc_final: 0.7292 (tp30) REVERT: C 880 LYS cc_start: 0.8053 (ptmt) cc_final: 0.7745 (ptmm) REVERT: C 912 GLN cc_start: 0.7739 (tt0) cc_final: 0.7502 (tt0) REVERT: C 933 CYS cc_start: 0.8247 (p) cc_final: 0.7920 (p) REVERT: C 1006 SER cc_start: 0.8224 (m) cc_final: 0.7831 (t) REVERT: C 1009 TYR cc_start: 0.6972 (m-80) cc_final: 0.6663 (m-80) REVERT: D 142 LYS cc_start: 0.7249 (tttm) cc_final: 0.6984 (tmtt) REVERT: D 164 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7192 (tt) REVERT: D 234 ILE cc_start: 0.6085 (OUTLIER) cc_final: 0.5733 (pt) REVERT: D 238 LYS cc_start: 0.7650 (tptt) cc_final: 0.7330 (tptp) REVERT: D 250 GLN cc_start: 0.7066 (tp40) cc_final: 0.6629 (tp40) REVERT: D 312 ASP cc_start: 0.7979 (t70) cc_final: 0.7388 (t0) REVERT: D 369 GLU cc_start: 0.7547 (tt0) cc_final: 0.7192 (tt0) REVERT: D 400 GLN cc_start: 0.7740 (tt0) cc_final: 0.7431 (tt0) REVERT: D 426 MET cc_start: 0.7066 (tpt) cc_final: 0.6832 (tpp) REVERT: D 524 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8249 (m) REVERT: D 611 TRP cc_start: 0.7732 (t60) cc_final: 0.7114 (t60) REVERT: D 614 VAL cc_start: 0.8516 (t) cc_final: 0.8304 (p) REVERT: D 640 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6987 (mm-30) REVERT: D 669 CYS cc_start: 0.7825 (m) cc_final: 0.7388 (p) REVERT: D 792 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8011 (mt) REVERT: D 853 THR cc_start: 0.8402 (t) cc_final: 0.7932 (p) REVERT: D 877 GLU cc_start: 0.7595 (pp20) cc_final: 0.7260 (pp20) REVERT: D 938 HIS cc_start: 0.7292 (t-90) cc_final: 0.6884 (t-170) REVERT: D 970 SER cc_start: 0.7243 (t) cc_final: 0.6786 (p) REVERT: D 973 LYS cc_start: 0.8150 (ptmt) cc_final: 0.7623 (ptpp) REVERT: D 983 ASP cc_start: 0.6175 (t0) cc_final: 0.5412 (t0) REVERT: D 987 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.6115 (mmm) REVERT: D 988 MET cc_start: 0.7218 (mmm) cc_final: 0.6836 (mmm) REVERT: D 991 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6303 (pm20) REVERT: D 1006 SER cc_start: 0.8027 (m) cc_final: 0.7676 (t) REVERT: D 1022 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7706 (tm-30) REVERT: D 1023 GLU cc_start: 0.6368 (mp0) cc_final: 0.5625 (mp0) REVERT: D 1029 THR cc_start: 0.8355 (m) cc_final: 0.7814 (p) REVERT: E 145 ARG cc_start: 0.7722 (ttp-110) cc_final: 0.7365 (ttm110) REVERT: E 172 ARG cc_start: 0.7352 (mtt90) cc_final: 0.6890 (mtt90) REVERT: E 175 LYS cc_start: 0.8170 (tttt) cc_final: 0.7883 (tttt) REVERT: E 269 GLN cc_start: 0.5337 (mp10) cc_final: 0.4861 (mp10) REVERT: E 277 MET cc_start: 0.6594 (ptm) cc_final: 0.6252 (ptm) REVERT: E 338 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7682 (mtpt) REVERT: E 367 HIS cc_start: 0.7349 (m-70) cc_final: 0.6971 (m90) REVERT: E 375 GLU cc_start: 0.7799 (tt0) cc_final: 0.7398 (tt0) REVERT: E 404 VAL cc_start: 0.8029 (t) cc_final: 0.7579 (p) REVERT: E 409 CYS cc_start: 0.8161 (m) cc_final: 0.7411 (t) REVERT: E 415 CYS cc_start: 0.7151 (m) cc_final: 0.6061 (m) REVERT: E 419 CYS cc_start: 0.7885 (m) cc_final: 0.7533 (m) REVERT: E 585 ASN cc_start: 0.7538 (t0) cc_final: 0.7282 (t0) REVERT: E 603 GLN cc_start: 0.7184 (tp40) cc_final: 0.6399 (tm-30) REVERT: E 648 ASP cc_start: 0.8027 (m-30) cc_final: 0.7685 (t0) REVERT: E 663 HIS cc_start: 0.7786 (m90) cc_final: 0.7499 (m-70) REVERT: E 731 ARG cc_start: 0.7308 (ttm170) cc_final: 0.6746 (ttm110) REVERT: E 745 GLU cc_start: 0.7457 (tt0) cc_final: 0.7183 (tt0) REVERT: E 777 LEU cc_start: 0.8302 (mp) cc_final: 0.7831 (mm) REVERT: E 785 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7851 (pt0) REVERT: E 853 THR cc_start: 0.8498 (t) cc_final: 0.8042 (p) REVERT: E 864 GLU cc_start: 0.7737 (tp30) cc_final: 0.7440 (tp30) REVERT: E 869 ASP cc_start: 0.7427 (t0) cc_final: 0.7195 (m-30) REVERT: E 933 CYS cc_start: 0.8366 (m) cc_final: 0.8056 (m) REVERT: E 973 LYS cc_start: 0.8159 (ptmt) cc_final: 0.7578 (ptpp) REVERT: E 991 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6606 (pm20) REVERT: E 1006 SER cc_start: 0.8124 (m) cc_final: 0.7777 (t) REVERT: E 1009 TYR cc_start: 0.6670 (m-80) cc_final: 0.6232 (m-80) REVERT: E 1019 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7287 (tp30) REVERT: E 1022 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7414 (tm-30) REVERT: E 1023 GLU cc_start: 0.6737 (pm20) cc_final: 0.6400 (pm20) REVERT: E 1029 THR cc_start: 0.8403 (m) cc_final: 0.7886 (p) REVERT: F 269 GLN cc_start: 0.5153 (mp10) cc_final: 0.4703 (mp10) REVERT: F 301 MET cc_start: 0.7509 (ttm) cc_final: 0.7119 (ttt) REVERT: F 312 ASP cc_start: 0.7792 (t70) cc_final: 0.7426 (t0) REVERT: F 367 HIS cc_start: 0.7447 (m-70) cc_final: 0.7200 (m90) REVERT: F 369 GLU cc_start: 0.7521 (tt0) cc_final: 0.6958 (tt0) REVERT: F 370 ILE cc_start: 0.8049 (mm) cc_final: 0.7693 (tp) REVERT: F 371 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7361 (mm) REVERT: F 379 LYS cc_start: 0.7384 (ttmt) cc_final: 0.7168 (ttmt) REVERT: F 563 GLU cc_start: 0.6934 (pp20) cc_final: 0.6586 (tm-30) REVERT: F 607 GLU cc_start: 0.7490 (tp30) cc_final: 0.7153 (tp30) REVERT: F 611 TRP cc_start: 0.7643 (t60) cc_final: 0.6869 (t60) REVERT: F 613 GLU cc_start: 0.7651 (tt0) cc_final: 0.7305 (tt0) REVERT: F 637 MET cc_start: 0.7945 (tpt) cc_final: 0.7558 (tpt) REVERT: F 641 ASP cc_start: 0.7271 (t0) cc_final: 0.7004 (t0) REVERT: F 644 GLN cc_start: 0.7713 (mm-40) cc_final: 0.6900 (mm-40) REVERT: F 645 ARG cc_start: 0.7403 (mtm110) cc_final: 0.7083 (mtm110) REVERT: F 647 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7681 (mtp) REVERT: F 649 TYR cc_start: 0.7529 (m-80) cc_final: 0.7184 (m-80) REVERT: F 652 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8167 (ttmt) REVERT: F 672 ASN cc_start: 0.8001 (p0) cc_final: 0.7275 (t0) REVERT: F 745 GLU cc_start: 0.7528 (tt0) cc_final: 0.7151 (tt0) REVERT: F 758 MET cc_start: 0.7728 (tpt) cc_final: 0.7397 (tpt) REVERT: F 785 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7583 (mt-10) REVERT: F 796 SER cc_start: 0.7139 (t) cc_final: 0.6675 (p) REVERT: F 853 THR cc_start: 0.8129 (t) cc_final: 0.7654 (p) REVERT: F 876 CYS cc_start: 0.8439 (m) cc_final: 0.7983 (m) REVERT: F 933 CYS cc_start: 0.8176 (m) cc_final: 0.7938 (m) REVERT: F 973 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7911 (mtmt) REVERT: F 987 MET cc_start: 0.7154 (mmt) cc_final: 0.6688 (mmt) REVERT: F 988 MET cc_start: 0.7321 (mmm) cc_final: 0.6793 (mmm) REVERT: F 991 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6697 (pm20) REVERT: F 1006 SER cc_start: 0.7975 (m) cc_final: 0.7718 (t) REVERT: F 1009 TYR cc_start: 0.6656 (m-80) cc_final: 0.6405 (m-80) REVERT: F 1019 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7714 (mm-30) REVERT: F 1022 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7589 (tm-30) REVERT: F 1029 THR cc_start: 0.8317 (m) cc_final: 0.7941 (p) outliers start: 160 outliers final: 107 residues processed: 956 average time/residue: 0.2382 time to fit residues: 373.0854 Evaluate side-chains 981 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 853 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 522 HIS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 632 TYR Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 632 TYR Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 785 GLU Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 840 THR Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 865 ASN Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 623 ILE Chi-restraints excluded: chain D residue 644 GLN Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain D residue 991 GLU Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 240 MET Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 288 HIS Chi-restraints excluded: chain E residue 522 HIS Chi-restraints excluded: chain E residue 573 LEU Chi-restraints excluded: chain E residue 624 GLN Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 765 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 793 VAL Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 929 ILE Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain E residue 991 GLU Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 522 HIS Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 600 ILE Chi-restraints excluded: chain F residue 647 MET Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 785 GLU Chi-restraints excluded: chain F residue 793 VAL Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 825 LEU Chi-restraints excluded: chain F residue 841 SER Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 927 LYS Chi-restraints excluded: chain F residue 929 ILE Chi-restraints excluded: chain F residue 948 LEU Chi-restraints excluded: chain F residue 973 LYS Chi-restraints excluded: chain F residue 991 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 76 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 378 optimal weight: 0.9990 chunk 310 optimal weight: 2.9990 chunk 351 optimal weight: 3.9990 chunk 406 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 133 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN ** A 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 HIS ** C 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN ** D 663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 956 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.177303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.144734 restraints weight = 61322.631| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 3.23 r_work: 0.3664 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39690 Z= 0.157 Angle : 0.697 14.215 53544 Z= 0.343 Chirality : 0.043 0.294 6078 Planarity : 0.005 0.077 6714 Dihedral : 7.365 141.901 5256 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.37 % Allowed : 21.83 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.12), residues: 4782 helix: 0.27 (0.11), residues: 2226 sheet: -1.95 (0.19), residues: 600 loop : -1.61 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 645 TYR 0.033 0.002 TYR E 143 PHE 0.029 0.001 PHE E 528 TRP 0.012 0.001 TRP A 243 HIS 0.005 0.001 HIS E 916 Details of bonding type rmsd covalent geometry : bond 0.00349 (39690) covalent geometry : angle 0.69725 (53544) hydrogen bonds : bond 0.04165 ( 1520) hydrogen bonds : angle 4.95632 ( 4488) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 856 time to evaluate : 1.463 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 143 TYR cc_start: 0.7235 (t80) cc_final: 0.6998 (t80) REVERT: A 147 ARG cc_start: 0.7483 (tmt170) cc_final: 0.7263 (tmt170) REVERT: A 172 ARG cc_start: 0.7089 (mtt90) cc_final: 0.6550 (mtt90) REVERT: A 220 HIS cc_start: 0.7000 (m-70) cc_final: 0.6297 (m-70) REVERT: A 239 MET cc_start: 0.7435 (ttp) cc_final: 0.7195 (ttp) REVERT: A 259 ILE cc_start: 0.7740 (mp) cc_final: 0.7137 (pt) REVERT: A 272 LEU cc_start: 0.8378 (tp) cc_final: 0.8159 (tp) REVERT: A 298 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6650 (pt) REVERT: A 371 LEU cc_start: 0.7691 (mm) cc_final: 0.7341 (mm) REVERT: A 419 CYS cc_start: 0.7914 (m) cc_final: 0.7688 (m) REVERT: A 442 VAL cc_start: 0.7404 (p) cc_final: 0.7153 (m) REVERT: A 505 MET cc_start: 0.4262 (ppp) cc_final: 0.3879 (ppp) REVERT: A 523 MET cc_start: 0.7714 (mmm) cc_final: 0.7434 (tpp) REVERT: A 603 GLN cc_start: 0.7381 (tp40) cc_final: 0.6767 (tm-30) REVERT: A 607 GLU cc_start: 0.7869 (tp30) cc_final: 0.7599 (tp30) REVERT: A 631 PHE cc_start: 0.7912 (m-10) cc_final: 0.7696 (m-80) REVERT: A 649 TYR cc_start: 0.7518 (m-80) cc_final: 0.7249 (m-80) REVERT: A 652 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7878 (ttmm) REVERT: A 662 ASP cc_start: 0.7851 (m-30) cc_final: 0.7441 (m-30) REVERT: A 669 CYS cc_start: 0.7592 (m) cc_final: 0.7127 (m) REVERT: A 671 GLU cc_start: 0.8130 (pp20) cc_final: 0.7717 (tm-30) REVERT: A 785 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7518 (pm20) REVERT: A 877 GLU cc_start: 0.7669 (pp20) cc_final: 0.7237 (pp20) REVERT: A 930 LYS cc_start: 0.8202 (mttt) cc_final: 0.7730 (mttt) REVERT: A 973 LYS cc_start: 0.8231 (ptmt) cc_final: 0.7906 (ptmm) REVERT: A 974 LEU cc_start: 0.8093 (tt) cc_final: 0.7879 (tt) REVERT: A 978 ASN cc_start: 0.7180 (p0) cc_final: 0.6906 (p0) REVERT: A 983 ASP cc_start: 0.6758 (OUTLIER) cc_final: 0.6547 (t70) REVERT: A 988 MET cc_start: 0.7415 (mmm) cc_final: 0.6308 (tmm) REVERT: A 991 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6376 (pm20) REVERT: A 1006 SER cc_start: 0.8327 (m) cc_final: 0.8056 (t) REVERT: A 1013 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7453 (tm-30) REVERT: B 145 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7444 (mtp85) REVERT: B 172 ARG cc_start: 0.6857 (mtt90) cc_final: 0.6433 (mtt90) REVERT: B 259 ILE cc_start: 0.7746 (mp) cc_final: 0.7179 (pt) REVERT: B 269 GLN cc_start: 0.6618 (mt0) cc_final: 0.6192 (mt0) REVERT: B 306 GLU cc_start: 0.6953 (mm-30) cc_final: 0.5601 (mm-30) REVERT: B 367 HIS cc_start: 0.7325 (m-70) cc_final: 0.6795 (m-70) REVERT: B 385 TYR cc_start: 0.8103 (t80) cc_final: 0.7644 (t80) REVERT: B 442 VAL cc_start: 0.7194 (p) cc_final: 0.6927 (m) REVERT: B 480 GLN cc_start: 0.6731 (mp10) cc_final: 0.6408 (mp10) REVERT: B 505 MET cc_start: 0.5249 (ppp) cc_final: 0.4954 (ppp) REVERT: B 523 MET cc_start: 0.7704 (tpt) cc_final: 0.7339 (tpt) REVERT: B 532 MET cc_start: 0.8201 (mmm) cc_final: 0.7956 (tpp) REVERT: B 613 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7126 (mm-30) REVERT: B 649 TYR cc_start: 0.7327 (m-80) cc_final: 0.6803 (m-80) REVERT: B 652 LYS cc_start: 0.8372 (ttmt) cc_final: 0.8091 (ttmm) REVERT: B 677 GLU cc_start: 0.7596 (tp30) cc_final: 0.7134 (tp30) REVERT: B 758 MET cc_start: 0.7239 (tpt) cc_final: 0.6915 (tpt) REVERT: B 845 GLN cc_start: 0.7908 (tp-100) cc_final: 0.7581 (tp-100) REVERT: B 864 GLU cc_start: 0.7829 (tp30) cc_final: 0.7562 (tp30) REVERT: B 1008 MET cc_start: 0.6636 (ttm) cc_final: 0.6350 (ttt) REVERT: B 1009 TYR cc_start: 0.6546 (m-80) cc_final: 0.6324 (m-80) REVERT: B 1013 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7463 (tm-30) REVERT: B 1029 THR cc_start: 0.8433 (m) cc_final: 0.8046 (p) REVERT: C 145 ARG cc_start: 0.7878 (ttp-110) cc_final: 0.7651 (ttm110) REVERT: C 172 ARG cc_start: 0.7218 (mtt90) cc_final: 0.6890 (mtp85) REVERT: C 259 ILE cc_start: 0.7803 (mp) cc_final: 0.7250 (pt) REVERT: C 262 ARG cc_start: 0.8186 (ttm-80) cc_final: 0.7764 (ttm-80) REVERT: C 298 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6669 (pt) REVERT: C 301 MET cc_start: 0.7770 (ttm) cc_final: 0.7126 (ttp) REVERT: C 367 HIS cc_start: 0.7460 (m-70) cc_final: 0.6911 (m-70) REVERT: C 371 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7535 (mm) REVERT: C 400 GLN cc_start: 0.7497 (tt0) cc_final: 0.7231 (tt0) REVERT: C 409 CYS cc_start: 0.7927 (m) cc_final: 0.7120 (t) REVERT: C 415 CYS cc_start: 0.7115 (m) cc_final: 0.5726 (m) REVERT: C 419 CYS cc_start: 0.8297 (m) cc_final: 0.7882 (m) REVERT: C 442 VAL cc_start: 0.7767 (p) cc_final: 0.7504 (m) REVERT: C 477 ILE cc_start: 0.7545 (pt) cc_final: 0.7179 (tp) REVERT: C 523 MET cc_start: 0.8079 (mmm) cc_final: 0.7796 (tpp) REVERT: C 607 GLU cc_start: 0.7752 (tp30) cc_final: 0.7527 (tp30) REVERT: C 613 GLU cc_start: 0.7855 (tt0) cc_final: 0.7516 (mt-10) REVERT: C 637 MET cc_start: 0.7488 (tpt) cc_final: 0.7226 (tpt) REVERT: C 641 ASP cc_start: 0.7512 (p0) cc_final: 0.7054 (t0) REVERT: C 774 ARG cc_start: 0.8051 (mtm110) cc_final: 0.7701 (mtm110) REVERT: C 785 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7871 (pt0) REVERT: C 864 GLU cc_start: 0.7524 (tp30) cc_final: 0.7291 (tp30) REVERT: C 880 LYS cc_start: 0.8086 (ptmt) cc_final: 0.7786 (ptmm) REVERT: C 912 GLN cc_start: 0.7736 (tt0) cc_final: 0.7504 (tt0) REVERT: C 933 CYS cc_start: 0.8242 (p) cc_final: 0.7897 (p) REVERT: C 1006 SER cc_start: 0.8222 (m) cc_final: 0.7839 (t) REVERT: C 1008 MET cc_start: 0.7128 (ttt) cc_final: 0.6889 (ttt) REVERT: C 1009 TYR cc_start: 0.6962 (m-80) cc_final: 0.6656 (m-80) REVERT: D 142 LYS cc_start: 0.7254 (tttm) cc_final: 0.7000 (tmtt) REVERT: D 164 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7197 (tt) REVERT: D 234 ILE cc_start: 0.6054 (OUTLIER) cc_final: 0.5594 (tt) REVERT: D 238 LYS cc_start: 0.7648 (tptt) cc_final: 0.7335 (tptp) REVERT: D 250 GLN cc_start: 0.7058 (tp40) cc_final: 0.6631 (tp40) REVERT: D 312 ASP cc_start: 0.8071 (t70) cc_final: 0.7656 (t70) REVERT: D 369 GLU cc_start: 0.7518 (tt0) cc_final: 0.7092 (tt0) REVERT: D 370 ILE cc_start: 0.7860 (mm) cc_final: 0.7455 (tp) REVERT: D 400 GLN cc_start: 0.7749 (tt0) cc_final: 0.7434 (tt0) REVERT: D 417 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7965 (mm) REVERT: D 426 MET cc_start: 0.7065 (tpt) cc_final: 0.6845 (tpp) REVERT: D 524 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8258 (m) REVERT: D 611 TRP cc_start: 0.7742 (t60) cc_final: 0.7119 (t60) REVERT: D 613 GLU cc_start: 0.7719 (tt0) cc_final: 0.7279 (tt0) REVERT: D 640 GLU cc_start: 0.7238 (mm-30) cc_final: 0.7004 (mm-30) REVERT: D 645 ARG cc_start: 0.7918 (mmm160) cc_final: 0.7239 (tpt90) REVERT: D 792 LEU cc_start: 0.8254 (mm) cc_final: 0.8001 (mt) REVERT: D 853 THR cc_start: 0.8420 (t) cc_final: 0.7958 (p) REVERT: D 877 GLU cc_start: 0.7538 (pp20) cc_final: 0.7206 (pp20) REVERT: D 938 HIS cc_start: 0.7286 (t-90) cc_final: 0.6854 (t-170) REVERT: D 970 SER cc_start: 0.7260 (t) cc_final: 0.6804 (p) REVERT: D 973 LYS cc_start: 0.8152 (ptmt) cc_final: 0.7658 (ptpp) REVERT: D 983 ASP cc_start: 0.6230 (t0) cc_final: 0.5389 (t0) REVERT: D 987 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.6095 (mmm) REVERT: D 988 MET cc_start: 0.7237 (mmm) cc_final: 0.6843 (mmm) REVERT: D 991 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6315 (pm20) REVERT: D 1006 SER cc_start: 0.8013 (m) cc_final: 0.7680 (t) REVERT: D 1022 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7694 (tm-30) REVERT: D 1029 THR cc_start: 0.8384 (m) cc_final: 0.7847 (p) REVERT: E 145 ARG cc_start: 0.7781 (ttp-110) cc_final: 0.7421 (ttm110) REVERT: E 172 ARG cc_start: 0.7355 (mtt90) cc_final: 0.6924 (mtt90) REVERT: E 175 LYS cc_start: 0.8157 (tttt) cc_final: 0.7869 (tttt) REVERT: E 269 GLN cc_start: 0.5326 (mp10) cc_final: 0.4874 (mp10) REVERT: E 277 MET cc_start: 0.6578 (ptm) cc_final: 0.6255 (ptm) REVERT: E 338 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7666 (mtpt) REVERT: E 367 HIS cc_start: 0.7337 (m-70) cc_final: 0.6971 (m-70) REVERT: E 375 GLU cc_start: 0.7824 (tt0) cc_final: 0.7407 (tt0) REVERT: E 404 VAL cc_start: 0.8039 (t) cc_final: 0.7598 (p) REVERT: E 409 CYS cc_start: 0.8137 (m) cc_final: 0.7346 (t) REVERT: E 415 CYS cc_start: 0.7111 (m) cc_final: 0.5988 (m) REVERT: E 419 CYS cc_start: 0.7879 (m) cc_final: 0.7511 (m) REVERT: E 585 ASN cc_start: 0.7559 (t0) cc_final: 0.7273 (t0) REVERT: E 603 GLN cc_start: 0.7111 (tp40) cc_final: 0.6322 (tm-30) REVERT: E 648 ASP cc_start: 0.8007 (m-30) cc_final: 0.7663 (t0) REVERT: E 663 HIS cc_start: 0.7791 (m90) cc_final: 0.7499 (m-70) REVERT: E 731 ARG cc_start: 0.7317 (ttm170) cc_final: 0.6755 (ttm110) REVERT: E 745 GLU cc_start: 0.7433 (tt0) cc_final: 0.7179 (tt0) REVERT: E 777 LEU cc_start: 0.8295 (mp) cc_final: 0.7849 (mm) REVERT: E 785 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7821 (pt0) REVERT: E 853 THR cc_start: 0.8444 (t) cc_final: 0.8022 (p) REVERT: E 864 GLU cc_start: 0.7802 (tp30) cc_final: 0.7485 (tp30) REVERT: E 869 ASP cc_start: 0.7420 (t0) cc_final: 0.7197 (m-30) REVERT: E 933 CYS cc_start: 0.8377 (m) cc_final: 0.8071 (m) REVERT: E 973 LYS cc_start: 0.8156 (ptmt) cc_final: 0.7666 (ptpp) REVERT: E 991 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6719 (pm20) REVERT: E 1006 SER cc_start: 0.8107 (m) cc_final: 0.7752 (t) REVERT: E 1009 TYR cc_start: 0.6652 (m-80) cc_final: 0.6221 (m-80) REVERT: E 1019 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7312 (tp30) REVERT: E 1022 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7426 (tm-30) REVERT: E 1023 GLU cc_start: 0.6702 (pm20) cc_final: 0.6385 (pm20) REVERT: E 1029 THR cc_start: 0.8401 (m) cc_final: 0.7867 (p) REVERT: F 269 GLN cc_start: 0.5155 (mp10) cc_final: 0.4684 (mp10) REVERT: F 301 MET cc_start: 0.7533 (ttm) cc_final: 0.7165 (ttt) REVERT: F 312 ASP cc_start: 0.7823 (t70) cc_final: 0.7480 (t0) REVERT: F 338 LYS cc_start: 0.7906 (mtmm) cc_final: 0.7612 (mtpp) REVERT: F 367 HIS cc_start: 0.7421 (m-70) cc_final: 0.7186 (m90) REVERT: F 369 GLU cc_start: 0.7513 (tt0) cc_final: 0.7076 (tt0) REVERT: F 371 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7301 (mm) REVERT: F 379 LYS cc_start: 0.7410 (ttmt) cc_final: 0.7168 (ttmt) REVERT: F 426 MET cc_start: 0.7425 (tpt) cc_final: 0.7218 (tpt) REVERT: F 607 GLU cc_start: 0.7460 (tp30) cc_final: 0.7124 (tp30) REVERT: F 611 TRP cc_start: 0.7648 (t60) cc_final: 0.6857 (t60) REVERT: F 613 GLU cc_start: 0.7646 (tt0) cc_final: 0.7307 (tt0) REVERT: F 637 MET cc_start: 0.7928 (tpt) cc_final: 0.7546 (tpt) REVERT: F 641 ASP cc_start: 0.7252 (t0) cc_final: 0.6973 (t0) REVERT: F 644 GLN cc_start: 0.7734 (mm-40) cc_final: 0.6939 (mm-40) REVERT: F 645 ARG cc_start: 0.7391 (mtm110) cc_final: 0.7059 (mtm110) REVERT: F 647 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7716 (mtm) REVERT: F 649 TYR cc_start: 0.7505 (m-80) cc_final: 0.7169 (m-80) REVERT: F 652 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8154 (ttmt) REVERT: F 672 ASN cc_start: 0.7978 (p0) cc_final: 0.7365 (t0) REVERT: F 745 GLU cc_start: 0.7517 (tt0) cc_final: 0.7153 (tt0) REVERT: F 758 MET cc_start: 0.7681 (tpt) cc_final: 0.7323 (tpt) REVERT: F 785 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: F 853 THR cc_start: 0.8094 (t) cc_final: 0.7625 (p) REVERT: F 876 CYS cc_start: 0.8415 (m) cc_final: 0.7774 (m) REVERT: F 933 CYS cc_start: 0.8158 (m) cc_final: 0.7897 (m) REVERT: F 973 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7898 (mtmt) REVERT: F 987 MET cc_start: 0.7131 (mmt) cc_final: 0.6710 (mmt) REVERT: F 988 MET cc_start: 0.7284 (mmm) cc_final: 0.6758 (mmm) REVERT: F 991 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6670 (pm20) REVERT: F 1006 SER cc_start: 0.7968 (m) cc_final: 0.7722 (t) REVERT: F 1009 TYR cc_start: 0.6675 (m-80) cc_final: 0.6420 (m-80) REVERT: F 1019 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7709 (mm-30) REVERT: F 1022 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7581 (tm-30) REVERT: F 1029 THR cc_start: 0.8301 (m) cc_final: 0.7921 (p) outliers start: 148 outliers final: 107 residues processed: 935 average time/residue: 0.2427 time to fit residues: 370.3999 Evaluate side-chains 975 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 847 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 522 HIS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 632 TYR Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 632 TYR Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 785 GLU Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 840 THR Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 865 ASN Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 623 ILE Chi-restraints excluded: chain D residue 644 GLN Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 849 SER Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain D residue 991 GLU Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 288 HIS Chi-restraints excluded: chain E residue 379 LYS Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 522 HIS Chi-restraints excluded: chain E residue 523 MET Chi-restraints excluded: chain E residue 573 LEU Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 765 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 793 VAL Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 929 ILE Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain E residue 991 GLU Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain F residue 522 HIS Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 600 ILE Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 647 MET Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 785 GLU Chi-restraints excluded: chain F residue 793 VAL Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 825 LEU Chi-restraints excluded: chain F residue 841 SER Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain F residue 929 ILE Chi-restraints excluded: chain F residue 948 LEU Chi-restraints excluded: chain F residue 973 LYS Chi-restraints excluded: chain F residue 991 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 452 optimal weight: 0.4980 chunk 234 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 373 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 449 optimal weight: 2.9990 chunk 345 optimal weight: 0.9990 chunk 368 optimal weight: 4.9990 chunk 221 optimal weight: 0.1980 chunk 469 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 644 GLN B 165 ASN B 526 GLN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 ASN ** C 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN ** D 663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 956 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.179283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.146885 restraints weight = 61502.363| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 3.26 r_work: 0.3683 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39690 Z= 0.126 Angle : 0.679 12.615 53544 Z= 0.330 Chirality : 0.042 0.286 6078 Planarity : 0.005 0.068 6714 Dihedral : 7.240 140.708 5256 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.16 % Allowed : 22.12 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.12), residues: 4782 helix: 0.40 (0.11), residues: 2226 sheet: -2.04 (0.18), residues: 642 loop : -1.44 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 645 TYR 0.030 0.001 TYR B 168 PHE 0.027 0.001 PHE F 396 TRP 0.014 0.001 TRP A 243 HIS 0.005 0.001 HIS E 916 Details of bonding type rmsd covalent geometry : bond 0.00281 (39690) covalent geometry : angle 0.67861 (53544) hydrogen bonds : bond 0.03708 ( 1520) hydrogen bonds : angle 4.83955 ( 4488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10266.20 seconds wall clock time: 177 minutes 2.92 seconds (10622.92 seconds total)