Starting phenix.real_space_refine on Sat Dec 28 14:01:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8swf_40811/12_2024/8swf_40811_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8swf_40811/12_2024/8swf_40811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8swf_40811/12_2024/8swf_40811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8swf_40811/12_2024/8swf_40811.map" model { file = "/net/cci-nas-00/data/ceres_data/8swf_40811/12_2024/8swf_40811_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8swf_40811/12_2024/8swf_40811_neut.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.013 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 456 5.16 5 C 33912 2.51 5 N 9048 2.21 5 O 9828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 238 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 53244 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6667 Classifications: {'peptide': 836} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 810} Chain breaks: 7 Chain: "B" Number of atoms: 6667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6667 Classifications: {'peptide': 836} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 810} Chain breaks: 7 Chain: "C" Number of atoms: 6644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6644 Classifications: {'peptide': 833} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 807} Chain breaks: 7 Chain: "D" Number of atoms: 6667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6667 Classifications: {'peptide': 836} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 810} Chain breaks: 7 Chain: "E" Number of atoms: 6644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6644 Classifications: {'peptide': 833} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 807} Chain breaks: 7 Chain: "F" Number of atoms: 6644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6644 Classifications: {'peptide': 833} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 807} Chain breaks: 7 Chain: "G" Number of atoms: 6667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6667 Classifications: {'peptide': 836} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 810} Chain breaks: 7 Chain: "H" Number of atoms: 6644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6644 Classifications: {'peptide': 833} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 807} Chain breaks: 7 Time building chain proxies: 22.41, per 1000 atoms: 0.42 Number of scatterers: 53244 At special positions: 0 Unit cell: (166.46, 191.06, 189.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 456 16.00 O 9828 8.00 N 9048 7.00 C 33912 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: 9.61 Conformation dependent library (CDL) restraints added in 5.0 seconds 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12648 Finding SS restraints... Secondary structure from input PDB file: 332 helices and 32 sheets defined 50.0% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.07 Creating SS restraints... Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.799A pdb=" N LYS A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.611A pdb=" N LEU A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 328 through 337 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 374 through 386 Processing helix chain 'A' and resid 388 through 401 removed outlier: 3.623A pdb=" N GLU A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 411 through 428 Processing helix chain 'A' and resid 439 through 452 Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.574A pdb=" N LEU A 469 " --> pdb=" O HIS A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 496 through 505 Processing helix chain 'A' and resid 522 through 534 removed outlier: 3.974A pdb=" N TYR A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 544 removed outlier: 3.870A pdb=" N ARG A 543 " --> pdb=" O LYS A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 564 Processing helix chain 'A' and resid 567 through 571 Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 597 through 618 Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.925A pdb=" N ARG A 645 " --> pdb=" O ASP A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 659 through 672 Processing helix chain 'A' and resid 727 through 729 No H-bonds generated for 'chain 'A' and resid 727 through 729' Processing helix chain 'A' and resid 730 through 738 removed outlier: 4.102A pdb=" N VAL A 736 " --> pdb=" O GLY A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 765 removed outlier: 4.129A pdb=" N VAL A 760 " --> pdb=" O PRO A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 795 removed outlier: 4.216A pdb=" N ASP A 789 " --> pdb=" O GLU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 823 removed outlier: 3.875A pdb=" N VAL A 820 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 842 No H-bonds generated for 'chain 'A' and resid 840 through 842' Processing helix chain 'A' and resid 843 through 854 removed outlier: 3.774A pdb=" N SER A 849 " --> pdb=" O GLN A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 880 removed outlier: 3.819A pdb=" N ILE A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 878 " --> pdb=" O ILE A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 899 No H-bonds generated for 'chain 'A' and resid 897 through 899' Processing helix chain 'A' and resid 900 through 911 Processing helix chain 'A' and resid 924 through 937 removed outlier: 3.727A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (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: 3.652A pdb=" N THR A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.640A pdb=" N MET A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE A 989 " --> pdb=" O GLY A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1025 Processing helix chain 'B' and resid 135 through 148 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.557A pdb=" N LEU B 235 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 328 through 337 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 358 through 362 Processing helix chain 'B' and resid 374 through 386 Processing helix chain 'B' and resid 388 through 401 Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 411 through 428 Processing helix chain 'B' and resid 439 through 452 Processing helix chain 'B' and resid 462 through 464 No H-bonds generated for 'chain 'B' and resid 462 through 464' Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.573A pdb=" N LEU B 469 " --> pdb=" O HIS B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 492 Processing helix chain 'B' and resid 496 through 505 Processing helix chain 'B' and resid 522 through 536 removed outlier: 4.066A pdb=" N TYR B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 544 removed outlier: 3.872A pdb=" N ARG B 543 " --> pdb=" O LYS B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 564 Processing helix chain 'B' and resid 567 through 571 Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 597 through 618 Processing helix chain 'B' and resid 627 through 637 Processing helix chain 'B' and resid 639 through 647 removed outlier: 3.916A pdb=" N ARG B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 650 No H-bonds generated for 'chain 'B' and resid 648 through 650' Processing helix chain 'B' and resid 659 through 672 Processing helix chain 'B' and resid 727 through 729 No H-bonds generated for 'chain 'B' and resid 727 through 729' Processing helix chain 'B' and resid 730 through 738 removed outlier: 4.156A pdb=" N VAL B 736 " --> pdb=" O GLY B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 765 removed outlier: 4.101A pdb=" N VAL B 760 " --> pdb=" O PRO B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 795 removed outlier: 4.231A pdb=" N ASP B 789 " --> pdb=" O GLU B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 823 removed outlier: 3.884A pdb=" N VAL B 820 " --> pdb=" O ARG B 816 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY B 821 " --> pdb=" O LEU B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 842 No H-bonds generated for 'chain 'B' and resid 840 through 842' Processing helix chain 'B' and resid 843 through 854 removed outlier: 3.769A pdb=" N SER B 849 " --> pdb=" O GLN B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 880 removed outlier: 3.834A pdb=" N ILE B 874 " --> pdb=" O SER B 870 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS B 878 " --> pdb=" O ILE B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 899 No H-bonds generated for 'chain 'B' and resid 897 through 899' Processing helix chain 'B' and resid 900 through 911 Processing helix chain 'B' and resid 924 through 937 removed outlier: 3.727A pdb=" N GLY B 935 " --> pdb=" O LEU B 931 " (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 Processing helix chain 'B' and resid 982 through 994 removed outlier: 3.636A pdb=" N MET B 988 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE B 989 " --> pdb=" O GLY B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1025 Processing helix chain 'C' and resid 136 through 148 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 231 through 245 Processing helix chain 'C' and resid 273 through 278 Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'C' and resid 328 through 337 Processing helix chain 'C' and resid 351 through 362 removed outlier: 4.700A pdb=" N GLU C 356 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLN C 359 " --> pdb=" O GLU C 356 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N HIS C 360 " --> 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 401 removed outlier: 3.677A pdb=" N GLU C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 3.525A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 428 Processing helix chain 'C' and resid 439 through 452 Processing helix chain 'C' and resid 462 through 464 No H-bonds generated for 'chain 'C' and resid 462 through 464' Processing helix chain 'C' and resid 465 through 479 Processing helix chain 'C' and resid 485 through 492 Processing helix chain 'C' and resid 496 through 505 Processing helix chain 'C' and resid 522 through 535 removed outlier: 3.923A pdb=" N TYR C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU C 535 " --> pdb=" O ALA C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 544 removed outlier: 4.008A pdb=" N ARG C 543 " --> pdb=" O LYS C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 564 Processing helix chain 'C' and resid 567 through 571 Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 598 through 618 Processing helix chain 'C' and resid 627 through 637 Processing helix chain 'C' and resid 639 through 647 removed outlier: 4.128A pdb=" N ARG C 645 " --> pdb=" O ASP C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 659 through 672 Processing helix chain 'C' and resid 727 through 729 No H-bonds generated for 'chain 'C' and resid 727 through 729' Processing helix chain 'C' and resid 730 through 738 removed outlier: 4.186A pdb=" N VAL C 736 " --> pdb=" O GLY C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 765 removed outlier: 3.985A pdb=" N VAL C 760 " --> pdb=" O PRO C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 795 removed outlier: 4.033A pdb=" N PHE C 788 " --> pdb=" O HIS C 784 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP C 789 " --> pdb=" O GLU C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 823 removed outlier: 3.825A pdb=" N VAL C 820 " --> pdb=" O ARG C 816 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY C 821 " --> pdb=" O LEU C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 842 No H-bonds generated for 'chain 'C' and resid 840 through 842' Processing helix chain 'C' and resid 843 through 854 removed outlier: 3.673A pdb=" N SER C 849 " --> pdb=" O GLN C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 880 removed outlier: 3.868A pdb=" N ILE C 874 " --> pdb=" O SER C 870 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 878 " --> pdb=" O ILE C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 899 No H-bonds generated for 'chain 'C' and resid 897 through 899' Processing helix chain 'C' and resid 900 through 911 Processing helix chain 'C' and resid 924 through 937 removed outlier: 3.853A pdb=" N GLY C 935 " --> pdb=" O LEU C 931 " (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 Processing helix chain 'C' and resid 982 through 994 Processing helix chain 'C' and resid 1011 through 1025 Processing helix chain 'D' and resid 135 through 148 removed outlier: 3.522A pdb=" N LYS D 139 " --> pdb=" O ASP D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 168 Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.583A pdb=" N LEU D 235 " --> pdb=" O GLY D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 278 Processing helix chain 'D' and resid 304 through 307 Processing helix chain 'D' and resid 328 through 337 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 358 through 362 Processing helix chain 'D' and resid 374 through 386 Processing helix chain 'D' and resid 388 through 401 removed outlier: 4.117A pdb=" N ALA D 395 " --> pdb=" O GLN D 391 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE D 396 " --> pdb=" O ALA D 392 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 409 Processing helix chain 'D' and resid 411 through 428 Processing helix chain 'D' and resid 439 through 452 Processing helix chain 'D' and resid 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.567A pdb=" N LEU D 469 " --> pdb=" O HIS D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 492 Processing helix chain 'D' and resid 496 through 505 Processing helix chain 'D' and resid 522 through 534 removed outlier: 3.932A pdb=" N TYR D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 544 removed outlier: 3.873A pdb=" N ARG D 543 " --> pdb=" O LYS D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 564 Processing helix chain 'D' and resid 567 through 571 Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 597 through 618 Processing helix chain 'D' and resid 627 through 637 Processing helix chain 'D' and resid 639 through 647 removed outlier: 3.919A pdb=" N ARG D 645 " --> pdb=" O ASP D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 650 No H-bonds generated for 'chain 'D' and resid 648 through 650' Processing helix chain 'D' and resid 659 through 672 Processing helix chain 'D' and resid 727 through 729 No H-bonds generated for 'chain 'D' and resid 727 through 729' Processing helix chain 'D' and resid 730 through 738 removed outlier: 4.129A pdb=" N VAL D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 754 through 765 removed outlier: 4.119A pdb=" N VAL D 760 " --> pdb=" O PRO D 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 795 removed outlier: 4.209A pdb=" N ASP D 789 " --> pdb=" O GLU D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 823 removed outlier: 3.914A pdb=" N VAL D 820 " --> pdb=" O ARG D 816 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY D 821 " --> pdb=" O LEU D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 842 No H-bonds generated for 'chain 'D' and resid 840 through 842' Processing helix chain 'D' and resid 843 through 854 removed outlier: 3.750A pdb=" N SER D 849 " --> pdb=" O GLN D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 880 removed outlier: 3.799A pdb=" N ILE D 874 " --> pdb=" O SER D 870 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS D 878 " --> pdb=" O ILE D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 899 No H-bonds generated for 'chain 'D' and resid 897 through 899' Processing helix chain 'D' and resid 900 through 911 Processing helix chain 'D' and resid 924 through 937 removed outlier: 3.801A pdb=" N GLY D 935 " --> pdb=" O LEU D 931 " (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: 3.646A pdb=" N THR D 966 " --> pdb=" O SER D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 994 removed outlier: 3.585A pdb=" N MET D 988 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE D 989 " --> pdb=" O GLY D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 1011 through 1025 Processing helix chain 'E' and resid 136 through 148 Processing helix chain 'E' and resid 164 through 168 Processing helix chain 'E' and resid 231 through 245 Processing helix chain 'E' and resid 273 through 278 Processing helix chain 'E' and resid 304 through 307 Processing helix chain 'E' and resid 328 through 337 Processing helix chain 'E' and resid 351 through 362 removed outlier: 4.624A pdb=" N GLU E 356 " --> pdb=" O VAL E 353 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN E 359 " --> pdb=" O GLU E 356 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N HIS E 360 " --> 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 401 removed outlier: 3.729A pdb=" N GLU E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 409 Processing helix chain 'E' and resid 411 through 428 Processing helix chain 'E' and resid 439 through 452 Processing helix chain 'E' and resid 462 through 464 No H-bonds generated for 'chain 'E' and resid 462 through 464' Processing helix chain 'E' and resid 465 through 479 Processing helix chain 'E' and resid 485 through 492 Processing helix chain 'E' and resid 496 through 505 Processing helix chain 'E' and resid 522 through 535 removed outlier: 3.889A pdb=" N TYR E 534 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU E 535 " --> pdb=" O ALA E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 544 removed outlier: 4.005A pdb=" N ARG E 543 " --> pdb=" O LYS E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 564 Processing helix chain 'E' and resid 567 through 571 Processing helix chain 'E' and resid 573 through 584 Processing helix chain 'E' and resid 598 through 618 Processing helix chain 'E' and resid 627 through 637 Processing helix chain 'E' and resid 639 through 647 removed outlier: 4.054A pdb=" N ARG E 645 " --> pdb=" O ASP E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 650 No H-bonds generated for 'chain 'E' and resid 648 through 650' Processing helix chain 'E' and resid 659 through 672 Processing helix chain 'E' and resid 727 through 729 No H-bonds generated for 'chain 'E' and resid 727 through 729' Processing helix chain 'E' and resid 730 through 738 removed outlier: 4.162A pdb=" N VAL E 736 " --> pdb=" O GLY E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 754 through 765 removed outlier: 3.995A pdb=" N VAL E 760 " --> pdb=" O PRO E 756 " (cutoff:3.500A) Processing helix chain 'E' and resid 784 through 795 removed outlier: 4.015A pdb=" N PHE E 788 " --> pdb=" O HIS E 784 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP E 789 " --> pdb=" O GLU E 785 " (cutoff:3.500A) Processing helix chain 'E' and resid 811 through 823 removed outlier: 3.825A pdb=" N VAL E 820 " --> pdb=" O ARG E 816 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY E 821 " --> pdb=" O LEU E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 840 through 842 No H-bonds generated for 'chain 'E' and resid 840 through 842' Processing helix chain 'E' and resid 843 through 854 removed outlier: 3.677A pdb=" N SER E 849 " --> pdb=" O GLN E 845 " (cutoff:3.500A) Processing helix chain 'E' and resid 868 through 880 removed outlier: 3.866A pdb=" N ILE E 874 " --> pdb=" O SER E 870 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS E 878 " --> pdb=" O ILE E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 899 No H-bonds generated for 'chain 'E' and resid 897 through 899' Processing helix chain 'E' and resid 900 through 911 Processing helix chain 'E' and resid 924 through 937 removed outlier: 3.822A pdb=" N GLY E 935 " --> pdb=" O LEU E 931 " (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 Processing helix chain 'E' and resid 982 through 994 Processing helix chain 'E' and resid 1011 through 1025 Processing helix chain 'F' and resid 136 through 148 Processing helix chain 'F' and resid 164 through 168 Processing helix chain 'F' and resid 231 through 245 removed outlier: 3.503A pdb=" N LEU F 235 " --> pdb=" O GLY F 231 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 278 Processing helix chain 'F' and resid 304 through 307 Processing helix chain 'F' and resid 328 through 337 Processing helix chain 'F' and resid 351 through 362 removed outlier: 4.699A pdb=" N GLU F 356 " --> pdb=" O VAL F 353 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN F 359 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N HIS F 360 " --> 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 401 removed outlier: 3.768A pdb=" N GLU F 401 " --> pdb=" O SER F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 409 Processing helix chain 'F' and resid 411 through 428 Processing helix chain 'F' and resid 439 through 452 Processing helix chain 'F' and resid 462 through 464 No H-bonds generated for 'chain 'F' and resid 462 through 464' Processing helix chain 'F' and resid 465 through 479 Processing helix chain 'F' and resid 485 through 492 Processing helix chain 'F' and resid 496 through 505 Processing helix chain 'F' and resid 522 through 535 removed outlier: 3.903A pdb=" N TYR F 534 " --> pdb=" O ALA F 530 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU F 535 " --> pdb=" O ALA F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 544 removed outlier: 4.023A pdb=" N ARG F 543 " --> pdb=" O LYS F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 564 Processing helix chain 'F' and resid 567 through 571 Processing helix chain 'F' and resid 573 through 584 Processing helix chain 'F' and resid 598 through 618 Processing helix chain 'F' and resid 627 through 637 Processing helix chain 'F' and resid 639 through 647 removed outlier: 4.121A pdb=" N ARG F 645 " --> pdb=" O ASP F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 650 No H-bonds generated for 'chain 'F' and resid 648 through 650' Processing helix chain 'F' and resid 659 through 672 Processing helix chain 'F' and resid 727 through 729 No H-bonds generated for 'chain 'F' and resid 727 through 729' Processing helix chain 'F' and resid 730 through 738 removed outlier: 4.182A pdb=" N VAL F 736 " --> pdb=" O GLY F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 754 through 765 removed outlier: 4.024A pdb=" N VAL F 760 " --> pdb=" O PRO F 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 784 through 795 removed outlier: 4.101A pdb=" N PHE F 788 " --> pdb=" O HIS F 784 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP F 789 " --> pdb=" O GLU F 785 " (cutoff:3.500A) Processing helix chain 'F' and resid 811 through 823 removed outlier: 3.830A pdb=" N VAL F 820 " --> pdb=" O ARG F 816 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY F 821 " --> pdb=" O LEU F 817 " (cutoff:3.500A) Processing helix chain 'F' and resid 840 through 842 No H-bonds generated for 'chain 'F' and resid 840 through 842' Processing helix chain 'F' and resid 843 through 854 removed outlier: 3.675A pdb=" N SER F 849 " --> pdb=" O GLN F 845 " (cutoff:3.500A) Processing helix chain 'F' and resid 868 through 880 removed outlier: 3.857A pdb=" N ILE F 874 " --> pdb=" O SER F 870 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS F 878 " --> pdb=" O ILE F 874 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 899 No H-bonds generated for 'chain 'F' and resid 897 through 899' Processing helix chain 'F' and resid 900 through 911 Processing helix chain 'F' and resid 924 through 937 removed outlier: 3.858A pdb=" N GLY F 935 " --> pdb=" O LEU F 931 " (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 Processing helix chain 'F' and resid 982 through 994 Processing helix chain 'F' and resid 1011 through 1025 Processing helix chain 'G' and resid 135 through 148 Processing helix chain 'G' and resid 164 through 168 Processing helix chain 'G' and resid 231 through 245 removed outlier: 3.544A pdb=" N LEU G 235 " --> pdb=" O GLY G 231 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET G 240 " --> pdb=" O ALA G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 278 Processing helix chain 'G' and resid 304 through 307 Processing helix chain 'G' and resid 328 through 337 Processing helix chain 'G' and resid 351 through 355 Processing helix chain 'G' and resid 358 through 362 Processing helix chain 'G' and resid 374 through 386 Processing helix chain 'G' and resid 388 through 401 Processing helix chain 'G' and resid 402 through 409 Processing helix chain 'G' and resid 411 through 428 Processing helix chain 'G' and resid 439 through 452 Processing helix chain 'G' and resid 462 through 464 No H-bonds generated for 'chain 'G' and resid 462 through 464' Processing helix chain 'G' and resid 465 through 479 removed outlier: 3.897A pdb=" N LEU G 469 " --> pdb=" O HIS G 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 492 Processing helix chain 'G' and resid 496 through 505 Processing helix chain 'G' and resid 522 through 536 removed outlier: 3.841A pdb=" N TYR G 534 " --> pdb=" O ALA G 530 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU G 535 " --> pdb=" O ALA G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 544 removed outlier: 3.865A pdb=" N ARG G 543 " --> pdb=" O LYS G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 564 Processing helix chain 'G' and resid 567 through 571 Processing helix chain 'G' and resid 573 through 584 Processing helix chain 'G' and resid 597 through 618 Processing helix chain 'G' and resid 627 through 637 Processing helix chain 'G' and resid 639 through 647 removed outlier: 3.927A pdb=" N ARG G 645 " --> pdb=" O ASP G 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 648 through 650 No H-bonds generated for 'chain 'G' and resid 648 through 650' Processing helix chain 'G' and resid 659 through 672 Processing helix chain 'G' and resid 727 through 729 No H-bonds generated for 'chain 'G' and resid 727 through 729' Processing helix chain 'G' and resid 730 through 738 removed outlier: 4.145A pdb=" N VAL G 736 " --> pdb=" O GLY G 732 " (cutoff:3.500A) Processing helix chain 'G' and resid 754 through 765 removed outlier: 4.125A pdb=" N VAL G 760 " --> pdb=" O PRO G 756 " (cutoff:3.500A) Processing helix chain 'G' and resid 785 through 795 removed outlier: 4.212A pdb=" N ASP G 789 " --> pdb=" O GLU G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 811 through 823 removed outlier: 3.881A pdb=" N VAL G 820 " --> pdb=" O ARG G 816 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY G 821 " --> pdb=" O LEU G 817 " (cutoff:3.500A) Processing helix chain 'G' and resid 840 through 842 No H-bonds generated for 'chain 'G' and resid 840 through 842' Processing helix chain 'G' and resid 843 through 854 removed outlier: 3.742A pdb=" N SER G 849 " --> pdb=" O GLN G 845 " (cutoff:3.500A) Processing helix chain 'G' and resid 868 through 880 removed outlier: 3.800A pdb=" N ILE G 874 " --> pdb=" O SER G 870 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS G 878 " --> pdb=" O ILE G 874 " (cutoff:3.500A) Processing helix chain 'G' and resid 897 through 899 No H-bonds generated for 'chain 'G' and resid 897 through 899' Processing helix chain 'G' and resid 900 through 911 Processing helix chain 'G' and resid 924 through 937 removed outlier: 3.798A pdb=" N GLY G 935 " --> pdb=" O LEU G 931 " (cutoff:3.500A) Processing helix chain 'G' and resid 954 through 956 No H-bonds generated for 'chain 'G' and resid 954 through 956' Processing helix chain 'G' and resid 957 through 968 removed outlier: 3.661A pdb=" N THR G 966 " --> pdb=" O SER G 962 " (cutoff:3.500A) Processing helix chain 'G' and resid 982 through 994 removed outlier: 3.614A pdb=" N MET G 988 " --> pdb=" O LEU G 984 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE G 989 " --> pdb=" O GLY G 985 " (cutoff:3.500A) Processing helix chain 'G' and resid 1011 through 1025 Processing helix chain 'H' and resid 136 through 148 Processing helix chain 'H' and resid 164 through 168 Processing helix chain 'H' and resid 231 through 245 Processing helix chain 'H' and resid 273 through 278 Processing helix chain 'H' and resid 304 through 307 Processing helix chain 'H' and resid 328 through 337 Processing helix chain 'H' and resid 351 through 362 removed outlier: 4.602A pdb=" N GLU H 356 " --> pdb=" O VAL H 353 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN H 359 " --> pdb=" O GLU H 356 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N HIS H 360 " --> pdb=" O LYS H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 386 removed outlier: 3.547A pdb=" N PHE H 386 " --> pdb=" O PHE H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 401 removed outlier: 3.730A pdb=" N GLU H 401 " --> pdb=" O SER H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 403 through 409 Processing helix chain 'H' and resid 411 through 428 Processing helix chain 'H' and resid 439 through 452 Processing helix chain 'H' and resid 462 through 464 No H-bonds generated for 'chain 'H' and resid 462 through 464' Processing helix chain 'H' and resid 465 through 479 removed outlier: 3.547A pdb=" N LEU H 469 " --> pdb=" O HIS H 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 485 through 492 Processing helix chain 'H' and resid 496 through 505 Processing helix chain 'H' and resid 522 through 535 removed outlier: 3.950A pdb=" N TYR H 534 " --> pdb=" O ALA H 530 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU H 535 " --> pdb=" O ALA H 531 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 544 removed outlier: 3.886A pdb=" N ARG H 543 " --> pdb=" O LYS H 540 " (cutoff:3.500A) Processing helix chain 'H' and resid 557 through 564 Processing helix chain 'H' and resid 567 through 571 Processing helix chain 'H' and resid 573 through 584 Processing helix chain 'H' and resid 598 through 618 Processing helix chain 'H' and resid 627 through 637 Processing helix chain 'H' and resid 639 through 647 removed outlier: 4.065A pdb=" N ARG H 645 " --> pdb=" O ASP H 641 " (cutoff:3.500A) Processing helix chain 'H' and resid 648 through 650 No H-bonds generated for 'chain 'H' and resid 648 through 650' Processing helix chain 'H' and resid 659 through 672 Processing helix chain 'H' and resid 727 through 729 No H-bonds generated for 'chain 'H' and resid 727 through 729' Processing helix chain 'H' and resid 730 through 738 removed outlier: 4.150A pdb=" N VAL H 736 " --> pdb=" O GLY H 732 " (cutoff:3.500A) Processing helix chain 'H' and resid 754 through 765 removed outlier: 4.054A pdb=" N VAL H 760 " --> pdb=" O PRO H 756 " (cutoff:3.500A) Processing helix chain 'H' and resid 784 through 795 removed outlier: 4.067A pdb=" N PHE H 788 " --> pdb=" O HIS H 784 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP H 789 " --> pdb=" O GLU H 785 " (cutoff:3.500A) Processing helix chain 'H' and resid 811 through 823 removed outlier: 3.831A pdb=" N VAL H 820 " --> pdb=" O ARG H 816 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY H 821 " --> pdb=" O LEU H 817 " (cutoff:3.500A) Processing helix chain 'H' and resid 840 through 842 No H-bonds generated for 'chain 'H' and resid 840 through 842' Processing helix chain 'H' and resid 843 through 854 removed outlier: 3.682A pdb=" N SER H 849 " --> pdb=" O GLN H 845 " (cutoff:3.500A) Processing helix chain 'H' and resid 868 through 880 removed outlier: 3.863A pdb=" N ILE H 874 " --> pdb=" O SER H 870 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS H 878 " --> pdb=" O ILE H 874 " (cutoff:3.500A) Processing helix chain 'H' and resid 897 through 899 No H-bonds generated for 'chain 'H' and resid 897 through 899' Processing helix chain 'H' and resid 900 through 911 Processing helix chain 'H' and resid 924 through 937 removed outlier: 3.857A pdb=" N GLY H 935 " --> pdb=" O LEU H 931 " (cutoff:3.500A) Processing helix chain 'H' and resid 954 through 956 No H-bonds generated for 'chain 'H' and resid 954 through 956' Processing helix chain 'H' and resid 957 through 968 Processing helix chain 'H' and resid 982 through 994 Processing helix chain 'H' and resid 1011 through 1025 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 203 removed outlier: 3.920A pdb=" N LEU A 173 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR A 221 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL A 368 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL A 223 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 509 Processing sheet with id=AA4, first strand: chain 'A' and resid 652 through 657 removed outlier: 6.601A pdb=" N ILE A 653 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLY A 682 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE A 655 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 679 " --> pdb=" O ASP A 747 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU A 946 " --> pdb=" O SER A 975 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 202 through 203 removed outlier: 3.982A pdb=" N LEU B 173 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR B 221 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL B 368 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL B 223 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B 297 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU B 347 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE B 299 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N THR B 349 " --> pdb=" O PHE B 299 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N MET B 301 " --> pdb=" O THR B 349 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AA7, first strand: chain 'B' and resid 508 through 509 Processing sheet with id=AA8, first strand: chain 'B' and resid 652 through 657 removed outlier: 6.589A pdb=" N ILE B 653 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLY B 682 " --> pdb=" O ILE B 653 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE B 655 " --> pdb=" O GLY B 682 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 679 " --> pdb=" O ASP B 747 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU B 946 " --> pdb=" O SER B 975 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 174 through 175 removed outlier: 6.861A pdb=" N THR C 221 " --> pdb=" O ARG C 366 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL C 368 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL C 223 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR C 255 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU C 300 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE C 257 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ASP C 302 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE C 259 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AB2, first strand: chain 'C' and resid 508 through 509 Processing sheet with id=AB3, first strand: chain 'C' and resid 652 through 657 removed outlier: 6.620A pdb=" N ILE C 653 " --> pdb=" O SER C 680 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLY C 682 " --> pdb=" O ILE C 653 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE C 655 " --> pdb=" O GLY C 682 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 679 " --> pdb=" O ASP C 747 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU C 946 " --> pdb=" O SER C 975 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 202 through 203 removed outlier: 3.818A pdb=" N LEU D 173 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR D 221 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL D 368 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL D 223 " --> pdb=" O VAL D 368 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 269 through 270 Processing sheet with id=AB6, first strand: chain 'D' and resid 508 through 509 Processing sheet with id=AB7, first strand: chain 'D' and resid 652 through 657 removed outlier: 6.590A pdb=" N ILE D 653 " --> pdb=" O SER D 680 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLY D 682 " --> pdb=" O ILE D 653 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE D 655 " --> pdb=" O GLY D 682 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU D 679 " --> pdb=" O ASP D 747 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 202 through 203 removed outlier: 4.313A pdb=" N LEU E 173 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TYR E 255 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU E 300 " --> pdb=" O TYR E 255 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE E 257 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP E 302 " --> pdb=" O PHE E 257 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE E 259 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 269 through 270 Processing sheet with id=AC1, first strand: chain 'E' and resid 508 through 509 Processing sheet with id=AC2, first strand: chain 'E' and resid 652 through 657 removed outlier: 6.622A pdb=" N ILE E 653 " --> pdb=" O SER E 680 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLY E 682 " --> pdb=" O ILE E 653 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE E 655 " --> pdb=" O GLY E 682 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU E 679 " --> pdb=" O ASP E 747 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU E 946 " --> pdb=" O SER E 975 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 202 through 203 removed outlier: 4.158A pdb=" N LEU F 173 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE F 297 " --> pdb=" O SER F 345 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU F 347 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE F 299 " --> pdb=" O LEU F 347 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N THR F 349 " --> pdb=" O PHE F 299 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N MET F 301 " --> pdb=" O THR F 349 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR F 255 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU F 300 " --> pdb=" O TYR F 255 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE F 257 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP F 302 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE F 259 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 269 through 270 Processing sheet with id=AC5, first strand: chain 'F' and resid 508 through 509 Processing sheet with id=AC6, first strand: chain 'F' and resid 652 through 657 removed outlier: 6.622A pdb=" N ILE F 653 " --> pdb=" O SER F 680 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLY F 682 " --> pdb=" O ILE F 653 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE F 655 " --> pdb=" O GLY F 682 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU F 679 " --> pdb=" O ASP F 747 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU F 946 " --> pdb=" O SER F 975 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 202 through 203 removed outlier: 3.820A pdb=" N LEU G 173 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR G 221 " --> pdb=" O ARG G 366 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL G 368 " --> pdb=" O THR G 221 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL G 223 " --> pdb=" O VAL G 368 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE G 297 " --> pdb=" O SER G 345 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU G 347 " --> pdb=" O ILE G 297 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE G 299 " --> pdb=" O LEU G 347 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N THR G 349 " --> pdb=" O PHE G 299 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N MET G 301 " --> pdb=" O THR G 349 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR G 255 " --> pdb=" O LEU G 298 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU G 300 " --> pdb=" O TYR G 255 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N PHE G 257 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP G 302 " --> pdb=" O PHE G 257 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE G 259 " --> pdb=" O ASP G 302 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 269 through 270 Processing sheet with id=AC9, first strand: chain 'G' and resid 508 through 509 Processing sheet with id=AD1, first strand: chain 'G' and resid 652 through 657 removed outlier: 6.608A pdb=" N ILE G 653 " --> pdb=" O SER G 680 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N GLY G 682 " --> pdb=" O ILE G 653 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE G 655 " --> pdb=" O GLY G 682 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU G 679 " --> pdb=" O ASP G 747 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU G 946 " --> pdb=" O SER G 975 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 174 through 175 removed outlier: 6.606A pdb=" N THR H 221 " --> pdb=" O ARG H 366 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL H 368 " --> pdb=" O THR H 221 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL H 223 " --> pdb=" O VAL H 368 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 269 through 270 Processing sheet with id=AD4, first strand: chain 'H' and resid 508 through 509 Processing sheet with id=AD5, first strand: chain 'H' and resid 652 through 657 removed outlier: 6.644A pdb=" N ILE H 653 " --> pdb=" O SER H 680 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N GLY H 682 " --> pdb=" O ILE H 653 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE H 655 " --> pdb=" O GLY H 682 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU H 679 " --> pdb=" O ASP H 747 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU H 946 " --> pdb=" O SER H 975 " (cutoff:3.500A) 2192 hydrogen bonds defined for protein. 6237 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: 21.97 Time building geometry restraints manager: 11.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8882 1.31 - 1.44: 13652 1.44 - 1.57: 30964 1.57 - 1.70: 94 1.70 - 1.83: 604 Bond restraints: 54196 Sorted by residual: bond pdb=" C ALA F 394 " pdb=" O ALA F 394 " ideal model delta sigma weight residual 1.237 1.321 -0.085 1.19e-02 7.06e+03 5.09e+01 bond pdb=" N ALA F 395 " pdb=" CA ALA F 395 " ideal model delta sigma weight residual 1.459 1.383 0.076 1.19e-02 7.06e+03 4.06e+01 bond pdb=" C ALA F 395 " pdb=" O ALA F 395 " ideal model delta sigma weight residual 1.236 1.176 0.061 1.15e-02 7.56e+03 2.80e+01 bond pdb=" C ALA F 394 " pdb=" N ALA F 395 " ideal model delta sigma weight residual 1.334 1.269 0.066 1.27e-02 6.20e+03 2.69e+01 bond pdb=" CA ALA F 394 " pdb=" C ALA F 394 " ideal model delta sigma weight residual 1.524 1.471 0.052 1.29e-02 6.01e+03 1.63e+01 ... (remaining 54191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 68323 2.15 - 4.30: 4116 4.30 - 6.44: 450 6.44 - 8.59: 114 8.59 - 10.74: 1 Bond angle restraints: 73004 Sorted by residual: angle pdb=" C ALA F 394 " pdb=" N ALA F 395 " pdb=" CA ALA F 395 " ideal model delta sigma weight residual 120.44 131.18 -10.74 1.30e+00 5.92e-01 6.83e+01 angle pdb=" C LYS B1025 " pdb=" N PRO B1026 " pdb=" CA PRO B1026 " ideal model delta sigma weight residual 119.56 127.18 -7.62 1.02e+00 9.61e-01 5.58e+01 angle pdb=" C LEU C 553 " pdb=" N PRO C 554 " pdb=" CA PRO C 554 " ideal model delta sigma weight residual 119.24 126.98 -7.74 1.04e+00 9.25e-01 5.54e+01 angle pdb=" C LYS A1025 " pdb=" N PRO A1026 " pdb=" CA PRO A1026 " ideal model delta sigma weight residual 119.56 127.13 -7.57 1.02e+00 9.61e-01 5.51e+01 angle pdb=" C LYS G1025 " pdb=" N PRO G1026 " pdb=" CA PRO G1026 " ideal model delta sigma weight residual 119.56 127.12 -7.56 1.02e+00 9.61e-01 5.49e+01 ... (remaining 72999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 31776 17.96 - 35.93: 861 35.93 - 53.89: 169 53.89 - 71.85: 115 71.85 - 89.81: 43 Dihedral angle restraints: 32964 sinusoidal: 13520 harmonic: 19444 Sorted by residual: dihedral pdb=" N ALA F 395 " pdb=" C ALA F 395 " pdb=" CA ALA F 395 " pdb=" CB ALA F 395 " ideal model delta harmonic sigma weight residual 122.90 132.99 -10.09 0 2.50e+00 1.60e-01 1.63e+01 dihedral pdb=" C ALA F 395 " pdb=" N ALA F 395 " pdb=" CA ALA F 395 " pdb=" CB ALA F 395 " ideal model delta harmonic sigma weight residual -122.60 -132.68 10.08 0 2.50e+00 1.60e-01 1.63e+01 dihedral pdb=" CB GLU D 214 " pdb=" CG GLU D 214 " pdb=" CD GLU D 214 " pdb=" OE1 GLU D 214 " ideal model delta sinusoidal sigma weight residual 0.00 89.81 -89.81 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 32961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 7475 0.108 - 0.215: 793 0.215 - 0.323: 43 0.323 - 0.430: 4 0.430 - 0.538: 1 Chirality restraints: 8316 Sorted by residual: chirality pdb=" CA ALA F 395 " pdb=" N ALA F 395 " pdb=" C ALA F 395 " pdb=" CB ALA F 395 " both_signs ideal model delta sigma weight residual False 2.48 1.95 0.54 2.00e-01 2.50e+01 7.22e+00 chirality pdb=" CB ILE B 370 " pdb=" CA ILE B 370 " pdb=" CG1 ILE B 370 " pdb=" CG2 ILE B 370 " both_signs ideal model delta sigma weight residual False 2.64 2.99 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CG LEU E 462 " pdb=" CB LEU E 462 " pdb=" CD1 LEU E 462 " pdb=" CD2 LEU E 462 " both_signs ideal model delta sigma weight residual False -2.59 -2.92 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 8313 not shown) Planarity restraints: 9212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 776 " 0.011 2.00e-02 2.50e+03 1.58e-02 6.20e+00 pdb=" CG TRP H 776 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP H 776 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP H 776 " 0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP H 776 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 776 " -0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP H 776 " -0.022 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 776 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 776 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP H 776 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 611 " -0.027 2.00e-02 2.50e+03 1.33e-02 4.43e+00 pdb=" CG TRP G 611 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP G 611 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP G 611 " 0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP G 611 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 611 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP G 611 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 611 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 611 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP G 611 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 381 " -0.025 2.00e-02 2.50e+03 1.46e-02 4.29e+00 pdb=" CG TYR F 381 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR F 381 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR F 381 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR F 381 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR F 381 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR F 381 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 381 " -0.025 2.00e-02 2.50e+03 ... (remaining 9209 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 13476 2.79 - 3.32: 51864 3.32 - 3.85: 87752 3.85 - 4.37: 113686 4.37 - 4.90: 182117 Nonbonded interactions: 448895 Sorted by model distance: nonbonded pdb=" OH TYR H 632 " pdb=" OD1 ASP H 662 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR F 632 " pdb=" OD1 ASP F 662 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR E 632 " pdb=" OD1 ASP E 662 " model vdw 2.287 3.040 nonbonded pdb=" NZ LYS D 238 " pdb=" OD1 ASP D 242 " model vdw 2.344 3.120 nonbonded pdb=" NZ LYS A 238 " pdb=" OD1 ASP A 242 " model vdw 2.348 3.120 ... (remaining 448890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 133 through 1035) selection = (chain 'B' and resid 133 through 1035) selection = chain 'C' selection = (chain 'D' and resid 133 through 1035) selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 133 through 1035) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.060 Extract box with map and model: 1.620 Check model and map are aligned: 0.310 Set scattering table: 0.370 Process input model: 91.490 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.012 0.085 54196 Z= 0.791 Angle : 1.168 10.741 73004 Z= 0.806 Chirality : 0.065 0.538 8316 Planarity : 0.004 0.029 9212 Dihedral : 10.727 89.815 20316 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.70 % Allowed : 3.74 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.10), residues: 6548 helix: -0.46 (0.08), residues: 2976 sheet: -0.36 (0.21), residues: 568 loop : -0.71 (0.11), residues: 3004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP G 611 HIS 0.007 0.001 HIS E 916 PHE 0.022 0.003 PHE B 529 TYR 0.026 0.004 TYR H 381 ARG 0.005 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1000 time to evaluate : 4.352 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 259 ILE cc_start: 0.8271 (mt) cc_final: 0.7871 (tp) REVERT: A 332 LEU cc_start: 0.8328 (mt) cc_final: 0.8117 (mt) REVERT: A 533 TYR cc_start: 0.7637 (t80) cc_final: 0.6992 (t80) REVERT: A 952 ASN cc_start: 0.7446 (t0) cc_final: 0.7089 (t0) REVERT: A 980 ASP cc_start: 0.5668 (t0) cc_final: 0.5465 (t0) REVERT: A 1025 LYS cc_start: 0.8406 (tttp) cc_final: 0.8081 (tttp) REVERT: B 533 TYR cc_start: 0.7398 (t80) cc_final: 0.7192 (t80) REVERT: B 559 THR cc_start: 0.8856 (m) cc_final: 0.8499 (p) REVERT: B 660 ARG cc_start: 0.7838 (ttm-80) cc_final: 0.7584 (tpp-160) REVERT: B 980 ASP cc_start: 0.5864 (t0) cc_final: 0.5555 (t0) REVERT: B 1025 LYS cc_start: 0.8364 (tttp) cc_final: 0.7972 (tttp) REVERT: C 277 MET cc_start: 0.2481 (mtm) cc_final: 0.1081 (ttm) REVERT: C 478 TRP cc_start: 0.4658 (t-100) cc_final: 0.4135 (m100) REVERT: C 505 MET cc_start: 0.3417 (mtm) cc_final: 0.2335 (mmt) REVERT: C 602 GLN cc_start: 0.6585 (tp40) cc_final: 0.6215 (mm-40) REVERT: C 671 GLU cc_start: 0.9041 (tt0) cc_final: 0.8785 (tm-30) REVERT: D 339 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8508 (mtmt) REVERT: D 533 TYR cc_start: 0.7402 (t80) cc_final: 0.6893 (t80) REVERT: D 559 THR cc_start: 0.8964 (m) cc_final: 0.8320 (m) REVERT: D 952 ASN cc_start: 0.7492 (t0) cc_final: 0.7121 (t0) REVERT: D 980 ASP cc_start: 0.5791 (t0) cc_final: 0.5470 (t0) REVERT: D 1025 LYS cc_start: 0.8416 (tttp) cc_final: 0.8110 (tttp) REVERT: E 277 MET cc_start: 0.1955 (mtm) cc_final: 0.1257 (ttm) REVERT: E 478 TRP cc_start: 0.4628 (t-100) cc_final: 0.4255 (m100) REVERT: E 505 MET cc_start: 0.2031 (mtm) cc_final: 0.1153 (mmt) REVERT: E 565 TYR cc_start: 0.4659 (t80) cc_final: 0.4439 (t80) REVERT: E 602 GLN cc_start: 0.6760 (tp40) cc_final: 0.6298 (mm-40) REVERT: E 1011 ASN cc_start: 0.7175 (p0) cc_final: 0.6939 (p0) REVERT: F 277 MET cc_start: 0.2124 (mtm) cc_final: 0.1290 (ttm) REVERT: F 478 TRP cc_start: 0.4586 (t-100) cc_final: 0.4115 (m100) REVERT: F 505 MET cc_start: 0.2882 (mtm) cc_final: 0.2055 (mmt) REVERT: F 565 TYR cc_start: 0.4941 (t80) cc_final: 0.4423 (t80) REVERT: F 1011 ASN cc_start: 0.7267 (p0) cc_final: 0.6983 (p0) REVERT: G 339 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8519 (mtmt) REVERT: G 445 PHE cc_start: 0.7331 (m-80) cc_final: 0.6481 (m-10) REVERT: G 533 TYR cc_start: 0.7556 (t80) cc_final: 0.7236 (t80) REVERT: G 557 ASP cc_start: 0.7741 (t0) cc_final: 0.7491 (t0) REVERT: G 559 THR cc_start: 0.8963 (m) cc_final: 0.8580 (p) REVERT: G 980 ASP cc_start: 0.7162 (t0) cc_final: 0.6713 (t0) REVERT: G 1025 LYS cc_start: 0.8461 (tttp) cc_final: 0.8130 (tttp) REVERT: H 277 MET cc_start: 0.2178 (mtm) cc_final: 0.1259 (ttm) REVERT: H 437 LYS cc_start: 0.6946 (tttt) cc_final: 0.6633 (ttmt) REVERT: H 478 TRP cc_start: 0.4700 (t-100) cc_final: 0.4284 (m100) REVERT: H 505 MET cc_start: 0.2741 (mtm) cc_final: 0.1814 (mmt) REVERT: H 565 TYR cc_start: 0.4787 (t80) cc_final: 0.4315 (t80) REVERT: H 602 GLN cc_start: 0.6455 (tp40) cc_final: 0.6190 (mm-40) REVERT: H 1011 ASN cc_start: 0.7210 (p0) cc_final: 0.6931 (p0) outliers start: 0 outliers final: 0 residues processed: 1000 average time/residue: 0.5153 time to fit residues: 858.5837 Evaluate side-chains 545 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 4.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 560 optimal weight: 1.9990 chunk 503 optimal weight: 10.0000 chunk 279 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 339 optimal weight: 7.9990 chunk 268 optimal weight: 7.9990 chunk 520 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 316 optimal weight: 0.9980 chunk 387 optimal weight: 0.9990 chunk 602 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN A 434 GLN A 824 HIS B 314 HIS ** B 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 798 GLN B 824 HIS C 656 ASN C 808 ASN C1022 GLN D 367 HIS ** D 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 GLN D 824 HIS E 808 ASN F 808 ASN G 314 HIS G 434 GLN G 509 GLN G 824 HIS H 492 HIS H1022 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 54196 Z= 0.239 Angle : 0.656 11.200 73004 Z= 0.338 Chirality : 0.041 0.161 8316 Planarity : 0.004 0.043 9212 Dihedral : 4.294 21.425 7124 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.30 % Favored : 94.47 % Rotamer: Outliers : 0.91 % Allowed : 4.92 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.10), residues: 6548 helix: 0.22 (0.09), residues: 3012 sheet: -0.58 (0.21), residues: 592 loop : -0.85 (0.11), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 467 HIS 0.007 0.001 HIS F 784 PHE 0.028 0.002 PHE B1032 TYR 0.020 0.002 TYR D 565 ARG 0.007 0.000 ARG E 660 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 645 time to evaluate : 4.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 HIS cc_start: 0.7537 (m170) cc_final: 0.6804 (t-170) REVERT: A 238 LYS cc_start: 0.8066 (tptp) cc_final: 0.7749 (ttpp) REVERT: A 259 ILE cc_start: 0.8352 (mt) cc_final: 0.7991 (tp) REVERT: A 280 CYS cc_start: 0.5617 (p) cc_final: 0.5365 (t) REVERT: A 533 TYR cc_start: 0.7635 (t80) cc_final: 0.7368 (t80) REVERT: A 952 ASN cc_start: 0.7775 (t0) cc_final: 0.7367 (t0) REVERT: A 1032 PHE cc_start: 0.6318 (t80) cc_final: 0.6112 (t80) REVERT: B 952 ASN cc_start: 0.7728 (t0) cc_final: 0.7306 (t0) REVERT: B 984 LEU cc_start: 0.8262 (tt) cc_final: 0.7812 (mp) REVERT: C 277 MET cc_start: 0.2194 (mtm) cc_final: 0.1212 (ttm) REVERT: C 478 TRP cc_start: 0.4366 (t-100) cc_final: 0.3963 (m100) REVERT: C 505 MET cc_start: 0.3065 (mtm) cc_final: 0.2020 (mmt) REVERT: C 634 LEU cc_start: 0.5908 (mt) cc_final: 0.5648 (mt) REVERT: C 647 MET cc_start: 0.8372 (mmm) cc_final: 0.7972 (mmm) REVERT: C 671 GLU cc_start: 0.8991 (tt0) cc_final: 0.8696 (tm-30) REVERT: C 672 ASN cc_start: 0.8098 (m-40) cc_final: 0.7541 (m-40) REVERT: D 220 HIS cc_start: 0.7528 (m170) cc_final: 0.6813 (t-170) REVERT: D 238 LYS cc_start: 0.7818 (tptp) cc_final: 0.7284 (ttpp) REVERT: D 240 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7741 (mtp) REVERT: D 533 TYR cc_start: 0.7470 (t80) cc_final: 0.7249 (t80) REVERT: D 557 ASP cc_start: 0.7436 (t0) cc_final: 0.7144 (t0) REVERT: D 952 ASN cc_start: 0.7765 (t0) cc_final: 0.7346 (t0) REVERT: D 984 LEU cc_start: 0.8253 (tt) cc_final: 0.8040 (mt) REVERT: E 277 MET cc_start: 0.1852 (mtm) cc_final: 0.1130 (ttm) REVERT: E 467 TRP cc_start: 0.2478 (t-100) cc_final: 0.1967 (t60) REVERT: E 478 TRP cc_start: 0.4470 (t-100) cc_final: 0.4067 (m100) REVERT: E 505 MET cc_start: 0.1643 (mtm) cc_final: 0.0892 (mmt) REVERT: E 523 MET cc_start: 0.6617 (ttt) cc_final: 0.6277 (mmm) REVERT: E 527 GLU cc_start: 0.6626 (mt-10) cc_final: 0.6130 (pt0) REVERT: E 634 LEU cc_start: 0.6156 (mt) cc_final: 0.5922 (mt) REVERT: E 647 MET cc_start: 0.8413 (mmm) cc_final: 0.8086 (mmm) REVERT: E 664 MET cc_start: 0.8510 (mmt) cc_final: 0.8058 (tpp) REVERT: E 1011 ASN cc_start: 0.7111 (p0) cc_final: 0.6729 (p0) REVERT: F 277 MET cc_start: 0.2015 (mtm) cc_final: 0.1272 (ttm) REVERT: F 467 TRP cc_start: 0.2605 (t-100) cc_final: 0.2380 (t-100) REVERT: F 478 TRP cc_start: 0.4385 (t-100) cc_final: 0.3929 (m100) REVERT: F 505 MET cc_start: 0.2795 (mtm) cc_final: 0.1978 (mmt) REVERT: F 565 TYR cc_start: 0.4500 (t80) cc_final: 0.3939 (t80) REVERT: F 568 PHE cc_start: 0.6582 (p90) cc_final: 0.6268 (t80) REVERT: F 647 MET cc_start: 0.8427 (mmm) cc_final: 0.8045 (mmm) REVERT: G 220 HIS cc_start: 0.7307 (m170) cc_final: 0.6579 (t70) REVERT: G 406 PHE cc_start: 0.7024 (OUTLIER) cc_final: 0.6581 (m-10) REVERT: G 533 TYR cc_start: 0.7562 (t80) cc_final: 0.7130 (t80) REVERT: G 952 ASN cc_start: 0.7798 (t0) cc_final: 0.7419 (t0) REVERT: G 980 ASP cc_start: 0.7023 (t0) cc_final: 0.6791 (t0) REVERT: H 277 MET cc_start: 0.2061 (mtm) cc_final: 0.1379 (ttm) REVERT: H 478 TRP cc_start: 0.4625 (t-100) cc_final: 0.4374 (m100) REVERT: H 505 MET cc_start: 0.2586 (mtm) cc_final: 0.1705 (mmt) REVERT: H 565 TYR cc_start: 0.4497 (t80) cc_final: 0.3928 (t80) REVERT: H 647 MET cc_start: 0.8488 (mmm) cc_final: 0.8191 (mmm) outliers start: 55 outliers final: 28 residues processed: 675 average time/residue: 0.4876 time to fit residues: 565.4707 Evaluate side-chains 515 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 485 time to evaluate : 4.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 927 LYS Chi-restraints excluded: chain D residue 962 SER Chi-restraints excluded: chain D residue 970 SER Chi-restraints excluded: chain D residue 983 ASP Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 406 PHE Chi-restraints excluded: chain G residue 576 VAL Chi-restraints excluded: chain G residue 826 LEU Chi-restraints excluded: chain G residue 869 ASP Chi-restraints excluded: chain G residue 927 LYS Chi-restraints excluded: chain G residue 962 SER Chi-restraints excluded: chain G residue 983 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 335 optimal weight: 3.9990 chunk 187 optimal weight: 50.0000 chunk 501 optimal weight: 40.0000 chunk 410 optimal weight: 2.9990 chunk 166 optimal weight: 50.0000 chunk 604 optimal weight: 30.0000 chunk 652 optimal weight: 3.9990 chunk 537 optimal weight: 9.9990 chunk 599 optimal weight: 20.0000 chunk 205 optimal weight: 20.0000 chunk 484 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 ASN B 564 ASN B 672 ASN B 686 ASN B 784 HIS C 465 HIS C 656 ASN C 922 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN D 672 ASN D 686 ASN E 922 ASN F 465 HIS F 922 ASN G 564 ASN G 672 ASN G 979 ASN H 808 ASN H 922 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 54196 Z= 0.399 Angle : 0.702 10.745 73004 Z= 0.354 Chirality : 0.043 0.184 8316 Planarity : 0.004 0.047 9212 Dihedral : 4.565 23.810 7124 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.75 % Favored : 93.16 % Rotamer: Outliers : 1.69 % Allowed : 6.28 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.10), residues: 6548 helix: 0.15 (0.09), residues: 3028 sheet: -1.28 (0.20), residues: 688 loop : -1.01 (0.12), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 467 HIS 0.008 0.001 HIS E 465 PHE 0.022 0.002 PHE D 224 TYR 0.026 0.002 TYR D 572 ARG 0.005 0.001 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 552 time to evaluate : 4.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LYS cc_start: 0.7979 (tptp) cc_final: 0.7551 (ttpp) REVERT: A 406 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6811 (m-10) REVERT: A 533 TYR cc_start: 0.7681 (t80) cc_final: 0.7448 (t80) REVERT: A 952 ASN cc_start: 0.8046 (t0) cc_final: 0.7744 (t0) REVERT: B 406 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6836 (m-10) REVERT: B 952 ASN cc_start: 0.8043 (t0) cc_final: 0.7694 (t0) REVERT: C 277 MET cc_start: 0.2144 (mtm) cc_final: 0.1184 (ttm) REVERT: C 467 TRP cc_start: 0.2722 (t-100) cc_final: 0.2236 (t-100) REVERT: C 478 TRP cc_start: 0.4236 (t-100) cc_final: 0.3924 (m100) REVERT: C 505 MET cc_start: 0.2975 (mtm) cc_final: 0.1989 (mmt) REVERT: C 664 MET cc_start: 0.8376 (mmt) cc_final: 0.7981 (tpp) REVERT: C 671 GLU cc_start: 0.8964 (tt0) cc_final: 0.8705 (tm-30) REVERT: C 672 ASN cc_start: 0.8211 (m-40) cc_final: 0.7430 (m-40) REVERT: D 238 LYS cc_start: 0.7960 (tptp) cc_final: 0.7547 (ttpp) REVERT: D 240 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7957 (mtp) REVERT: D 384 LYS cc_start: 0.7308 (tmtt) cc_final: 0.7037 (ptmm) REVERT: D 952 ASN cc_start: 0.8079 (t0) cc_final: 0.7736 (t0) REVERT: D 984 LEU cc_start: 0.8444 (tt) cc_final: 0.8213 (mt) REVERT: E 277 MET cc_start: 0.1802 (mtm) cc_final: 0.1240 (ttm) REVERT: E 410 PHE cc_start: 0.4505 (p90) cc_final: 0.4268 (t80) REVERT: E 478 TRP cc_start: 0.4532 (t-100) cc_final: 0.4186 (m100) REVERT: E 527 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6289 (pt0) REVERT: E 565 TYR cc_start: 0.4165 (t80) cc_final: 0.3882 (t80) REVERT: E 980 ASP cc_start: 0.7479 (p0) cc_final: 0.7090 (p0) REVERT: F 277 MET cc_start: 0.1874 (mtm) cc_final: 0.1379 (ttm) REVERT: F 467 TRP cc_start: 0.2632 (t-100) cc_final: 0.2345 (t-100) REVERT: F 478 TRP cc_start: 0.4256 (t-100) cc_final: 0.3927 (m100) REVERT: F 505 MET cc_start: 0.2458 (mtm) cc_final: 0.1619 (mmt) REVERT: F 565 TYR cc_start: 0.4673 (t80) cc_final: 0.4180 (t80) REVERT: F 568 PHE cc_start: 0.6563 (p90) cc_final: 0.6309 (t80) REVERT: G 406 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6546 (m-10) REVERT: G 533 TYR cc_start: 0.7619 (t80) cc_final: 0.7301 (t80) REVERT: G 952 ASN cc_start: 0.8019 (t0) cc_final: 0.7696 (t0) REVERT: G 984 LEU cc_start: 0.8424 (tt) cc_final: 0.8121 (mt) REVERT: H 277 MET cc_start: 0.2073 (mtm) cc_final: 0.1502 (ttm) REVERT: H 505 MET cc_start: 0.2426 (mtm) cc_final: 0.1615 (mmt) REVERT: H 565 TYR cc_start: 0.4592 (t80) cc_final: 0.4066 (t80) REVERT: H 980 ASP cc_start: 0.7546 (p0) cc_final: 0.7291 (p0) outliers start: 102 outliers final: 72 residues processed: 615 average time/residue: 0.4704 time to fit residues: 504.2104 Evaluate side-chains 548 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 472 time to evaluate : 4.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 755 ASP Chi-restraints excluded: chain B residue 820 VAL Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain C residue 382 PHE Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 755 ASP Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 419 CYS Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 812 ASP Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 910 THR Chi-restraints excluded: chain D residue 927 LYS Chi-restraints excluded: chain D residue 962 SER Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain D residue 970 SER Chi-restraints excluded: chain D residue 983 ASP Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 446 PHE Chi-restraints excluded: chain E residue 678 SER Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 755 ASP Chi-restraints excluded: chain E residue 965 LEU Chi-restraints excluded: chain E residue 1008 MET Chi-restraints excluded: chain F residue 382 PHE Chi-restraints excluded: chain F residue 446 PHE Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 755 ASP Chi-restraints excluded: chain F residue 812 ASP Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 406 PHE Chi-restraints excluded: chain G residue 576 VAL Chi-restraints excluded: chain G residue 736 VAL Chi-restraints excluded: chain G residue 755 ASP Chi-restraints excluded: chain G residue 812 ASP Chi-restraints excluded: chain G residue 820 VAL Chi-restraints excluded: chain G residue 826 LEU Chi-restraints excluded: chain G residue 869 ASP Chi-restraints excluded: chain G residue 910 THR Chi-restraints excluded: chain G residue 927 LYS Chi-restraints excluded: chain G residue 962 SER Chi-restraints excluded: chain G residue 983 ASP Chi-restraints excluded: chain H residue 446 PHE Chi-restraints excluded: chain H residue 684 LEU Chi-restraints excluded: chain H residue 755 ASP Chi-restraints excluded: chain H residue 984 LEU Chi-restraints excluded: chain H residue 1008 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 596 optimal weight: 10.0000 chunk 454 optimal weight: 6.9990 chunk 313 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 288 optimal weight: 9.9990 chunk 405 optimal weight: 0.9980 chunk 606 optimal weight: 40.0000 chunk 641 optimal weight: 0.9980 chunk 316 optimal weight: 0.9990 chunk 574 optimal weight: 0.7980 chunk 172 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 HIS ** D 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 808 ASN H 808 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 54196 Z= 0.171 Angle : 0.575 11.769 73004 Z= 0.292 Chirality : 0.039 0.204 8316 Planarity : 0.004 0.049 9212 Dihedral : 4.238 21.009 7124 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.96 % Favored : 94.00 % Rotamer: Outliers : 1.11 % Allowed : 7.49 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.10), residues: 6548 helix: 0.44 (0.09), residues: 3040 sheet: -1.47 (0.20), residues: 700 loop : -0.93 (0.12), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 467 HIS 0.012 0.001 HIS E 465 PHE 0.022 0.001 PHE F1032 TYR 0.027 0.001 TYR D 565 ARG 0.005 0.000 ARG F 605 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 544 time to evaluate : 4.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LYS cc_start: 0.7954 (tptp) cc_final: 0.7526 (ttpp) REVERT: A 406 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.6891 (m-10) REVERT: A 952 ASN cc_start: 0.7900 (t0) cc_final: 0.7543 (t0) REVERT: A 984 LEU cc_start: 0.8309 (tt) cc_final: 0.7972 (mt) REVERT: B 343 GLU cc_start: 0.7590 (tt0) cc_final: 0.7183 (tt0) REVERT: B 952 ASN cc_start: 0.7881 (t0) cc_final: 0.7524 (t0) REVERT: B 984 LEU cc_start: 0.8305 (tt) cc_final: 0.7927 (mt) REVERT: C 277 MET cc_start: 0.2059 (mtm) cc_final: 0.1279 (ttm) REVERT: C 467 TRP cc_start: 0.2767 (t-100) cc_final: 0.1855 (t60) REVERT: C 478 TRP cc_start: 0.4256 (t-100) cc_final: 0.3910 (m100) REVERT: C 505 MET cc_start: 0.3046 (mtm) cc_final: 0.2108 (mmt) REVERT: C 664 MET cc_start: 0.8315 (mmt) cc_final: 0.7985 (tpp) REVERT: C 671 GLU cc_start: 0.8921 (tt0) cc_final: 0.8675 (tm-30) REVERT: C 672 ASN cc_start: 0.8195 (m-40) cc_final: 0.7422 (m-40) REVERT: C 812 ASP cc_start: 0.6884 (m-30) cc_final: 0.6580 (m-30) REVERT: D 238 LYS cc_start: 0.7885 (tptp) cc_final: 0.7382 (ttpp) REVERT: D 249 TYR cc_start: 0.8400 (m-80) cc_final: 0.8109 (m-80) REVERT: D 339 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8645 (mtmt) REVERT: D 343 GLU cc_start: 0.7503 (tt0) cc_final: 0.7170 (tt0) REVERT: D 533 TYR cc_start: 0.7135 (t80) cc_final: 0.6593 (t80) REVERT: D 952 ASN cc_start: 0.7901 (t0) cc_final: 0.7536 (t0) REVERT: D 984 LEU cc_start: 0.8350 (tt) cc_final: 0.8128 (mt) REVERT: E 277 MET cc_start: 0.1763 (mtm) cc_final: 0.1262 (ttm) REVERT: E 478 TRP cc_start: 0.4545 (t-100) cc_final: 0.4236 (m100) REVERT: E 565 TYR cc_start: 0.4079 (t80) cc_final: 0.3665 (t80) REVERT: E 664 MET cc_start: 0.8719 (mmt) cc_final: 0.8312 (tpp) REVERT: E 812 ASP cc_start: 0.6828 (m-30) cc_final: 0.6439 (m-30) REVERT: E 980 ASP cc_start: 0.7325 (p0) cc_final: 0.7115 (p0) REVERT: F 277 MET cc_start: 0.1780 (mtm) cc_final: 0.1470 (ttm) REVERT: F 382 PHE cc_start: 0.5031 (OUTLIER) cc_final: 0.4821 (t80) REVERT: F 467 TRP cc_start: 0.2674 (t-100) cc_final: 0.1784 (t-100) REVERT: F 478 TRP cc_start: 0.4269 (t-100) cc_final: 0.3893 (m100) REVERT: F 505 MET cc_start: 0.2682 (mtm) cc_final: 0.1913 (mmt) REVERT: F 565 TYR cc_start: 0.4399 (t80) cc_final: 0.3895 (t80) REVERT: F 568 PHE cc_start: 0.6553 (p90) cc_final: 0.6270 (t80) REVERT: F 937 LEU cc_start: 0.8557 (mt) cc_final: 0.7990 (pp) REVERT: G 205 MET cc_start: 0.7894 (tpp) cc_final: 0.7609 (tpp) REVERT: G 255 TYR cc_start: 0.8457 (m-80) cc_final: 0.8201 (m-80) REVERT: G 339 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8637 (mtmt) REVERT: G 384 LYS cc_start: 0.7572 (tptp) cc_final: 0.7282 (ttmt) REVERT: G 406 PHE cc_start: 0.7023 (OUTLIER) cc_final: 0.6480 (m-10) REVERT: G 952 ASN cc_start: 0.7898 (t0) cc_final: 0.7556 (t0) REVERT: G 980 ASP cc_start: 0.6916 (t0) cc_final: 0.6482 (t0) REVERT: G 984 LEU cc_start: 0.8333 (tt) cc_final: 0.8034 (mt) REVERT: H 277 MET cc_start: 0.2047 (mtm) cc_final: 0.1475 (ttm) REVERT: H 505 MET cc_start: 0.2647 (mtm) cc_final: 0.1860 (mmt) REVERT: H 565 TYR cc_start: 0.4261 (t80) cc_final: 0.3837 (t80) REVERT: H 980 ASP cc_start: 0.7368 (p0) cc_final: 0.7125 (p0) outliers start: 67 outliers final: 40 residues processed: 575 average time/residue: 0.4654 time to fit residues: 467.3500 Evaluate side-chains 527 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 484 time to evaluate : 4.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 367 HIS Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 927 LYS Chi-restraints excluded: chain D residue 962 SER Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 446 PHE Chi-restraints excluded: chain E residue 655 ILE Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 755 ASP Chi-restraints excluded: chain E residue 965 LEU Chi-restraints excluded: chain E residue 1008 MET Chi-restraints excluded: chain F residue 382 PHE Chi-restraints excluded: chain F residue 446 PHE Chi-restraints excluded: chain F residue 736 VAL Chi-restraints excluded: chain F residue 929 ILE Chi-restraints excluded: chain G residue 406 PHE Chi-restraints excluded: chain G residue 736 VAL Chi-restraints excluded: chain G residue 752 SER Chi-restraints excluded: chain G residue 869 ASP Chi-restraints excluded: chain G residue 927 LYS Chi-restraints excluded: chain G residue 962 SER Chi-restraints excluded: chain H residue 446 PHE Chi-restraints excluded: chain H residue 526 GLN Chi-restraints excluded: chain H residue 736 VAL Chi-restraints excluded: chain H residue 984 LEU Chi-restraints excluded: chain H residue 1008 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 534 optimal weight: 9.9990 chunk 364 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 477 optimal weight: 4.9990 chunk 264 optimal weight: 30.0000 chunk 547 optimal weight: 5.9990 chunk 443 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 chunk 576 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN A 434 GLN B 220 HIS C 771 ASN ** D 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 HIS E 808 ASN ** F 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 771 ASN F 845 GLN G 686 ASN H 808 ASN H 922 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 54196 Z= 0.395 Angle : 0.684 11.152 73004 Z= 0.344 Chirality : 0.043 0.186 8316 Planarity : 0.004 0.052 9212 Dihedral : 4.564 22.311 7124 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.82 % Favored : 92.12 % Rotamer: Outliers : 1.93 % Allowed : 7.60 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.10), residues: 6548 helix: 0.31 (0.09), residues: 3036 sheet: -1.56 (0.20), residues: 688 loop : -1.19 (0.12), residues: 2824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 467 HIS 0.010 0.001 HIS E 465 PHE 0.018 0.002 PHE G 224 TYR 0.030 0.002 TYR D 136 ARG 0.006 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 517 time to evaluate : 4.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.8090 (tpp) cc_final: 0.7776 (tpt) REVERT: A 238 LYS cc_start: 0.7985 (tptp) cc_final: 0.7538 (ttpp) REVERT: A 249 TYR cc_start: 0.8476 (m-80) cc_final: 0.8175 (m-80) REVERT: A 406 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.6792 (m-10) REVERT: A 952 ASN cc_start: 0.8043 (t0) cc_final: 0.7687 (t0) REVERT: B 204 LYS cc_start: 0.7290 (tptp) cc_final: 0.6888 (ptmm) REVERT: B 239 MET cc_start: 0.8705 (tpp) cc_final: 0.8430 (tpp) REVERT: B 406 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6881 (m-10) REVERT: B 952 ASN cc_start: 0.8023 (t0) cc_final: 0.7706 (t0) REVERT: C 277 MET cc_start: 0.2044 (mtm) cc_final: 0.1243 (ttm) REVERT: C 467 TRP cc_start: 0.2803 (t-100) cc_final: 0.2440 (t-100) REVERT: C 478 TRP cc_start: 0.4347 (t-100) cc_final: 0.4054 (m100) REVERT: C 505 MET cc_start: 0.3174 (mtm) cc_final: 0.2267 (mmt) REVERT: C 664 MET cc_start: 0.8339 (mmt) cc_final: 0.8017 (tpp) REVERT: C 671 GLU cc_start: 0.8933 (tt0) cc_final: 0.8726 (tm-30) REVERT: D 238 LYS cc_start: 0.7924 (tptp) cc_final: 0.7444 (ttpp) REVERT: D 820 VAL cc_start: 0.8795 (p) cc_final: 0.8547 (m) REVERT: D 952 ASN cc_start: 0.8090 (t0) cc_final: 0.7720 (t0) REVERT: E 277 MET cc_start: 0.1717 (mtm) cc_final: 0.1223 (ttm) REVERT: E 478 TRP cc_start: 0.4674 (t-100) cc_final: 0.4420 (m100) REVERT: E 565 TYR cc_start: 0.4509 (t80) cc_final: 0.4291 (t80) REVERT: E 637 MET cc_start: 0.5196 (ptp) cc_final: 0.4878 (ptp) REVERT: E 812 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6689 (m-30) REVERT: F 277 MET cc_start: 0.1841 (mtm) cc_final: 0.1547 (ttm) REVERT: F 382 PHE cc_start: 0.5065 (OUTLIER) cc_final: 0.4785 (t80) REVERT: F 467 TRP cc_start: 0.2578 (t-100) cc_final: 0.2145 (t-100) REVERT: F 478 TRP cc_start: 0.4351 (t-100) cc_final: 0.4002 (m100) REVERT: F 505 MET cc_start: 0.2961 (mtm) cc_final: 0.2175 (mmt) REVERT: F 565 TYR cc_start: 0.4746 (t80) cc_final: 0.4259 (t80) REVERT: F 812 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6597 (m-30) REVERT: F 1011 ASN cc_start: 0.7416 (p0) cc_final: 0.7116 (p0) REVERT: G 205 MET cc_start: 0.7945 (tpp) cc_final: 0.7660 (tpp) REVERT: G 406 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.6565 (m-10) REVERT: G 952 ASN cc_start: 0.8083 (t0) cc_final: 0.7731 (t0) REVERT: G 980 ASP cc_start: 0.7142 (t0) cc_final: 0.6745 (t0) REVERT: H 277 MET cc_start: 0.2039 (mtm) cc_final: 0.1406 (ttm) REVERT: H 505 MET cc_start: 0.2683 (mtm) cc_final: 0.1925 (mmt) REVERT: H 565 TYR cc_start: 0.4430 (t80) cc_final: 0.4031 (t80) outliers start: 117 outliers final: 76 residues processed: 582 average time/residue: 0.4637 time to fit residues: 472.6482 Evaluate side-chains 567 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 485 time to evaluate : 4.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 755 ASP Chi-restraints excluded: chain B residue 820 VAL Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 568 PHE Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 755 ASP Chi-restraints excluded: chain C residue 786 CYS Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 812 ASP Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 910 THR Chi-restraints excluded: chain D residue 927 LYS Chi-restraints excluded: chain D residue 962 SER Chi-restraints excluded: chain D residue 983 ASP Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 446 PHE Chi-restraints excluded: chain E residue 655 ILE Chi-restraints excluded: chain E residue 678 SER Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 755 ASP Chi-restraints excluded: chain E residue 786 CYS Chi-restraints excluded: chain E residue 812 ASP Chi-restraints excluded: chain E residue 965 LEU Chi-restraints excluded: chain E residue 1008 MET Chi-restraints excluded: chain F residue 382 PHE Chi-restraints excluded: chain F residue 446 PHE Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 736 VAL Chi-restraints excluded: chain F residue 755 ASP Chi-restraints excluded: chain F residue 786 CYS Chi-restraints excluded: chain F residue 812 ASP Chi-restraints excluded: chain F residue 929 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 406 PHE Chi-restraints excluded: chain G residue 525 PHE Chi-restraints excluded: chain G residue 736 VAL Chi-restraints excluded: chain G residue 755 ASP Chi-restraints excluded: chain G residue 812 ASP Chi-restraints excluded: chain G residue 820 VAL Chi-restraints excluded: chain G residue 826 LEU Chi-restraints excluded: chain G residue 869 ASP Chi-restraints excluded: chain G residue 910 THR Chi-restraints excluded: chain G residue 927 LYS Chi-restraints excluded: chain G residue 962 SER Chi-restraints excluded: chain G residue 966 THR Chi-restraints excluded: chain H residue 446 PHE Chi-restraints excluded: chain H residue 684 LEU Chi-restraints excluded: chain H residue 736 VAL Chi-restraints excluded: chain H residue 755 ASP Chi-restraints excluded: chain H residue 786 CYS Chi-restraints excluded: chain H residue 922 ASN Chi-restraints excluded: chain H residue 1008 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 215 optimal weight: 5.9990 chunk 577 optimal weight: 0.0970 chunk 126 optimal weight: 9.9990 chunk 376 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 642 optimal weight: 1.9990 chunk 533 optimal weight: 10.0000 chunk 297 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 212 optimal weight: 6.9990 chunk 337 optimal weight: 50.0000 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS C 465 HIS ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 808 ASN G 771 ASN H 808 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 54196 Z= 0.259 Angle : 0.613 12.593 73004 Z= 0.309 Chirality : 0.040 0.210 8316 Planarity : 0.004 0.051 9212 Dihedral : 4.404 21.641 7124 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.55 % Allowed : 8.71 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.10), residues: 6548 helix: 0.40 (0.09), residues: 3048 sheet: -1.69 (0.20), residues: 684 loop : -1.20 (0.12), residues: 2816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 467 HIS 0.011 0.001 HIS C 465 PHE 0.016 0.001 PHE G 224 TYR 0.028 0.002 TYR G 565 ARG 0.006 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 522 time to evaluate : 4.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.7986 (tpp) cc_final: 0.7755 (tpt) REVERT: A 238 LYS cc_start: 0.8015 (tptp) cc_final: 0.7528 (ttpp) REVERT: A 406 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.6816 (m-10) REVERT: A 952 ASN cc_start: 0.8040 (t0) cc_final: 0.7666 (t0) REVERT: A 1033 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7195 (pt0) REVERT: B 204 LYS cc_start: 0.7266 (tptp) cc_final: 0.6837 (ptmm) REVERT: B 239 MET cc_start: 0.8675 (tpp) cc_final: 0.8363 (tpp) REVERT: B 343 GLU cc_start: 0.7631 (tt0) cc_final: 0.7241 (tt0) REVERT: B 406 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6865 (m-10) REVERT: B 408 MET cc_start: 0.7870 (ptp) cc_final: 0.7639 (ptm) REVERT: B 952 ASN cc_start: 0.8020 (t0) cc_final: 0.7655 (t0) REVERT: C 277 MET cc_start: 0.1917 (mtm) cc_final: 0.1158 (ttm) REVERT: C 478 TRP cc_start: 0.4378 (t-100) cc_final: 0.4097 (m100) REVERT: C 505 MET cc_start: 0.3200 (mtm) cc_final: 0.2394 (mmt) REVERT: C 671 GLU cc_start: 0.8861 (tt0) cc_final: 0.8635 (tm-30) REVERT: C 672 ASN cc_start: 0.8208 (m-40) cc_final: 0.7318 (m-40) REVERT: C 755 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: D 238 LYS cc_start: 0.7838 (tptp) cc_final: 0.7406 (ttpp) REVERT: D 820 VAL cc_start: 0.8731 (p) cc_final: 0.8443 (m) REVERT: D 952 ASN cc_start: 0.8063 (t0) cc_final: 0.7701 (t0) REVERT: D 984 LEU cc_start: 0.8417 (tt) cc_final: 0.8118 (mt) REVERT: E 277 MET cc_start: 0.1748 (mtm) cc_final: 0.1343 (ttm) REVERT: E 478 TRP cc_start: 0.4679 (t-100) cc_final: 0.4430 (m100) REVERT: E 812 ASP cc_start: 0.6996 (m-30) cc_final: 0.6612 (m-30) REVERT: F 382 PHE cc_start: 0.5031 (OUTLIER) cc_final: 0.4793 (t80) REVERT: F 478 TRP cc_start: 0.4399 (t-100) cc_final: 0.4056 (m100) REVERT: F 505 MET cc_start: 0.2866 (mtm) cc_final: 0.2111 (mmt) REVERT: F 565 TYR cc_start: 0.4717 (t80) cc_final: 0.4286 (t80) REVERT: G 205 MET cc_start: 0.7917 (tpp) cc_final: 0.7674 (tpp) REVERT: G 255 TYR cc_start: 0.8591 (m-80) cc_final: 0.8292 (m-80) REVERT: G 406 PHE cc_start: 0.7009 (OUTLIER) cc_final: 0.6588 (m-10) REVERT: G 557 ASP cc_start: 0.7029 (t0) cc_final: 0.6741 (t0) REVERT: G 559 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8485 (p) REVERT: G 952 ASN cc_start: 0.8028 (t0) cc_final: 0.7658 (t0) REVERT: G 980 ASP cc_start: 0.7004 (t0) cc_final: 0.6608 (t0) REVERT: H 277 MET cc_start: 0.2000 (mtm) cc_final: 0.1367 (ttm) REVERT: H 505 MET cc_start: 0.2966 (mtm) cc_final: 0.2227 (mmt) REVERT: H 565 TYR cc_start: 0.4495 (t80) cc_final: 0.4139 (t80) REVERT: H 664 MET cc_start: 0.8767 (mmt) cc_final: 0.8540 (tpp) outliers start: 94 outliers final: 65 residues processed: 567 average time/residue: 0.4812 time to fit residues: 477.8785 Evaluate side-chains 560 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 488 time to evaluate : 4.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 568 PHE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 755 ASP Chi-restraints excluded: chain C residue 812 ASP Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 812 ASP Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 910 THR Chi-restraints excluded: chain D residue 927 LYS Chi-restraints excluded: chain D residue 962 SER Chi-restraints excluded: chain D residue 983 ASP Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 446 PHE Chi-restraints excluded: chain E residue 664 MET Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 755 ASP Chi-restraints excluded: chain E residue 929 ILE Chi-restraints excluded: chain E residue 965 LEU Chi-restraints excluded: chain E residue 1008 MET Chi-restraints excluded: chain F residue 382 PHE Chi-restraints excluded: chain F residue 446 PHE Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 736 VAL Chi-restraints excluded: chain F residue 755 ASP Chi-restraints excluded: chain F residue 929 ILE Chi-restraints excluded: chain G residue 406 PHE Chi-restraints excluded: chain G residue 525 PHE Chi-restraints excluded: chain G residue 559 THR Chi-restraints excluded: chain G residue 655 ILE Chi-restraints excluded: chain G residue 736 VAL Chi-restraints excluded: chain G residue 755 ASP Chi-restraints excluded: chain G residue 869 ASP Chi-restraints excluded: chain G residue 910 THR Chi-restraints excluded: chain G residue 927 LYS Chi-restraints excluded: chain G residue 962 SER Chi-restraints excluded: chain G residue 966 THR Chi-restraints excluded: chain H residue 446 PHE Chi-restraints excluded: chain H residue 684 LEU Chi-restraints excluded: chain H residue 736 VAL Chi-restraints excluded: chain H residue 755 ASP Chi-restraints excluded: chain H residue 786 CYS Chi-restraints excluded: chain H residue 922 ASN Chi-restraints excluded: chain H residue 1008 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 619 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 366 optimal weight: 1.9990 chunk 469 optimal weight: 2.9990 chunk 363 optimal weight: 5.9990 chunk 540 optimal weight: 7.9990 chunk 358 optimal weight: 10.0000 chunk 639 optimal weight: 0.7980 chunk 400 optimal weight: 3.9990 chunk 390 optimal weight: 2.9990 chunk 295 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1022 GLN D 402 ASN E 314 HIS H 314 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 54196 Z= 0.192 Angle : 0.587 13.549 73004 Z= 0.294 Chirality : 0.039 0.211 8316 Planarity : 0.003 0.051 9212 Dihedral : 4.234 21.435 7124 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.37 % Allowed : 9.68 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.11), residues: 6548 helix: 0.50 (0.09), residues: 3072 sheet: -1.79 (0.20), residues: 696 loop : -1.13 (0.12), residues: 2780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 467 HIS 0.004 0.001 HIS F 465 PHE 0.019 0.001 PHE F1032 TYR 0.027 0.001 TYR D 572 ARG 0.008 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 530 time to evaluate : 4.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.7920 (tpp) cc_final: 0.7718 (tpt) REVERT: A 238 LYS cc_start: 0.7952 (tptp) cc_final: 0.7429 (ttpp) REVERT: A 249 TYR cc_start: 0.8434 (m-80) cc_final: 0.8066 (m-80) REVERT: A 406 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6779 (m-10) REVERT: A 533 TYR cc_start: 0.7283 (t80) cc_final: 0.6607 (t80) REVERT: A 952 ASN cc_start: 0.8010 (t0) cc_final: 0.7650 (t0) REVERT: B 204 LYS cc_start: 0.7159 (tptp) cc_final: 0.6769 (ptmm) REVERT: B 239 MET cc_start: 0.8690 (tpp) cc_final: 0.8324 (tpp) REVERT: B 406 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6873 (m-10) REVERT: B 559 THR cc_start: 0.8604 (m) cc_final: 0.8307 (p) REVERT: B 952 ASN cc_start: 0.7960 (t0) cc_final: 0.7620 (t0) REVERT: C 277 MET cc_start: 0.1862 (mtm) cc_final: 0.1146 (ttm) REVERT: C 467 TRP cc_start: 0.2999 (t-100) cc_final: 0.2216 (t-100) REVERT: C 478 TRP cc_start: 0.4371 (t-100) cc_final: 0.4115 (m100) REVERT: C 505 MET cc_start: 0.3068 (mtm) cc_final: 0.2334 (mmt) REVERT: C 664 MET cc_start: 0.8587 (mmt) cc_final: 0.8206 (tpp) REVERT: C 755 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: C 980 ASP cc_start: 0.7205 (p0) cc_final: 0.6957 (p0) REVERT: D 238 LYS cc_start: 0.7863 (tptp) cc_final: 0.7321 (ttpp) REVERT: D 239 MET cc_start: 0.8593 (ttp) cc_final: 0.8284 (ttm) REVERT: D 820 VAL cc_start: 0.8600 (p) cc_final: 0.8310 (m) REVERT: D 952 ASN cc_start: 0.7980 (t0) cc_final: 0.7636 (t0) REVERT: D 984 LEU cc_start: 0.8404 (tt) cc_final: 0.8126 (mt) REVERT: E 277 MET cc_start: 0.1668 (mtm) cc_final: 0.1339 (ttm) REVERT: E 467 TRP cc_start: 0.3020 (t-100) cc_final: 0.2200 (t60) REVERT: E 478 TRP cc_start: 0.4674 (t-100) cc_final: 0.4452 (m100) REVERT: E 527 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6123 (pt0) REVERT: E 664 MET cc_start: 0.8586 (mmm) cc_final: 0.8229 (tpp) REVERT: E 812 ASP cc_start: 0.6952 (m-30) cc_final: 0.6560 (m-30) REVERT: E 980 ASP cc_start: 0.7257 (p0) cc_final: 0.6978 (p0) REVERT: F 382 PHE cc_start: 0.5055 (OUTLIER) cc_final: 0.4788 (t80) REVERT: F 408 MET cc_start: 0.3990 (tmm) cc_final: 0.3629 (ptt) REVERT: F 467 TRP cc_start: 0.2883 (t-100) cc_final: 0.2184 (t-100) REVERT: F 478 TRP cc_start: 0.4452 (t-100) cc_final: 0.4115 (m100) REVERT: F 505 MET cc_start: 0.2700 (mtm) cc_final: 0.2023 (mmt) REVERT: G 406 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.6463 (m-10) REVERT: G 408 MET cc_start: 0.8064 (ptp) cc_final: 0.6828 (mmt) REVERT: G 505 MET cc_start: 0.2218 (mtp) cc_final: 0.2008 (mtm) REVERT: G 533 TYR cc_start: 0.7167 (t80) cc_final: 0.6545 (t80) REVERT: G 557 ASP cc_start: 0.6958 (t0) cc_final: 0.6634 (t0) REVERT: G 559 THR cc_start: 0.8746 (m) cc_final: 0.8410 (p) REVERT: G 952 ASN cc_start: 0.7979 (t0) cc_final: 0.7629 (t0) REVERT: G 980 ASP cc_start: 0.6919 (t0) cc_final: 0.6526 (t0) REVERT: H 277 MET cc_start: 0.1910 (mtm) cc_final: 0.1584 (ttm) REVERT: H 505 MET cc_start: 0.2747 (mtm) cc_final: 0.2085 (mmt) REVERT: H 565 TYR cc_start: 0.4499 (t80) cc_final: 0.3963 (t80) REVERT: H 637 MET cc_start: 0.4526 (OUTLIER) cc_final: 0.4186 (ptt) outliers start: 83 outliers final: 56 residues processed: 574 average time/residue: 0.4655 time to fit residues: 467.1001 Evaluate side-chains 548 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 486 time to evaluate : 4.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 755 ASP Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 910 THR Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 962 SER Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 446 PHE Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 755 ASP Chi-restraints excluded: chain E residue 965 LEU Chi-restraints excluded: chain E residue 1008 MET Chi-restraints excluded: chain F residue 382 PHE Chi-restraints excluded: chain F residue 446 PHE Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 736 VAL Chi-restraints excluded: chain F residue 755 ASP Chi-restraints excluded: chain F residue 786 CYS Chi-restraints excluded: chain F residue 929 ILE Chi-restraints excluded: chain G residue 406 PHE Chi-restraints excluded: chain G residue 525 PHE Chi-restraints excluded: chain G residue 736 VAL Chi-restraints excluded: chain G residue 820 VAL Chi-restraints excluded: chain G residue 826 LEU Chi-restraints excluded: chain G residue 869 ASP Chi-restraints excluded: chain G residue 910 THR Chi-restraints excluded: chain G residue 927 LYS Chi-restraints excluded: chain G residue 962 SER Chi-restraints excluded: chain H residue 446 PHE Chi-restraints excluded: chain H residue 637 MET Chi-restraints excluded: chain H residue 736 VAL Chi-restraints excluded: chain H residue 786 CYS Chi-restraints excluded: chain H residue 943 LEU Chi-restraints excluded: chain H residue 1008 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 395 optimal weight: 2.9990 chunk 255 optimal weight: 0.1980 chunk 382 optimal weight: 5.9990 chunk 192 optimal weight: 20.0000 chunk 125 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 406 optimal weight: 0.9980 chunk 436 optimal weight: 20.0000 chunk 316 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 503 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN B 220 HIS C 672 ASN ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 771 ASN G1022 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 54196 Z= 0.175 Angle : 0.582 14.571 73004 Z= 0.290 Chirality : 0.039 0.210 8316 Planarity : 0.003 0.051 9212 Dihedral : 4.138 22.430 7124 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 1.34 % Allowed : 10.19 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.11), residues: 6548 helix: 0.57 (0.10), residues: 3076 sheet: -1.79 (0.20), residues: 696 loop : -1.10 (0.12), residues: 2776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 467 HIS 0.004 0.001 HIS F 465 PHE 0.015 0.001 PHE B 568 TYR 0.032 0.001 TYR D 572 ARG 0.011 0.000 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 513 time to evaluate : 4.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.7923 (tpp) cc_final: 0.7686 (tpt) REVERT: A 238 LYS cc_start: 0.7864 (tptp) cc_final: 0.7361 (ttpp) REVERT: A 249 TYR cc_start: 0.8433 (m-80) cc_final: 0.8188 (m-80) REVERT: A 406 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6776 (m-10) REVERT: A 952 ASN cc_start: 0.7966 (t0) cc_final: 0.7625 (t0) REVERT: B 408 MET cc_start: 0.7946 (ptp) cc_final: 0.7691 (ptm) REVERT: B 559 THR cc_start: 0.8577 (m) cc_final: 0.8258 (p) REVERT: B 952 ASN cc_start: 0.7925 (t0) cc_final: 0.7599 (t0) REVERT: B 1033 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.6752 (pt0) REVERT: C 240 MET cc_start: 0.2205 (tpt) cc_final: 0.0932 (mpp) REVERT: C 277 MET cc_start: 0.1812 (mtm) cc_final: 0.1245 (ttm) REVERT: C 467 TRP cc_start: 0.2984 (t-100) cc_final: 0.2236 (t-100) REVERT: C 478 TRP cc_start: 0.4380 (t-100) cc_final: 0.4166 (m100) REVERT: C 505 MET cc_start: 0.3022 (mtm) cc_final: 0.2261 (mmt) REVERT: C 664 MET cc_start: 0.8538 (mmt) cc_final: 0.8165 (tpp) REVERT: C 980 ASP cc_start: 0.7188 (p0) cc_final: 0.6941 (p0) REVERT: D 238 LYS cc_start: 0.7799 (tptp) cc_final: 0.7127 (ttpp) REVERT: D 343 GLU cc_start: 0.7591 (tt0) cc_final: 0.7256 (tt0) REVERT: D 820 VAL cc_start: 0.8535 (p) cc_final: 0.8228 (m) REVERT: D 952 ASN cc_start: 0.7978 (t0) cc_final: 0.7635 (t0) REVERT: D 984 LEU cc_start: 0.8428 (tt) cc_final: 0.8204 (mt) REVERT: E 277 MET cc_start: 0.1628 (mtm) cc_final: 0.1313 (ttm) REVERT: E 467 TRP cc_start: 0.2950 (t-100) cc_final: 0.2274 (t60) REVERT: E 478 TRP cc_start: 0.4726 (t-100) cc_final: 0.4513 (m100) REVERT: E 527 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6110 (pt0) REVERT: E 664 MET cc_start: 0.8525 (mmm) cc_final: 0.8184 (tpp) REVERT: E 812 ASP cc_start: 0.6945 (m-30) cc_final: 0.6563 (m-30) REVERT: E 980 ASP cc_start: 0.7251 (p0) cc_final: 0.6977 (p0) REVERT: F 382 PHE cc_start: 0.5094 (OUTLIER) cc_final: 0.4755 (t80) REVERT: F 408 MET cc_start: 0.3974 (tmm) cc_final: 0.3508 (ptt) REVERT: F 467 TRP cc_start: 0.2888 (t-100) cc_final: 0.2239 (t-100) REVERT: F 478 TRP cc_start: 0.4464 (t-100) cc_final: 0.4191 (m100) REVERT: F 505 MET cc_start: 0.2703 (mtm) cc_final: 0.2006 (mmt) REVERT: F 937 LEU cc_start: 0.8552 (mt) cc_final: 0.7980 (pp) REVERT: F 948 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8128 (mt) REVERT: G 254 ASP cc_start: 0.6989 (m-30) cc_final: 0.6659 (p0) REVERT: G 266 LEU cc_start: 0.8023 (mt) cc_final: 0.7806 (tp) REVERT: G 406 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6459 (m-10) REVERT: G 533 TYR cc_start: 0.7017 (t80) cc_final: 0.6499 (t80) REVERT: G 952 ASN cc_start: 0.7953 (t0) cc_final: 0.7610 (t0) REVERT: G 980 ASP cc_start: 0.6962 (t0) cc_final: 0.6555 (t0) REVERT: H 277 MET cc_start: 0.1909 (mtm) cc_final: 0.1500 (ttm) REVERT: H 505 MET cc_start: 0.2816 (mtm) cc_final: 0.2135 (mmt) REVERT: H 565 TYR cc_start: 0.4574 (t80) cc_final: 0.4029 (t80) REVERT: H 637 MET cc_start: 0.4515 (OUTLIER) cc_final: 0.4181 (ptt) REVERT: H 664 MET cc_start: 0.8961 (tpp) cc_final: 0.8661 (mmt) REVERT: H 765 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8379 (tp) REVERT: H 980 ASP cc_start: 0.7269 (p0) cc_final: 0.6969 (p0) outliers start: 81 outliers final: 59 residues processed: 556 average time/residue: 0.4592 time to fit residues: 448.5755 Evaluate side-chains 549 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 483 time to evaluate : 4.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 820 VAL Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 1033 GLU Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 568 PHE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 962 SER Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 437 LYS Chi-restraints excluded: chain E residue 446 PHE Chi-restraints excluded: chain E residue 965 LEU Chi-restraints excluded: chain E residue 1008 MET Chi-restraints excluded: chain F residue 382 PHE Chi-restraints excluded: chain F residue 446 PHE Chi-restraints excluded: chain F residue 568 PHE Chi-restraints excluded: chain F residue 736 VAL Chi-restraints excluded: chain F residue 755 ASP Chi-restraints excluded: chain F residue 786 CYS Chi-restraints excluded: chain F residue 929 ILE Chi-restraints excluded: chain F residue 948 LEU Chi-restraints excluded: chain G residue 406 PHE Chi-restraints excluded: chain G residue 525 PHE Chi-restraints excluded: chain G residue 736 VAL Chi-restraints excluded: chain G residue 820 VAL Chi-restraints excluded: chain G residue 826 LEU Chi-restraints excluded: chain G residue 869 ASP Chi-restraints excluded: chain G residue 910 THR Chi-restraints excluded: chain G residue 927 LYS Chi-restraints excluded: chain G residue 948 LEU Chi-restraints excluded: chain G residue 962 SER Chi-restraints excluded: chain H residue 446 PHE Chi-restraints excluded: chain H residue 637 MET Chi-restraints excluded: chain H residue 736 VAL Chi-restraints excluded: chain H residue 765 LEU Chi-restraints excluded: chain H residue 786 CYS Chi-restraints excluded: chain H residue 943 LEU Chi-restraints excluded: chain H residue 1008 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 582 optimal weight: 20.0000 chunk 613 optimal weight: 0.4980 chunk 559 optimal weight: 0.9990 chunk 596 optimal weight: 3.9990 chunk 612 optimal weight: 0.4980 chunk 358 optimal weight: 4.9990 chunk 259 optimal weight: 6.9990 chunk 468 optimal weight: 0.9990 chunk 183 optimal weight: 50.0000 chunk 538 optimal weight: 0.3980 chunk 564 optimal weight: 2.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 GLN B 220 HIS B 425 GLN B 602 GLN C 672 ASN ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 54196 Z= 0.151 Angle : 0.577 14.491 73004 Z= 0.287 Chirality : 0.038 0.263 8316 Planarity : 0.003 0.050 9212 Dihedral : 4.017 21.381 7124 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.11 % Allowed : 10.59 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.11), residues: 6548 helix: 0.73 (0.10), residues: 3072 sheet: -1.76 (0.20), residues: 692 loop : -1.08 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 467 HIS 0.004 0.000 HIS F 465 PHE 0.019 0.001 PHE E 568 TYR 0.039 0.001 TYR D 572 ARG 0.007 0.000 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 530 time to evaluate : 4.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.7813 (tpp) cc_final: 0.7585 (tpt) REVERT: A 238 LYS cc_start: 0.7828 (tptp) cc_final: 0.7258 (ttpp) REVERT: A 406 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.6820 (m-10) REVERT: A 952 ASN cc_start: 0.7921 (t0) cc_final: 0.7615 (t0) REVERT: B 249 TYR cc_start: 0.8491 (m-80) cc_final: 0.8191 (m-80) REVERT: B 408 MET cc_start: 0.7910 (ptp) cc_final: 0.7647 (ptm) REVERT: B 559 THR cc_start: 0.8508 (m) cc_final: 0.8213 (p) REVERT: B 952 ASN cc_start: 0.7880 (t0) cc_final: 0.7574 (t0) REVERT: B 1033 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.6805 (pt0) REVERT: C 277 MET cc_start: 0.1776 (mtm) cc_final: 0.1219 (ttm) REVERT: C 467 TRP cc_start: 0.3137 (t-100) cc_final: 0.2425 (t-100) REVERT: C 505 MET cc_start: 0.2961 (mtm) cc_final: 0.2217 (mmt) REVERT: C 664 MET cc_start: 0.8500 (mmt) cc_final: 0.8150 (tpp) REVERT: C 812 ASP cc_start: 0.6904 (m-30) cc_final: 0.6545 (m-30) REVERT: C 965 LEU cc_start: 0.9131 (mm) cc_final: 0.8910 (mp) REVERT: C 980 ASP cc_start: 0.7107 (p0) cc_final: 0.6792 (p0) REVERT: D 238 LYS cc_start: 0.7679 (tptp) cc_final: 0.7284 (ttpp) REVERT: D 820 VAL cc_start: 0.8356 (p) cc_final: 0.8055 (m) REVERT: D 952 ASN cc_start: 0.7903 (t0) cc_final: 0.7608 (t0) REVERT: D 984 LEU cc_start: 0.8347 (tt) cc_final: 0.8038 (mp) REVERT: E 277 MET cc_start: 0.1586 (mtm) cc_final: 0.1304 (ttm) REVERT: E 527 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6085 (pt0) REVERT: E 565 TYR cc_start: 0.4836 (t80) cc_final: 0.4526 (t80) REVERT: E 664 MET cc_start: 0.8504 (mmm) cc_final: 0.8191 (tpp) REVERT: E 812 ASP cc_start: 0.6852 (m-30) cc_final: 0.6484 (m-30) REVERT: E 980 ASP cc_start: 0.7221 (p0) cc_final: 0.6929 (p0) REVERT: E 987 MET cc_start: 0.8378 (mmt) cc_final: 0.8139 (mmm) REVERT: F 382 PHE cc_start: 0.5291 (OUTLIER) cc_final: 0.5043 (t80) REVERT: F 408 MET cc_start: 0.4083 (tmm) cc_final: 0.3415 (ptt) REVERT: F 467 TRP cc_start: 0.2950 (t-100) cc_final: 0.2333 (t-100) REVERT: F 478 TRP cc_start: 0.4581 (t-100) cc_final: 0.4335 (m100) REVERT: F 505 MET cc_start: 0.2729 (mtm) cc_final: 0.2022 (mmt) REVERT: F 812 ASP cc_start: 0.6848 (m-30) cc_final: 0.6558 (m-30) REVERT: F 937 LEU cc_start: 0.8516 (mt) cc_final: 0.7960 (pp) REVERT: G 254 ASP cc_start: 0.6854 (m-30) cc_final: 0.6628 (p0) REVERT: G 255 TYR cc_start: 0.8337 (m-80) cc_final: 0.8050 (m-80) REVERT: G 406 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6682 (m-80) REVERT: G 533 TYR cc_start: 0.6977 (t80) cc_final: 0.6405 (t80) REVERT: G 559 THR cc_start: 0.8754 (m) cc_final: 0.8358 (p) REVERT: G 952 ASN cc_start: 0.7888 (t0) cc_final: 0.7639 (t0) REVERT: G 980 ASP cc_start: 0.6879 (t0) cc_final: 0.6462 (t0) REVERT: H 240 MET cc_start: 0.2095 (tpt) cc_final: 0.0921 (mpp) REVERT: H 277 MET cc_start: 0.1884 (mtm) cc_final: 0.1486 (ttm) REVERT: H 505 MET cc_start: 0.2898 (mtm) cc_final: 0.2253 (mmt) REVERT: H 565 TYR cc_start: 0.4537 (t80) cc_final: 0.4000 (t80) REVERT: H 664 MET cc_start: 0.8973 (tpp) cc_final: 0.8652 (mmt) REVERT: H 980 ASP cc_start: 0.7246 (p0) cc_final: 0.6942 (p0) outliers start: 67 outliers final: 45 residues processed: 562 average time/residue: 0.4639 time to fit residues: 459.3905 Evaluate side-chains 539 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 490 time to evaluate : 4.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 1033 GLU Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 962 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 446 PHE Chi-restraints excluded: chain E residue 1008 MET Chi-restraints excluded: chain F residue 382 PHE Chi-restraints excluded: chain F residue 446 PHE Chi-restraints excluded: chain F residue 736 VAL Chi-restraints excluded: chain F residue 786 CYS Chi-restraints excluded: chain F residue 929 ILE Chi-restraints excluded: chain G residue 406 PHE Chi-restraints excluded: chain G residue 525 PHE Chi-restraints excluded: chain G residue 736 VAL Chi-restraints excluded: chain G residue 826 LEU Chi-restraints excluded: chain G residue 869 ASP Chi-restraints excluded: chain G residue 927 LYS Chi-restraints excluded: chain G residue 948 LEU Chi-restraints excluded: chain G residue 962 SER Chi-restraints excluded: chain H residue 446 PHE Chi-restraints excluded: chain H residue 736 VAL Chi-restraints excluded: chain H residue 786 CYS Chi-restraints excluded: chain H residue 943 LEU Chi-restraints excluded: chain H residue 1008 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 594 optimal weight: 50.0000 chunk 391 optimal weight: 1.9990 chunk 630 optimal weight: 9.9990 chunk 384 optimal weight: 8.9990 chunk 299 optimal weight: 0.9990 chunk 438 optimal weight: 40.0000 chunk 661 optimal weight: 8.9990 chunk 608 optimal weight: 0.9980 chunk 526 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 406 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN B 220 HIS C 314 HIS ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 54196 Z= 0.267 Angle : 0.633 13.741 73004 Z= 0.314 Chirality : 0.041 0.220 8316 Planarity : 0.004 0.052 9212 Dihedral : 4.219 22.234 7124 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 1.02 % Allowed : 11.30 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.11), residues: 6548 helix: 0.63 (0.10), residues: 3052 sheet: -1.87 (0.20), residues: 688 loop : -1.16 (0.12), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 467 HIS 0.006 0.001 HIS H 522 PHE 0.043 0.001 PHE E1032 TYR 0.048 0.002 TYR D 572 ARG 0.008 0.000 ARG A 675 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13096 Ramachandran restraints generated. 6548 Oldfield, 0 Emsley, 6548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 484 time to evaluate : 4.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.7908 (tpp) cc_final: 0.7699 (tpt) REVERT: A 238 LYS cc_start: 0.7779 (tptp) cc_final: 0.7396 (ttpp) REVERT: A 406 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.6712 (m-10) REVERT: A 952 ASN cc_start: 0.8006 (t0) cc_final: 0.7705 (t0) REVERT: B 204 LYS cc_start: 0.7080 (tptp) cc_final: 0.6696 (ptmm) REVERT: B 408 MET cc_start: 0.8353 (ptp) cc_final: 0.8101 (ptm) REVERT: B 559 THR cc_start: 0.8559 (m) cc_final: 0.8197 (p) REVERT: B 952 ASN cc_start: 0.7981 (t0) cc_final: 0.7683 (t0) REVERT: B 1033 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7172 (pt0) REVERT: C 240 MET cc_start: 0.2338 (tpt) cc_final: 0.1193 (mpp) REVERT: C 277 MET cc_start: 0.1841 (mtm) cc_final: 0.1272 (ttm) REVERT: C 467 TRP cc_start: 0.3157 (t-100) cc_final: 0.2446 (t-100) REVERT: C 505 MET cc_start: 0.2941 (mtm) cc_final: 0.2230 (mmt) REVERT: C 664 MET cc_start: 0.8501 (mmt) cc_final: 0.8139 (tpp) REVERT: C 980 ASP cc_start: 0.7299 (p0) cc_final: 0.7029 (p0) REVERT: D 238 LYS cc_start: 0.7694 (tptp) cc_final: 0.7205 (ttpp) REVERT: D 820 VAL cc_start: 0.8489 (p) cc_final: 0.8195 (m) REVERT: D 952 ASN cc_start: 0.7986 (t0) cc_final: 0.7708 (t0) REVERT: D 984 LEU cc_start: 0.8375 (tt) cc_final: 0.8050 (mp) REVERT: E 277 MET cc_start: 0.1665 (mtm) cc_final: 0.1283 (ttm) REVERT: E 664 MET cc_start: 0.8526 (mmm) cc_final: 0.8213 (tpp) REVERT: F 382 PHE cc_start: 0.5214 (OUTLIER) cc_final: 0.4983 (t80) REVERT: F 408 MET cc_start: 0.4186 (tmm) cc_final: 0.3463 (ptt) REVERT: F 467 TRP cc_start: 0.2981 (t-100) cc_final: 0.2382 (t-100) REVERT: F 478 TRP cc_start: 0.4650 (t-100) cc_final: 0.4414 (m100) REVERT: F 505 MET cc_start: 0.2746 (mtm) cc_final: 0.2090 (mmt) REVERT: G 149 GLN cc_start: 0.8025 (mt0) cc_final: 0.7751 (mm-40) REVERT: G 254 ASP cc_start: 0.7158 (m-30) cc_final: 0.6886 (p0) REVERT: G 406 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6601 (m-80) REVERT: G 533 TYR cc_start: 0.6977 (t80) cc_final: 0.6409 (t80) REVERT: G 820 VAL cc_start: 0.8754 (p) cc_final: 0.8518 (m) REVERT: G 952 ASN cc_start: 0.7983 (t0) cc_final: 0.7731 (t0) REVERT: G 980 ASP cc_start: 0.7016 (t0) cc_final: 0.6623 (t0) REVERT: H 240 MET cc_start: 0.1948 (tpt) cc_final: 0.0793 (mpp) REVERT: H 277 MET cc_start: 0.1964 (mtm) cc_final: 0.1579 (ttm) REVERT: H 505 MET cc_start: 0.2909 (mtm) cc_final: 0.2298 (mmt) REVERT: H 565 TYR cc_start: 0.4230 (t80) cc_final: 0.3683 (t80) REVERT: H 664 MET cc_start: 0.8993 (tpp) cc_final: 0.8668 (mmt) outliers start: 62 outliers final: 50 residues processed: 520 average time/residue: 0.4697 time to fit residues: 430.2596 Evaluate side-chains 524 residues out of total 6052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 470 time to evaluate : 4.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 820 VAL Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 1033 GLU Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 962 SER Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 437 LYS Chi-restraints excluded: chain E residue 446 PHE Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 1008 MET Chi-restraints excluded: chain F residue 382 PHE Chi-restraints excluded: chain F residue 446 PHE Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 736 VAL Chi-restraints excluded: chain F residue 786 CYS Chi-restraints excluded: chain F residue 929 ILE Chi-restraints excluded: chain F residue 1006 SER Chi-restraints excluded: chain G residue 406 PHE Chi-restraints excluded: chain G residue 525 PHE Chi-restraints excluded: chain G residue 736 VAL Chi-restraints excluded: chain G residue 752 SER Chi-restraints excluded: chain G residue 826 LEU Chi-restraints excluded: chain G residue 869 ASP Chi-restraints excluded: chain G residue 927 LYS Chi-restraints excluded: chain G residue 962 SER Chi-restraints excluded: chain H residue 446 PHE Chi-restraints excluded: chain H residue 736 VAL Chi-restraints excluded: chain H residue 786 CYS Chi-restraints excluded: chain H residue 943 LEU Chi-restraints excluded: chain H residue 1008 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 322 optimal weight: 1.9990 chunk 418 optimal weight: 8.9990 chunk 561 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 485 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 527 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 541 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 HIS C 808 ASN D 771 ASN F1002 ASN G 391 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.252152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.197169 restraints weight = 72030.528| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 2.28 r_work: 0.4049 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 54196 Z= 0.188 Angle : 0.603 14.117 73004 Z= 0.299 Chirality : 0.039 0.223 8316 Planarity : 0.003 0.051 9212 Dihedral : 4.117 21.218 7124 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.02 % Allowed : 11.45 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.11), residues: 6548 helix: 0.72 (0.10), residues: 3052 sheet: -1.88 (0.20), residues: 692 loop : -1.09 (0.12), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 467 HIS 0.004 0.001 HIS F 465 PHE 0.038 0.001 PHE E1032 TYR 0.049 0.001 TYR D 572 ARG 0.007 0.000 ARG A 675 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10490.18 seconds wall clock time: 185 minutes 57.82 seconds (11157.82 seconds total)