Starting phenix.real_space_refine on Tue Mar 19 02:04:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x29_21997/03_2024/6x29_21997.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x29_21997/03_2024/6x29_21997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x29_21997/03_2024/6x29_21997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x29_21997/03_2024/6x29_21997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x29_21997/03_2024/6x29_21997.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x29_21997/03_2024/6x29_21997.pdb" } resolution = 2.7 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= 0.003 sd= 0.084 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 105 5.16 5 C 14580 2.51 5 N 3786 2.21 5 O 4335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22806 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "B" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "C" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Time building chain proxies: 12.58, per 1000 atoms: 0.55 Number of scatterers: 22806 At special positions: 0 Unit cell: (129.93, 136.32, 171.465, 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 105 16.00 O 4335 8.00 N 3786 7.00 C 14580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 985 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS C 383 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS C 985 " distance=2.01 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 7.97 Conformation dependent library (CDL) restraints added in 4.5 seconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 54 sheets defined 25.7% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.638A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.764A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.209A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.501A pdb=" N LYS A 386 " --> pdb=" O CYS A 383 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.916A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.975A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.121A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.627A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.525A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.904A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.870A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.562A pdb=" N ALA A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 944 removed outlier: 3.602A pdb=" N ALA A 944 " --> pdb=" O THR A 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 941 through 944' Processing helix chain 'A' and resid 945 through 963 removed outlier: 3.862A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 968 Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.783A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.184A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.638A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.765A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.209A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.501A pdb=" N LYS B 386 " --> pdb=" O CYS B 383 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.916A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.976A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.121A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.627A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.526A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.905A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.870A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.563A pdb=" N ALA B 930 " --> pdb=" O GLN B 926 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 944 removed outlier: 3.603A pdb=" N ALA B 944 " --> pdb=" O THR B 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 941 through 944' Processing helix chain 'B' and resid 945 through 963 removed outlier: 3.861A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 968 Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.783A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.184A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.638A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.763A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.210A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.501A pdb=" N LYS C 386 " --> pdb=" O CYS C 383 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.915A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.977A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.121A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 759 through 783 removed outlier: 3.627A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.525A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.904A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.870A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.562A pdb=" N ALA C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 944 removed outlier: 3.603A pdb=" N ALA C 944 " --> pdb=" O THR C 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 941 through 944' Processing helix chain 'C' and resid 945 through 963 removed outlier: 3.861A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 968 Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.783A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.184A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.575A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.568A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.619A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.503A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.503A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 229 removed outlier: 5.681A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.516A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.763A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.251A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 539 removed outlier: 5.568A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.913A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.763A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.345A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.345A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.880A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.575A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.620A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 224 through 229 removed outlier: 5.682A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 118 through 121 removed outlier: 3.515A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.763A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AD2, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.251A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD4, first strand: chain 'B' and resid 538 through 539 removed outlier: 5.568A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.914A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.676A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.345A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.345A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE3, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.575A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.619A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.504A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.504A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 224 through 229 removed outlier: 5.680A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.515A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.762A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AF2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.250A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.913A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.346A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.346A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF9, first strand: chain 'C' and resid 1094 through 1097 790 hydrogen bonds defined for protein. 2145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.47 Time building geometry restraints manager: 8.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7351 1.35 - 1.47: 6097 1.47 - 1.60: 9733 1.60 - 1.73: 0 1.73 - 1.86: 129 Bond restraints: 23310 Sorted by residual: bond pdb=" CG LEU B 878 " pdb=" CD1 LEU B 878 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.22e+00 bond pdb=" CG LEU C 878 " pdb=" CD1 LEU C 878 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.13e+00 bond pdb=" CG LEU A 878 " pdb=" CD1 LEU A 878 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.06e+00 bond pdb=" CB GLU B1072 " pdb=" CG GLU B1072 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.84e+00 bond pdb=" CB GLU A1072 " pdb=" CG GLU A1072 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.79e+00 ... (remaining 23305 not shown) Histogram of bond angle deviations from ideal: 98.78 - 107.03: 748 107.03 - 115.27: 13948 115.27 - 123.51: 16348 123.51 - 131.76: 639 131.76 - 140.00: 24 Bond angle restraints: 31707 Sorted by residual: angle pdb=" C VAL C 83 " pdb=" N LEU C 84 " pdb=" CA LEU C 84 " ideal model delta sigma weight residual 120.94 140.00 -19.06 1.90e+00 2.77e-01 1.01e+02 angle pdb=" C VAL A 83 " pdb=" N LEU A 84 " pdb=" CA LEU A 84 " ideal model delta sigma weight residual 120.94 139.96 -19.02 1.90e+00 2.77e-01 1.00e+02 angle pdb=" C VAL B 83 " pdb=" N LEU B 84 " pdb=" CA LEU B 84 " ideal model delta sigma weight residual 120.94 139.92 -18.98 1.90e+00 2.77e-01 9.98e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 115.64 -4.94 1.22e+00 6.72e-01 1.64e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.62 -4.92 1.22e+00 6.72e-01 1.62e+01 ... (remaining 31702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 13477 17.91 - 35.82: 334 35.82 - 53.73: 79 53.73 - 71.64: 9 71.64 - 89.55: 12 Dihedral angle restraints: 13911 sinusoidal: 5421 harmonic: 8490 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -175.55 89.55 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -175.52 89.52 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -175.48 89.48 1 1.00e+01 1.00e-02 9.51e+01 ... (remaining 13908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2006 0.043 - 0.085: 1187 0.085 - 0.128: 365 0.128 - 0.170: 60 0.170 - 0.213: 15 Chirality restraints: 3633 Sorted by residual: chirality pdb=" CB THR C 581 " pdb=" CA THR C 581 " pdb=" OG1 THR C 581 " pdb=" CG2 THR C 581 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB THR B 581 " pdb=" CA THR B 581 " pdb=" OG1 THR B 581 " pdb=" CG2 THR B 581 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB THR A 581 " pdb=" CA THR A 581 " pdb=" OG1 THR A 581 " pdb=" CG2 THR A 581 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 3630 not shown) Planarity restraints: 4098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 86 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C PHE B 86 " 0.060 2.00e-02 2.50e+03 pdb=" O PHE B 86 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN B 87 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 86 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C PHE C 86 " 0.059 2.00e-02 2.50e+03 pdb=" O PHE C 86 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN C 87 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 86 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C PHE A 86 " 0.059 2.00e-02 2.50e+03 pdb=" O PHE A 86 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN A 87 " -0.020 2.00e-02 2.50e+03 ... (remaining 4095 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 477 2.68 - 3.23: 20603 3.23 - 3.79: 34748 3.79 - 4.34: 46282 4.34 - 4.90: 78352 Nonbonded interactions: 180462 Sorted by model distance: nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.123 2.520 nonbonded pdb=" NZ LYS C 811 " pdb=" OD2 ASP C 820 " model vdw 2.123 2.520 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.123 2.520 nonbonded pdb=" NZ LYS C 557 " pdb=" OD2 ASP C 574 " model vdw 2.207 2.520 nonbonded pdb=" NZ LYS B 557 " pdb=" OD2 ASP B 574 " model vdw 2.208 2.520 ... (remaining 180457 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 7.220 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 60.960 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5648 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 : 0.009 0.077 23310 Z= 0.590 Angle : 0.873 19.061 31707 Z= 0.478 Chirality : 0.056 0.213 3633 Planarity : 0.007 0.080 4098 Dihedral : 8.822 76.066 8310 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.12 % Allowed : 0.47 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.11 % 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: -4.56 (0.12), residues: 2844 helix: -4.57 (0.07), residues: 714 sheet: -2.33 (0.17), residues: 660 loop : -2.48 (0.13), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 64 HIS 0.013 0.002 HIS A1048 PHE 0.031 0.004 PHE B 800 TYR 0.025 0.003 TYR C 38 ARG 0.013 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 500 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.6822 (mtm-85) cc_final: 0.6500 (mtp-110) REVERT: A 326 ILE cc_start: 0.5706 (mm) cc_final: 0.5486 (mp) REVERT: A 340 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7974 (mp0) REVERT: A 360 ASN cc_start: 0.7609 (m-40) cc_final: 0.7113 (t0) REVERT: A 365 TYR cc_start: 0.7186 (m-80) cc_final: 0.6751 (m-80) REVERT: A 394 ASN cc_start: 0.6804 (m-40) cc_final: 0.6588 (m-40) REVERT: A 529 LYS cc_start: 0.8219 (mttt) cc_final: 0.7582 (tmtt) REVERT: A 530 SER cc_start: 0.7694 (p) cc_final: 0.7374 (m) REVERT: A 532 ASN cc_start: 0.7398 (t0) cc_final: 0.7073 (t0) REVERT: A 537 LYS cc_start: 0.6658 (ttpt) cc_final: 0.6371 (ptmt) REVERT: A 574 ASP cc_start: 0.5792 (t70) cc_final: 0.5470 (t0) REVERT: A 588 THR cc_start: 0.6729 (m) cc_final: 0.6229 (t) REVERT: A 592 PHE cc_start: 0.6798 (p90) cc_final: 0.6508 (p90) REVERT: A 607 GLN cc_start: 0.7530 (tt0) cc_final: 0.7177 (tt0) REVERT: A 614 ASP cc_start: 0.7701 (t0) cc_final: 0.7202 (m-30) REVERT: A 656 VAL cc_start: 0.6491 (t) cc_final: 0.6257 (m) REVERT: A 661 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6884 (tt0) REVERT: A 702 GLU cc_start: 0.8166 (tt0) cc_final: 0.7914 (tp30) REVERT: A 745 ASP cc_start: 0.7544 (m-30) cc_final: 0.7085 (p0) REVERT: A 748 GLU cc_start: 0.7570 (mp0) cc_final: 0.7096 (mp0) REVERT: A 814 LYS cc_start: 0.7622 (mttt) cc_final: 0.7220 (mptp) REVERT: A 819 GLU cc_start: 0.5851 (mt-10) cc_final: 0.5413 (mt-10) REVERT: A 872 GLN cc_start: 0.6795 (mt0) cc_final: 0.6520 (tt0) REVERT: A 875 SER cc_start: 0.6229 (t) cc_final: 0.6012 (m) REVERT: A 990 GLU cc_start: 0.6272 (mt-10) cc_final: 0.5920 (mp0) REVERT: A 995 ARG cc_start: 0.6169 (mtt180) cc_final: 0.5884 (mtp180) REVERT: A 1045 LYS cc_start: 0.7565 (ttpp) cc_final: 0.7179 (tmmt) REVERT: A 1050 MET cc_start: 0.7367 (ptt) cc_final: 0.7143 (ptm) REVERT: A 1073 LYS cc_start: 0.6462 (mttt) cc_final: 0.6020 (mtpp) REVERT: A 1092 GLU cc_start: 0.7619 (mt-10) cc_final: 0.6922 (mp0) REVERT: A 1119 ASN cc_start: 0.6929 (m-40) cc_final: 0.6636 (m110) REVERT: A 1138 TYR cc_start: 0.7040 (t80) cc_final: 0.6815 (t80) REVERT: B 224 GLU cc_start: 0.4614 (pm20) cc_final: 0.4347 (mp0) REVERT: B 282 ASN cc_start: 0.6485 (m-40) cc_final: 0.5999 (m-40) REVERT: B 287 ASP cc_start: 0.5593 (t0) cc_final: 0.5306 (m-30) REVERT: B 314 GLN cc_start: 0.7428 (tt0) cc_final: 0.6952 (tp40) REVERT: B 316 SER cc_start: 0.6920 (t) cc_final: 0.6386 (p) REVERT: B 319 ARG cc_start: 0.6948 (mtm-85) cc_final: 0.6594 (mtp-110) REVERT: B 340 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7880 (mp0) REVERT: B 351 TYR cc_start: 0.6915 (p90) cc_final: 0.6031 (p90) REVERT: B 360 ASN cc_start: 0.7745 (m-40) cc_final: 0.7280 (t0) REVERT: B 365 TYR cc_start: 0.6875 (m-80) cc_final: 0.6582 (m-80) REVERT: B 394 ASN cc_start: 0.6626 (m-40) cc_final: 0.6195 (m-40) REVERT: B 529 LYS cc_start: 0.8188 (mttt) cc_final: 0.7594 (tmtt) REVERT: B 532 ASN cc_start: 0.7437 (t0) cc_final: 0.6902 (t0) REVERT: B 537 LYS cc_start: 0.6774 (ttpt) cc_final: 0.6335 (ptmt) REVERT: B 574 ASP cc_start: 0.5880 (t70) cc_final: 0.5582 (t0) REVERT: B 607 GLN cc_start: 0.7363 (tt0) cc_final: 0.7079 (tt0) REVERT: B 614 ASP cc_start: 0.7634 (t0) cc_final: 0.7080 (m-30) REVERT: B 651 ILE cc_start: 0.7513 (mt) cc_final: 0.7312 (mm) REVERT: B 656 VAL cc_start: 0.6424 (t) cc_final: 0.6173 (m) REVERT: B 661 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6059 (mm-30) REVERT: B 745 ASP cc_start: 0.7334 (m-30) cc_final: 0.7133 (p0) REVERT: B 748 GLU cc_start: 0.7509 (mp0) cc_final: 0.7055 (mp0) REVERT: B 794 ILE cc_start: 0.7380 (mt) cc_final: 0.7086 (pp) REVERT: B 814 LYS cc_start: 0.7608 (mttt) cc_final: 0.7232 (mptp) REVERT: B 819 GLU cc_start: 0.5883 (mt-10) cc_final: 0.5584 (mt-10) REVERT: B 868 GLU cc_start: 0.7171 (tt0) cc_final: 0.6855 (tt0) REVERT: B 872 GLN cc_start: 0.6538 (mt0) cc_final: 0.6145 (mt0) REVERT: B 947 LYS cc_start: 0.7636 (mttt) cc_final: 0.7425 (mtmt) REVERT: B 987 PRO cc_start: 0.7774 (Cg_exo) cc_final: 0.7540 (Cg_endo) REVERT: B 995 ARG cc_start: 0.6377 (mtt180) cc_final: 0.6047 (mtp180) REVERT: B 1050 MET cc_start: 0.7396 (ptt) cc_final: 0.7041 (ptm) REVERT: B 1073 LYS cc_start: 0.6811 (mttt) cc_final: 0.6340 (mtpt) REVERT: B 1092 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6687 (mp0) REVERT: B 1100 THR cc_start: 0.7303 (p) cc_final: 0.6966 (p) REVERT: B 1101 HIS cc_start: 0.6843 (m90) cc_final: 0.6338 (m170) REVERT: C 237 ARG cc_start: 0.4936 (mtt90) cc_final: 0.4730 (mtm180) REVERT: C 287 ASP cc_start: 0.5562 (t0) cc_final: 0.5202 (m-30) REVERT: C 305 SER cc_start: 0.7997 (t) cc_final: 0.7728 (t) REVERT: C 340 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8005 (mp0) REVERT: C 360 ASN cc_start: 0.7520 (m-40) cc_final: 0.6985 (t0) REVERT: C 365 TYR cc_start: 0.6997 (m-80) cc_final: 0.6353 (m-80) REVERT: C 394 ASN cc_start: 0.6668 (m-40) cc_final: 0.6299 (m-40) REVERT: C 521 PRO cc_start: 0.7418 (Cg_exo) cc_final: 0.7113 (Cg_endo) REVERT: C 532 ASN cc_start: 0.7356 (t0) cc_final: 0.7076 (t0) REVERT: C 537 LYS cc_start: 0.6759 (ttpt) cc_final: 0.6225 (ptmt) REVERT: C 574 ASP cc_start: 0.5688 (t70) cc_final: 0.5391 (t0) REVERT: C 592 PHE cc_start: 0.6971 (p90) cc_final: 0.6709 (p90) REVERT: C 607 GLN cc_start: 0.7337 (tt0) cc_final: 0.6901 (tt0) REVERT: C 614 ASP cc_start: 0.7396 (t0) cc_final: 0.7070 (m-30) REVERT: C 651 ILE cc_start: 0.7747 (mt) cc_final: 0.7528 (mp) REVERT: C 661 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6771 (tt0) REVERT: C 697 MET cc_start: 0.7203 (ptt) cc_final: 0.6990 (ptt) REVERT: C 748 GLU cc_start: 0.7734 (mp0) cc_final: 0.7341 (mp0) REVERT: C 794 ILE cc_start: 0.7592 (mt) cc_final: 0.7205 (pp) REVERT: C 814 LYS cc_start: 0.7726 (mttt) cc_final: 0.7298 (mptp) REVERT: C 819 GLU cc_start: 0.6113 (mt-10) cc_final: 0.5675 (mt-10) REVERT: C 872 GLN cc_start: 0.6426 (mt0) cc_final: 0.6147 (tt0) REVERT: C 947 LYS cc_start: 0.7719 (mttt) cc_final: 0.7493 (mtpt) REVERT: C 987 PRO cc_start: 0.8032 (Cg_exo) cc_final: 0.7689 (Cg_endo) REVERT: C 995 ARG cc_start: 0.6213 (mtt180) cc_final: 0.5929 (mtp180) REVERT: C 1002 GLN cc_start: 0.6327 (tt0) cc_final: 0.6056 (tt0) REVERT: C 1045 LYS cc_start: 0.7563 (ttpp) cc_final: 0.7343 (ttpt) REVERT: C 1092 GLU cc_start: 0.7556 (mt-10) cc_final: 0.6947 (mp0) outliers start: 3 outliers final: 2 residues processed: 503 average time/residue: 1.2312 time to fit residues: 714.6791 Evaluate side-chains 291 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 289 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain C residue 391 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 117 optimal weight: 0.0170 chunk 228 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 264 optimal weight: 0.6980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 501 ASN A 603 ASN A 613 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1005 GLN A1101 HIS B 66 HIS ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 536 ASN B 603 ASN B 613 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN B1119 ASN C 66 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 603 ASN C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1101 HIS C1142 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5616 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23310 Z= 0.188 Angle : 0.554 9.039 31707 Z= 0.295 Chirality : 0.045 0.183 3633 Planarity : 0.005 0.047 4098 Dihedral : 5.285 47.434 3101 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.00 % Allowed : 6.96 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.97 (0.13), residues: 2844 helix: -2.45 (0.15), residues: 666 sheet: -1.74 (0.20), residues: 591 loop : -1.82 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.004 0.001 HIS B1048 PHE 0.020 0.002 PHE C 32 TYR 0.016 0.001 TYR B 313 ARG 0.007 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 306 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.6250 (tp) cc_final: 0.5706 (mt) REVERT: A 202 LYS cc_start: 0.5174 (mttm) cc_final: 0.4846 (mtmt) REVERT: A 206 LYS cc_start: 0.6540 (tptt) cc_final: 0.6024 (tptp) REVERT: A 207 HIS cc_start: 0.6514 (m170) cc_final: 0.6306 (m90) REVERT: A 287 ASP cc_start: 0.6267 (OUTLIER) cc_final: 0.6023 (m-30) REVERT: A 340 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8055 (mp0) REVERT: A 360 ASN cc_start: 0.7267 (m-40) cc_final: 0.7018 (t0) REVERT: A 365 TYR cc_start: 0.6975 (m-80) cc_final: 0.6706 (m-80) REVERT: A 394 ASN cc_start: 0.6513 (m-40) cc_final: 0.6288 (t0) REVERT: A 529 LYS cc_start: 0.8263 (mttt) cc_final: 0.7621 (tmtt) REVERT: A 530 SER cc_start: 0.7916 (p) cc_final: 0.7692 (m) REVERT: A 532 ASN cc_start: 0.7286 (t0) cc_final: 0.7079 (t0) REVERT: A 564 GLN cc_start: 0.6038 (mm110) cc_final: 0.5801 (mm-40) REVERT: A 574 ASP cc_start: 0.5880 (t70) cc_final: 0.5487 (t0) REVERT: A 588 THR cc_start: 0.6774 (m) cc_final: 0.6257 (t) REVERT: A 592 PHE cc_start: 0.6933 (p90) cc_final: 0.6716 (p90) REVERT: A 607 GLN cc_start: 0.7468 (tt0) cc_final: 0.7127 (tt0) REVERT: A 614 ASP cc_start: 0.7390 (t0) cc_final: 0.6871 (m-30) REVERT: A 646 ARG cc_start: 0.7923 (mtp180) cc_final: 0.7678 (ttm170) REVERT: A 661 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6863 (tt0) REVERT: A 702 GLU cc_start: 0.8147 (tt0) cc_final: 0.7804 (tp30) REVERT: A 745 ASP cc_start: 0.7621 (m-30) cc_final: 0.7222 (p0) REVERT: A 748 GLU cc_start: 0.7565 (mp0) cc_final: 0.7149 (mp0) REVERT: A 750 SER cc_start: 0.6055 (t) cc_final: 0.5833 (m) REVERT: A 776 LYS cc_start: 0.5685 (tttt) cc_final: 0.5472 (tttm) REVERT: A 780 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6294 (mm-30) REVERT: A 790 LYS cc_start: 0.7809 (pttt) cc_final: 0.7489 (ptmt) REVERT: A 811 LYS cc_start: 0.5564 (mmtp) cc_final: 0.5262 (tttm) REVERT: A 814 LYS cc_start: 0.7585 (mttt) cc_final: 0.7125 (mptp) REVERT: A 995 ARG cc_start: 0.5850 (mtt180) cc_final: 0.5604 (mtp180) REVERT: A 1045 LYS cc_start: 0.7326 (ttpp) cc_final: 0.7051 (tmmt) REVERT: A 1073 LYS cc_start: 0.6034 (mttt) cc_final: 0.5637 (mtpp) REVERT: A 1092 GLU cc_start: 0.7545 (mt-10) cc_final: 0.6891 (mp0) REVERT: A 1119 ASN cc_start: 0.7071 (m-40) cc_final: 0.6842 (m110) REVERT: B 202 LYS cc_start: 0.4704 (mttm) cc_final: 0.4334 (mtmt) REVERT: B 287 ASP cc_start: 0.5758 (t0) cc_final: 0.5492 (m-30) REVERT: B 314 GLN cc_start: 0.7654 (tt0) cc_final: 0.7057 (tp40) REVERT: B 316 SER cc_start: 0.5622 (t) cc_final: 0.5345 (m) REVERT: B 355 ARG cc_start: 0.8168 (ttt90) cc_final: 0.7910 (mtp180) REVERT: B 360 ASN cc_start: 0.7519 (m-40) cc_final: 0.7298 (t0) REVERT: B 529 LYS cc_start: 0.8282 (mttt) cc_final: 0.7595 (tmtt) REVERT: B 532 ASN cc_start: 0.7668 (t0) cc_final: 0.7228 (t0) REVERT: B 537 LYS cc_start: 0.6566 (ttpt) cc_final: 0.5888 (ptmt) REVERT: B 574 ASP cc_start: 0.6043 (t70) cc_final: 0.5616 (t0) REVERT: B 607 GLN cc_start: 0.7237 (tt0) cc_final: 0.7017 (tt0) REVERT: B 614 ASP cc_start: 0.7222 (t0) cc_final: 0.6838 (m-30) REVERT: B 661 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6030 (mm-30) REVERT: B 745 ASP cc_start: 0.7687 (m-30) cc_final: 0.7352 (p0) REVERT: B 748 GLU cc_start: 0.7649 (mp0) cc_final: 0.7300 (mp0) REVERT: B 750 SER cc_start: 0.6115 (t) cc_final: 0.5832 (m) REVERT: B 776 LYS cc_start: 0.5763 (tttt) cc_final: 0.5514 (ttpp) REVERT: B 790 LYS cc_start: 0.7603 (pttt) cc_final: 0.7311 (pttm) REVERT: B 811 LYS cc_start: 0.5315 (mmtp) cc_final: 0.5008 (tttm) REVERT: B 814 LYS cc_start: 0.7685 (mttt) cc_final: 0.7194 (mptp) REVERT: B 947 LYS cc_start: 0.7453 (mttt) cc_final: 0.7180 (mtmt) REVERT: B 1010 GLN cc_start: 0.6351 (mm-40) cc_final: 0.6060 (mp10) REVERT: B 1050 MET cc_start: 0.7267 (ptt) cc_final: 0.7028 (ptm) REVERT: B 1073 LYS cc_start: 0.6292 (mttt) cc_final: 0.5873 (mtpt) REVERT: B 1092 GLU cc_start: 0.7575 (mt-10) cc_final: 0.6690 (mp0) REVERT: C 118 LEU cc_start: 0.6062 (tp) cc_final: 0.5518 (mt) REVERT: C 202 LYS cc_start: 0.5056 (mttm) cc_final: 0.4771 (mtmt) REVERT: C 207 HIS cc_start: 0.6828 (m170) cc_final: 0.6597 (m90) REVERT: C 287 ASP cc_start: 0.5748 (t0) cc_final: 0.5542 (m-30) REVERT: C 305 SER cc_start: 0.8153 (t) cc_final: 0.7947 (t) REVERT: C 340 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8064 (mp0) REVERT: C 355 ARG cc_start: 0.8219 (ttt90) cc_final: 0.7797 (mmm160) REVERT: C 357 ARG cc_start: 0.7841 (mtp-110) cc_final: 0.7531 (mmm-85) REVERT: C 360 ASN cc_start: 0.7294 (m-40) cc_final: 0.6909 (t0) REVERT: C 365 TYR cc_start: 0.6897 (m-80) cc_final: 0.6478 (m-80) REVERT: C 394 ASN cc_start: 0.6504 (m-40) cc_final: 0.6139 (m-40) REVERT: C 396 TYR cc_start: 0.6166 (m-80) cc_final: 0.5964 (m-80) REVERT: C 528 LYS cc_start: 0.6395 (OUTLIER) cc_final: 0.5971 (mtpm) REVERT: C 529 LYS cc_start: 0.8251 (mttt) cc_final: 0.7611 (ttpp) REVERT: C 532 ASN cc_start: 0.7269 (t0) cc_final: 0.6901 (t0) REVERT: C 537 LYS cc_start: 0.6568 (ttpt) cc_final: 0.5689 (ptmt) REVERT: C 574 ASP cc_start: 0.6155 (t70) cc_final: 0.5682 (t0) REVERT: C 607 GLN cc_start: 0.7171 (tt0) cc_final: 0.6692 (tt0) REVERT: C 614 ASP cc_start: 0.7300 (t0) cc_final: 0.7009 (m-30) REVERT: C 661 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6738 (tt0) REVERT: C 748 GLU cc_start: 0.7530 (mp0) cc_final: 0.7173 (mp0) REVERT: C 750 SER cc_start: 0.6341 (t) cc_final: 0.6129 (m) REVERT: C 776 LYS cc_start: 0.5611 (tttt) cc_final: 0.5247 (ttpp) REVERT: C 790 LYS cc_start: 0.7733 (pttt) cc_final: 0.7442 (ptmt) REVERT: C 794 ILE cc_start: 0.7733 (mt) cc_final: 0.7236 (pp) REVERT: C 814 LYS cc_start: 0.7658 (mttt) cc_final: 0.7254 (mptp) REVERT: C 825 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7087 (mtpt) REVERT: C 947 LYS cc_start: 0.7586 (mttt) cc_final: 0.7338 (mtpt) REVERT: C 1045 LYS cc_start: 0.7405 (ttpp) cc_final: 0.7188 (ttpt) REVERT: C 1073 LYS cc_start: 0.5825 (mttt) cc_final: 0.5449 (mtpp) REVERT: C 1092 GLU cc_start: 0.7578 (mt-10) cc_final: 0.6837 (mp0) outliers start: 51 outliers final: 16 residues processed: 337 average time/residue: 1.2045 time to fit residues: 469.9459 Evaluate side-chains 261 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 242 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 825 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 219 optimal weight: 0.0070 chunk 179 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 264 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 chunk 262 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 212 optimal weight: 6.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1119 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN B1002 GLN B1101 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5621 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23310 Z= 0.275 Angle : 0.564 8.541 31707 Z= 0.298 Chirality : 0.045 0.152 3633 Planarity : 0.004 0.039 4098 Dihedral : 5.101 58.634 3101 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.27 % Allowed : 8.72 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.13 (0.14), residues: 2844 helix: -1.09 (0.19), residues: 681 sheet: -1.23 (0.19), residues: 645 loop : -1.61 (0.14), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 886 HIS 0.004 0.001 HIS B1101 PHE 0.025 0.002 PHE C 515 TYR 0.020 0.002 TYR A 313 ARG 0.004 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 243 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.6325 (tp) cc_final: 0.5905 (mt) REVERT: A 202 LYS cc_start: 0.5388 (mttm) cc_final: 0.5003 (mtmt) REVERT: A 207 HIS cc_start: 0.6536 (m170) cc_final: 0.6272 (m90) REVERT: A 287 ASP cc_start: 0.5992 (OUTLIER) cc_final: 0.5725 (m-30) REVERT: A 340 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8017 (mp0) REVERT: A 351 TYR cc_start: 0.7144 (p90) cc_final: 0.6394 (p90) REVERT: A 360 ASN cc_start: 0.7283 (m-40) cc_final: 0.7011 (t0) REVERT: A 365 TYR cc_start: 0.7048 (m-80) cc_final: 0.6715 (m-80) REVERT: A 394 ASN cc_start: 0.6499 (m-40) cc_final: 0.6195 (m-40) REVERT: A 400 PHE cc_start: 0.7148 (p90) cc_final: 0.6936 (p90) REVERT: A 529 LYS cc_start: 0.8181 (mttt) cc_final: 0.7555 (tmtt) REVERT: A 532 ASN cc_start: 0.7639 (t0) cc_final: 0.7331 (t0) REVERT: A 558 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.7133 (pmmt) REVERT: A 574 ASP cc_start: 0.6013 (t70) cc_final: 0.5538 (t0) REVERT: A 603 ASN cc_start: 0.7747 (t0) cc_final: 0.7319 (t0) REVERT: A 614 ASP cc_start: 0.7462 (t0) cc_final: 0.6918 (m-30) REVERT: A 661 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6810 (tt0) REVERT: A 697 MET cc_start: 0.7154 (ptt) cc_final: 0.6894 (ptm) REVERT: A 702 GLU cc_start: 0.8017 (tt0) cc_final: 0.7611 (tp30) REVERT: A 745 ASP cc_start: 0.7543 (m-30) cc_final: 0.7094 (p0) REVERT: A 748 GLU cc_start: 0.7634 (mp0) cc_final: 0.7207 (mp0) REVERT: A 776 LYS cc_start: 0.5334 (tttt) cc_final: 0.5128 (tttm) REVERT: A 780 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6209 (mm-30) REVERT: A 790 LYS cc_start: 0.7715 (pttt) cc_final: 0.7383 (ptmt) REVERT: A 811 LYS cc_start: 0.5656 (mmtp) cc_final: 0.5151 (tttm) REVERT: A 814 LYS cc_start: 0.7548 (mttt) cc_final: 0.7117 (mptp) REVERT: A 995 ARG cc_start: 0.5886 (mtt180) cc_final: 0.5610 (mtp180) REVERT: A 1045 LYS cc_start: 0.7124 (ttpp) cc_final: 0.6838 (ttpt) REVERT: A 1092 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6889 (mp0) REVERT: B 202 LYS cc_start: 0.5077 (mttm) cc_final: 0.4624 (mtmt) REVERT: B 287 ASP cc_start: 0.5799 (t0) cc_final: 0.5530 (m-30) REVERT: B 307 THR cc_start: 0.7725 (m) cc_final: 0.7523 (t) REVERT: B 314 GLN cc_start: 0.7629 (tt0) cc_final: 0.7365 (tt0) REVERT: B 360 ASN cc_start: 0.7453 (m-40) cc_final: 0.7195 (t0) REVERT: B 529 LYS cc_start: 0.8364 (mttt) cc_final: 0.7737 (tmtt) REVERT: B 532 ASN cc_start: 0.7488 (t0) cc_final: 0.7100 (t0) REVERT: B 537 LYS cc_start: 0.6518 (ttpt) cc_final: 0.6232 (tttt) REVERT: B 574 ASP cc_start: 0.5829 (t70) cc_final: 0.5431 (t0) REVERT: B 614 ASP cc_start: 0.7225 (t0) cc_final: 0.6866 (m-30) REVERT: B 661 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6691 (tt0) REVERT: B 745 ASP cc_start: 0.7633 (m-30) cc_final: 0.7208 (p0) REVERT: B 748 GLU cc_start: 0.7694 (mp0) cc_final: 0.7348 (mp0) REVERT: B 790 LYS cc_start: 0.7385 (pttt) cc_final: 0.6994 (pttm) REVERT: B 814 LYS cc_start: 0.7705 (mttt) cc_final: 0.7375 (mptp) REVERT: B 1010 GLN cc_start: 0.6353 (mm-40) cc_final: 0.6046 (mm110) REVERT: B 1050 MET cc_start: 0.7475 (ptt) cc_final: 0.7244 (ptm) REVERT: B 1092 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6505 (mp0) REVERT: C 118 LEU cc_start: 0.5884 (tp) cc_final: 0.5529 (mt) REVERT: C 202 LYS cc_start: 0.5024 (mttm) cc_final: 0.4654 (mtmt) REVERT: C 305 SER cc_start: 0.7985 (t) cc_final: 0.7742 (t) REVERT: C 351 TYR cc_start: 0.7083 (p90) cc_final: 0.6703 (p90) REVERT: C 360 ASN cc_start: 0.7217 (m-40) cc_final: 0.6882 (t0) REVERT: C 365 TYR cc_start: 0.7018 (m-80) cc_final: 0.6591 (m-80) REVERT: C 394 ASN cc_start: 0.6644 (m-40) cc_final: 0.6324 (m-40) REVERT: C 529 LYS cc_start: 0.8260 (mttt) cc_final: 0.7618 (tmtt) REVERT: C 532 ASN cc_start: 0.7421 (t0) cc_final: 0.7109 (t0) REVERT: C 537 LYS cc_start: 0.6717 (ttpt) cc_final: 0.6327 (ptmt) REVERT: C 574 ASP cc_start: 0.5942 (t70) cc_final: 0.5483 (t0) REVERT: C 603 ASN cc_start: 0.7785 (t0) cc_final: 0.7504 (t0) REVERT: C 614 ASP cc_start: 0.7289 (t0) cc_final: 0.6946 (m-30) REVERT: C 661 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6744 (tt0) REVERT: C 748 GLU cc_start: 0.7611 (mp0) cc_final: 0.7279 (mp0) REVERT: C 776 LYS cc_start: 0.5614 (tttt) cc_final: 0.5205 (ttpp) REVERT: C 790 LYS cc_start: 0.7721 (pttt) cc_final: 0.7437 (ptmt) REVERT: C 794 ILE cc_start: 0.7600 (mt) cc_final: 0.7102 (pp) REVERT: C 814 LYS cc_start: 0.7696 (mttt) cc_final: 0.7435 (mptp) REVERT: C 825 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.7081 (mtpt) REVERT: C 947 LYS cc_start: 0.7338 (mttt) cc_final: 0.7056 (mtpt) REVERT: C 1092 GLU cc_start: 0.7549 (mt-10) cc_final: 0.6847 (mp0) outliers start: 58 outliers final: 28 residues processed: 281 average time/residue: 1.0291 time to fit residues: 343.5018 Evaluate side-chains 248 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 217 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 177 optimal weight: 0.4980 chunk 265 optimal weight: 0.0980 chunk 281 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 580 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 901 GLN B 935 GLN B 969 ASN B1002 GLN B1119 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 969 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5611 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23310 Z= 0.221 Angle : 0.519 9.605 31707 Z= 0.270 Chirality : 0.044 0.145 3633 Planarity : 0.004 0.062 4098 Dihedral : 4.838 58.568 3101 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.00 % Allowed : 10.49 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.65 (0.15), residues: 2844 helix: -0.38 (0.20), residues: 681 sheet: -1.05 (0.19), residues: 645 loop : -1.41 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 353 HIS 0.003 0.001 HIS B 655 PHE 0.020 0.002 PHE C 32 TYR 0.028 0.001 TYR B 396 ARG 0.008 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 231 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.5021 (mttm) cc_final: 0.4629 (mtmt) REVERT: A 206 LYS cc_start: 0.6645 (tptt) cc_final: 0.6255 (tptp) REVERT: A 207 HIS cc_start: 0.6474 (m170) cc_final: 0.6201 (m90) REVERT: A 351 TYR cc_start: 0.7157 (p90) cc_final: 0.6426 (p90) REVERT: A 360 ASN cc_start: 0.7304 (m-40) cc_final: 0.7012 (t0) REVERT: A 394 ASN cc_start: 0.6555 (m-40) cc_final: 0.6342 (m-40) REVERT: A 529 LYS cc_start: 0.8351 (mttt) cc_final: 0.7729 (tmtt) REVERT: A 532 ASN cc_start: 0.7527 (t0) cc_final: 0.7256 (t0) REVERT: A 558 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7172 (pmmt) REVERT: A 574 ASP cc_start: 0.6001 (t70) cc_final: 0.5498 (t0) REVERT: A 603 ASN cc_start: 0.7618 (t0) cc_final: 0.7346 (p0) REVERT: A 614 ASP cc_start: 0.7135 (t0) cc_final: 0.6802 (m-30) REVERT: A 661 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6875 (tt0) REVERT: A 702 GLU cc_start: 0.8038 (tt0) cc_final: 0.7575 (tp30) REVERT: A 745 ASP cc_start: 0.7540 (m-30) cc_final: 0.7094 (p0) REVERT: A 776 LYS cc_start: 0.5461 (tttt) cc_final: 0.5200 (tttm) REVERT: A 780 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6182 (mm-30) REVERT: A 790 LYS cc_start: 0.7624 (pttt) cc_final: 0.7140 (ptmm) REVERT: A 814 LYS cc_start: 0.7552 (mttt) cc_final: 0.7103 (mptp) REVERT: A 995 ARG cc_start: 0.5859 (mtt180) cc_final: 0.5532 (mtp180) REVERT: A 1045 LYS cc_start: 0.6947 (ttpp) cc_final: 0.6727 (ttpt) REVERT: A 1092 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6851 (mp0) REVERT: B 202 LYS cc_start: 0.5103 (mttm) cc_final: 0.4670 (mtmt) REVERT: B 287 ASP cc_start: 0.5973 (t0) cc_final: 0.5698 (m-30) REVERT: B 314 GLN cc_start: 0.7682 (tt0) cc_final: 0.7393 (tt0) REVERT: B 360 ASN cc_start: 0.7483 (m-40) cc_final: 0.7225 (t0) REVERT: B 529 LYS cc_start: 0.8518 (mttt) cc_final: 0.7898 (tmtt) REVERT: B 532 ASN cc_start: 0.7558 (t0) cc_final: 0.7217 (t0) REVERT: B 537 LYS cc_start: 0.6494 (ttpt) cc_final: 0.6254 (tttt) REVERT: B 574 ASP cc_start: 0.5745 (t70) cc_final: 0.5321 (t0) REVERT: B 592 PHE cc_start: 0.6866 (p90) cc_final: 0.6483 (p90) REVERT: B 603 ASN cc_start: 0.7708 (t0) cc_final: 0.7358 (t0) REVERT: B 614 ASP cc_start: 0.7297 (t0) cc_final: 0.7005 (m-30) REVERT: B 661 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6619 (tt0) REVERT: B 745 ASP cc_start: 0.7536 (m-30) cc_final: 0.7122 (p0) REVERT: B 748 GLU cc_start: 0.7603 (mp0) cc_final: 0.7282 (mp0) REVERT: B 790 LYS cc_start: 0.7371 (pttt) cc_final: 0.6979 (pttm) REVERT: B 814 LYS cc_start: 0.7786 (mttt) cc_final: 0.7431 (mptp) REVERT: B 947 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7251 (mtmt) REVERT: B 1010 GLN cc_start: 0.6386 (mm-40) cc_final: 0.6160 (mm-40) REVERT: B 1092 GLU cc_start: 0.7515 (mt-10) cc_final: 0.6503 (mp0) REVERT: C 305 SER cc_start: 0.7999 (t) cc_final: 0.7759 (t) REVERT: C 351 TYR cc_start: 0.6995 (p90) cc_final: 0.6609 (p90) REVERT: C 360 ASN cc_start: 0.7501 (m-40) cc_final: 0.7198 (t0) REVERT: C 365 TYR cc_start: 0.6978 (m-80) cc_final: 0.6544 (m-80) REVERT: C 396 TYR cc_start: 0.6059 (m-80) cc_final: 0.5683 (m-80) REVERT: C 529 LYS cc_start: 0.8364 (mttt) cc_final: 0.7675 (tmtt) REVERT: C 532 ASN cc_start: 0.7528 (t0) cc_final: 0.7235 (t0) REVERT: C 537 LYS cc_start: 0.6590 (ttpt) cc_final: 0.6188 (ptmt) REVERT: C 574 ASP cc_start: 0.5910 (t70) cc_final: 0.5436 (t0) REVERT: C 603 ASN cc_start: 0.7656 (t0) cc_final: 0.7338 (p0) REVERT: C 614 ASP cc_start: 0.7299 (t0) cc_final: 0.6871 (m-30) REVERT: C 661 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6756 (tt0) REVERT: C 776 LYS cc_start: 0.5636 (tttt) cc_final: 0.5239 (ttpp) REVERT: C 790 LYS cc_start: 0.7656 (pttt) cc_final: 0.7428 (ptmt) REVERT: C 794 ILE cc_start: 0.7643 (mt) cc_final: 0.7040 (pp) REVERT: C 814 LYS cc_start: 0.7672 (mttt) cc_final: 0.7384 (mptp) REVERT: C 947 LYS cc_start: 0.7346 (mttt) cc_final: 0.6998 (mtpt) REVERT: C 1092 GLU cc_start: 0.7541 (mt-10) cc_final: 0.6815 (mp0) outliers start: 51 outliers final: 27 residues processed: 262 average time/residue: 0.9591 time to fit residues: 301.7254 Evaluate side-chains 246 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 217 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 209 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 252 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 901 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 914 ASN B 969 ASN B1002 GLN B1119 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 901 GLN C 914 ASN C 969 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5632 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 23310 Z= 0.550 Angle : 0.668 9.187 31707 Z= 0.350 Chirality : 0.051 0.225 3633 Planarity : 0.005 0.046 4098 Dihedral : 5.365 56.785 3101 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.70 % Allowed : 10.41 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.81 (0.15), residues: 2844 helix: -0.44 (0.20), residues: 681 sheet: -1.35 (0.18), residues: 660 loop : -1.45 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 353 HIS 0.007 0.002 HIS A1058 PHE 0.022 0.003 PHE B 515 TYR 0.026 0.003 TYR B 396 ARG 0.008 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 219 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.7382 (p90) cc_final: 0.6688 (p90) REVERT: A 360 ASN cc_start: 0.7478 (m-40) cc_final: 0.7225 (t0) REVERT: A 529 LYS cc_start: 0.8185 (mttt) cc_final: 0.7564 (tmtt) REVERT: A 532 ASN cc_start: 0.7352 (t0) cc_final: 0.6890 (t0) REVERT: A 574 ASP cc_start: 0.6029 (t70) cc_final: 0.5556 (t0) REVERT: A 603 ASN cc_start: 0.7851 (t0) cc_final: 0.7466 (t0) REVERT: A 614 ASP cc_start: 0.7515 (t0) cc_final: 0.6982 (m-30) REVERT: A 661 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6801 (tt0) REVERT: A 702 GLU cc_start: 0.8004 (tt0) cc_final: 0.7688 (tp30) REVERT: A 745 ASP cc_start: 0.7519 (m-30) cc_final: 0.7092 (p0) REVERT: A 780 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6278 (mm-30) REVERT: A 790 LYS cc_start: 0.7367 (pttt) cc_final: 0.7002 (ptmm) REVERT: A 814 LYS cc_start: 0.7444 (mttt) cc_final: 0.7150 (mptp) REVERT: A 815 ARG cc_start: 0.6086 (OUTLIER) cc_final: 0.5492 (mtp180) REVERT: A 1092 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6680 (mp0) REVERT: B 314 GLN cc_start: 0.7512 (tt0) cc_final: 0.7229 (tt0) REVERT: B 360 ASN cc_start: 0.7618 (m-40) cc_final: 0.7361 (t0) REVERT: B 508 TYR cc_start: 0.6347 (m-80) cc_final: 0.5877 (m-80) REVERT: B 529 LYS cc_start: 0.8377 (mttt) cc_final: 0.7779 (tmtt) REVERT: B 537 LYS cc_start: 0.6486 (ttpt) cc_final: 0.6255 (tttt) REVERT: B 556 ASN cc_start: 0.7822 (p0) cc_final: 0.7348 (p0) REVERT: B 574 ASP cc_start: 0.5785 (t70) cc_final: 0.5349 (t0) REVERT: B 603 ASN cc_start: 0.7852 (t0) cc_final: 0.7525 (t0) REVERT: B 614 ASP cc_start: 0.7255 (t0) cc_final: 0.6834 (m-30) REVERT: B 661 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6681 (tt0) REVERT: B 745 ASP cc_start: 0.7575 (m-30) cc_final: 0.7150 (p0) REVERT: B 790 LYS cc_start: 0.7205 (pttt) cc_final: 0.6967 (ptmm) REVERT: B 814 LYS cc_start: 0.7686 (mttt) cc_final: 0.7430 (mptp) REVERT: B 1092 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6643 (mp0) REVERT: B 1142 GLN cc_start: 0.7290 (tp40) cc_final: 0.7013 (tp-100) REVERT: C 351 TYR cc_start: 0.7052 (p90) cc_final: 0.6683 (p90) REVERT: C 360 ASN cc_start: 0.7448 (m-40) cc_final: 0.7158 (t0) REVERT: C 529 LYS cc_start: 0.8396 (mttt) cc_final: 0.7793 (tmtt) REVERT: C 532 ASN cc_start: 0.7423 (t0) cc_final: 0.6945 (t0) REVERT: C 556 ASN cc_start: 0.7616 (p0) cc_final: 0.7263 (p0) REVERT: C 574 ASP cc_start: 0.5889 (t70) cc_final: 0.5443 (t0) REVERT: C 603 ASN cc_start: 0.7954 (t0) cc_final: 0.7687 (t0) REVERT: C 614 ASP cc_start: 0.7252 (t0) cc_final: 0.6880 (m-30) REVERT: C 661 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6625 (tt0) REVERT: C 776 LYS cc_start: 0.5606 (tttt) cc_final: 0.5121 (ttpp) REVERT: C 780 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6395 (mm-30) REVERT: C 790 LYS cc_start: 0.7380 (pttt) cc_final: 0.6968 (ptmm) REVERT: C 794 ILE cc_start: 0.7619 (mt) cc_final: 0.6992 (pp) REVERT: C 814 LYS cc_start: 0.7524 (mttt) cc_final: 0.7182 (mptp) REVERT: C 947 LYS cc_start: 0.7149 (mttt) cc_final: 0.6894 (mtmt) REVERT: C 1092 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7001 (mp0) outliers start: 69 outliers final: 45 residues processed: 267 average time/residue: 0.9254 time to fit residues: 299.0059 Evaluate side-chains 247 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 201 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 2.9990 chunk 253 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 165 optimal weight: 0.8980 chunk 69 optimal weight: 0.0980 chunk 281 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 130 optimal weight: 0.0870 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 804 GLN C1142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5596 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23310 Z= 0.155 Angle : 0.495 9.870 31707 Z= 0.256 Chirality : 0.043 0.149 3633 Planarity : 0.004 0.062 4098 Dihedral : 4.677 53.218 3101 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.64 % Allowed : 12.44 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.18 (0.15), residues: 2844 helix: 0.44 (0.21), residues: 681 sheet: -1.00 (0.18), residues: 675 loop : -1.23 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 353 HIS 0.002 0.000 HIS B 655 PHE 0.023 0.001 PHE A 168 TYR 0.017 0.001 TYR B 170 ARG 0.008 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 244 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.6632 (tptt) cc_final: 0.6346 (tppt) REVERT: A 351 TYR cc_start: 0.7264 (p90) cc_final: 0.6551 (p90) REVERT: A 400 PHE cc_start: 0.7247 (p90) cc_final: 0.6949 (p90) REVERT: A 529 LYS cc_start: 0.8472 (mttt) cc_final: 0.7871 (tmtt) REVERT: A 532 ASN cc_start: 0.7391 (t0) cc_final: 0.6892 (t0) REVERT: A 574 ASP cc_start: 0.5913 (t70) cc_final: 0.5435 (t0) REVERT: A 614 ASP cc_start: 0.7147 (t0) cc_final: 0.6824 (m-30) REVERT: A 661 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6683 (tt0) REVERT: A 702 GLU cc_start: 0.8064 (tt0) cc_final: 0.7727 (tp30) REVERT: A 745 ASP cc_start: 0.7589 (m-30) cc_final: 0.7104 (p0) REVERT: A 780 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6154 (mm-30) REVERT: A 790 LYS cc_start: 0.7404 (pttt) cc_final: 0.7012 (ptmm) REVERT: A 814 LYS cc_start: 0.7478 (mttt) cc_final: 0.7090 (mptp) REVERT: A 912 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.7003 (p) REVERT: A 988 GLU cc_start: 0.7459 (mp0) cc_final: 0.6731 (mp0) REVERT: A 1045 LYS cc_start: 0.7079 (ttpp) cc_final: 0.6554 (mtpm) REVERT: A 1092 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6848 (mp0) REVERT: B 190 ARG cc_start: 0.6049 (mtm180) cc_final: 0.5811 (mtt-85) REVERT: B 314 GLN cc_start: 0.7619 (tt0) cc_final: 0.7350 (tt0) REVERT: B 360 ASN cc_start: 0.7677 (m-40) cc_final: 0.7445 (t0) REVERT: B 394 ASN cc_start: 0.6000 (t0) cc_final: 0.5715 (m-40) REVERT: B 529 LYS cc_start: 0.8453 (mttt) cc_final: 0.7862 (tmtt) REVERT: B 537 LYS cc_start: 0.6482 (ttpt) cc_final: 0.6256 (tttt) REVERT: B 556 ASN cc_start: 0.7758 (p0) cc_final: 0.7320 (p0) REVERT: B 574 ASP cc_start: 0.5560 (t70) cc_final: 0.5179 (t0) REVERT: B 592 PHE cc_start: 0.6305 (p90) cc_final: 0.5994 (p90) REVERT: B 603 ASN cc_start: 0.7540 (t0) cc_final: 0.7297 (p0) REVERT: B 614 ASP cc_start: 0.7304 (t0) cc_final: 0.7018 (m-30) REVERT: B 661 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6637 (tt0) REVERT: B 745 ASP cc_start: 0.7574 (m-30) cc_final: 0.7174 (p0) REVERT: B 790 LYS cc_start: 0.7353 (pttt) cc_final: 0.7047 (pttt) REVERT: B 814 LYS cc_start: 0.7625 (mttt) cc_final: 0.7344 (mptp) REVERT: B 969 ASN cc_start: 0.6679 (m110) cc_final: 0.6214 (m-40) REVERT: B 994 ASP cc_start: 0.6237 (t0) cc_final: 0.5878 (m-30) REVERT: B 1092 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6495 (mp0) REVERT: B 1142 GLN cc_start: 0.7335 (tp40) cc_final: 0.7098 (tp-100) REVERT: C 305 SER cc_start: 0.7940 (t) cc_final: 0.7709 (t) REVERT: C 351 TYR cc_start: 0.6989 (p90) cc_final: 0.6532 (p90) REVERT: C 360 ASN cc_start: 0.7417 (m-40) cc_final: 0.7147 (t0) REVERT: C 529 LYS cc_start: 0.8269 (mttt) cc_final: 0.7553 (tmtt) REVERT: C 532 ASN cc_start: 0.7485 (t0) cc_final: 0.6832 (t0) REVERT: C 574 ASP cc_start: 0.5874 (t70) cc_final: 0.5409 (t0) REVERT: C 603 ASN cc_start: 0.7607 (t0) cc_final: 0.7348 (p0) REVERT: C 614 ASP cc_start: 0.7306 (t0) cc_final: 0.6959 (m-30) REVERT: C 661 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6412 (mm-30) REVERT: C 780 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6316 (mm-30) REVERT: C 790 LYS cc_start: 0.7464 (pttt) cc_final: 0.7082 (ptmm) REVERT: C 794 ILE cc_start: 0.7676 (mt) cc_final: 0.7050 (pp) REVERT: C 814 LYS cc_start: 0.7711 (mttt) cc_final: 0.7287 (mptp) REVERT: C 947 LYS cc_start: 0.7180 (mttt) cc_final: 0.6879 (mtpt) REVERT: C 1092 GLU cc_start: 0.7532 (mt-10) cc_final: 0.6904 (mp0) outliers start: 42 outliers final: 23 residues processed: 270 average time/residue: 0.9060 time to fit residues: 297.6739 Evaluate side-chains 254 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 230 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 159 optimal weight: 0.9980 chunk 237 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 280 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 129 optimal weight: 0.0070 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A1005 GLN A1142 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23310 Z= 0.177 Angle : 0.498 10.041 31707 Z= 0.257 Chirality : 0.043 0.147 3633 Planarity : 0.004 0.051 4098 Dihedral : 4.517 53.310 3101 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.76 % Allowed : 13.18 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.89 (0.15), residues: 2844 helix: 0.84 (0.21), residues: 684 sheet: -0.81 (0.19), residues: 669 loop : -1.14 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 353 HIS 0.003 0.001 HIS B 655 PHE 0.024 0.001 PHE A 168 TYR 0.035 0.001 TYR A 265 ARG 0.008 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 241 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.5991 (tt) cc_final: 0.5336 (mt) REVERT: A 169 GLU cc_start: 0.7513 (tt0) cc_final: 0.6789 (tm-30) REVERT: A 206 LYS cc_start: 0.6675 (tptt) cc_final: 0.6328 (tptp) REVERT: A 351 TYR cc_start: 0.7264 (p90) cc_final: 0.6575 (p90) REVERT: A 400 PHE cc_start: 0.7262 (p90) cc_final: 0.7002 (p90) REVERT: A 529 LYS cc_start: 0.8475 (mttt) cc_final: 0.7867 (tmtt) REVERT: A 532 ASN cc_start: 0.7349 (t0) cc_final: 0.6817 (t0) REVERT: A 556 ASN cc_start: 0.7639 (p0) cc_final: 0.7354 (p0) REVERT: A 574 ASP cc_start: 0.5909 (t70) cc_final: 0.5432 (t0) REVERT: A 614 ASP cc_start: 0.7187 (t0) cc_final: 0.6875 (m-30) REVERT: A 661 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6696 (tt0) REVERT: A 702 GLU cc_start: 0.8051 (tt0) cc_final: 0.7696 (tp30) REVERT: A 745 ASP cc_start: 0.7599 (m-30) cc_final: 0.7052 (p0) REVERT: A 780 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6147 (mm-30) REVERT: A 790 LYS cc_start: 0.7441 (pttt) cc_final: 0.6855 (ptmm) REVERT: A 811 LYS cc_start: 0.5637 (mmtp) cc_final: 0.5099 (tttm) REVERT: A 814 LYS cc_start: 0.7440 (mttt) cc_final: 0.7062 (mptp) REVERT: A 912 THR cc_start: 0.7448 (OUTLIER) cc_final: 0.6925 (p) REVERT: A 988 GLU cc_start: 0.7479 (mp0) cc_final: 0.6731 (mp0) REVERT: A 995 ARG cc_start: 0.5661 (mtt180) cc_final: 0.5439 (mtp180) REVERT: A 1092 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6735 (mp0) REVERT: B 190 ARG cc_start: 0.6090 (mtm180) cc_final: 0.5865 (mtt-85) REVERT: B 314 GLN cc_start: 0.7619 (tt0) cc_final: 0.7386 (tt0) REVERT: B 360 ASN cc_start: 0.7650 (m-40) cc_final: 0.7424 (t0) REVERT: B 529 LYS cc_start: 0.8438 (mttt) cc_final: 0.7827 (tmtt) REVERT: B 537 LYS cc_start: 0.6477 (ttpt) cc_final: 0.6032 (ptmt) REVERT: B 556 ASN cc_start: 0.7745 (p0) cc_final: 0.7313 (p0) REVERT: B 574 ASP cc_start: 0.5560 (t70) cc_final: 0.5176 (t0) REVERT: B 592 PHE cc_start: 0.6521 (p90) cc_final: 0.6019 (p90) REVERT: B 661 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6342 (mm-30) REVERT: B 745 ASP cc_start: 0.7617 (m-30) cc_final: 0.7140 (p0) REVERT: B 790 LYS cc_start: 0.7383 (pttt) cc_final: 0.7047 (pttt) REVERT: B 814 LYS cc_start: 0.7658 (mttt) cc_final: 0.7330 (mptp) REVERT: B 969 ASN cc_start: 0.6659 (m110) cc_final: 0.6151 (m-40) REVERT: B 1092 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6501 (mp0) REVERT: B 1142 GLN cc_start: 0.7342 (tp40) cc_final: 0.7122 (tp-100) REVERT: C 305 SER cc_start: 0.8013 (t) cc_final: 0.7772 (t) REVERT: C 351 TYR cc_start: 0.6998 (p90) cc_final: 0.6516 (p90) REVERT: C 360 ASN cc_start: 0.7519 (m-40) cc_final: 0.7239 (t0) REVERT: C 529 LYS cc_start: 0.8265 (mttt) cc_final: 0.7568 (tmtt) REVERT: C 532 ASN cc_start: 0.7411 (t0) cc_final: 0.7197 (m-40) REVERT: C 556 ASN cc_start: 0.7616 (p0) cc_final: 0.7046 (p0) REVERT: C 574 ASP cc_start: 0.5951 (t70) cc_final: 0.5482 (t0) REVERT: C 614 ASP cc_start: 0.7273 (t0) cc_final: 0.6852 (m-30) REVERT: C 661 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6424 (mm-30) REVERT: C 780 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6366 (mm-30) REVERT: C 790 LYS cc_start: 0.7561 (pttt) cc_final: 0.7123 (ptmm) REVERT: C 794 ILE cc_start: 0.7667 (mt) cc_final: 0.7039 (pp) REVERT: C 814 LYS cc_start: 0.7611 (mttt) cc_final: 0.7180 (mptp) REVERT: C 947 LYS cc_start: 0.7185 (mttt) cc_final: 0.6894 (mtpt) REVERT: C 1092 GLU cc_start: 0.7533 (mt-10) cc_final: 0.6758 (mp0) outliers start: 45 outliers final: 22 residues processed: 268 average time/residue: 0.9481 time to fit residues: 307.6122 Evaluate side-chains 251 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 228 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 0.4980 chunk 112 optimal weight: 0.5980 chunk 167 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 55 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 191 optimal weight: 0.0270 chunk 138 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 220 optimal weight: 8.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 394 ASN C1142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5591 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23310 Z= 0.131 Angle : 0.487 12.183 31707 Z= 0.247 Chirality : 0.043 0.177 3633 Planarity : 0.004 0.049 4098 Dihedral : 4.345 52.383 3101 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.68 % Allowed : 13.58 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.52 (0.16), residues: 2844 helix: 1.43 (0.21), residues: 666 sheet: -0.59 (0.19), residues: 645 loop : -1.03 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 353 HIS 0.002 0.000 HIS B 655 PHE 0.026 0.001 PHE C 168 TYR 0.029 0.001 TYR A 265 ARG 0.011 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 235 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.5759 (tt) cc_final: 0.5151 (mt) REVERT: A 169 GLU cc_start: 0.7374 (tt0) cc_final: 0.6537 (tm-30) REVERT: A 206 LYS cc_start: 0.6700 (tptt) cc_final: 0.6371 (tptm) REVERT: A 335 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6713 (mm) REVERT: A 351 TYR cc_start: 0.7231 (p90) cc_final: 0.6528 (p90) REVERT: A 353 TRP cc_start: 0.5887 (p-90) cc_final: 0.5657 (p-90) REVERT: A 357 ARG cc_start: 0.7733 (mmm-85) cc_final: 0.7503 (mmm-85) REVERT: A 400 PHE cc_start: 0.7205 (p90) cc_final: 0.6857 (p90) REVERT: A 529 LYS cc_start: 0.8449 (mttt) cc_final: 0.7837 (tmtt) REVERT: A 532 ASN cc_start: 0.7375 (t0) cc_final: 0.6821 (t0) REVERT: A 556 ASN cc_start: 0.7671 (p0) cc_final: 0.7359 (p0) REVERT: A 574 ASP cc_start: 0.5911 (t70) cc_final: 0.5549 (t0) REVERT: A 614 ASP cc_start: 0.7204 (t0) cc_final: 0.6931 (m-30) REVERT: A 661 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6676 (tt0) REVERT: A 702 GLU cc_start: 0.8058 (tt0) cc_final: 0.7787 (tp30) REVERT: A 740 MET cc_start: 0.6959 (ttt) cc_final: 0.6697 (tmm) REVERT: A 745 ASP cc_start: 0.7603 (m-30) cc_final: 0.7049 (p0) REVERT: A 780 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6119 (mm-30) REVERT: A 790 LYS cc_start: 0.7283 (pttt) cc_final: 0.6890 (ptmm) REVERT: A 811 LYS cc_start: 0.5546 (mmtp) cc_final: 0.5071 (tttp) REVERT: A 814 LYS cc_start: 0.7524 (mttt) cc_final: 0.7173 (mptp) REVERT: A 912 THR cc_start: 0.7444 (OUTLIER) cc_final: 0.6946 (p) REVERT: A 988 GLU cc_start: 0.7451 (mp0) cc_final: 0.6699 (mp0) REVERT: A 1092 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6671 (mp0) REVERT: B 190 ARG cc_start: 0.6020 (mtm180) cc_final: 0.5761 (mtt-85) REVERT: B 314 GLN cc_start: 0.7613 (tt0) cc_final: 0.7363 (tt0) REVERT: B 360 ASN cc_start: 0.7613 (m-40) cc_final: 0.7382 (t0) REVERT: B 529 LYS cc_start: 0.8424 (mttt) cc_final: 0.7792 (tmtt) REVERT: B 532 ASN cc_start: 0.7762 (m-40) cc_final: 0.7535 (m-40) REVERT: B 537 LYS cc_start: 0.6363 (ttpt) cc_final: 0.5907 (ptmt) REVERT: B 556 ASN cc_start: 0.7746 (p0) cc_final: 0.7320 (p0) REVERT: B 574 ASP cc_start: 0.5564 (t70) cc_final: 0.5280 (t0) REVERT: B 661 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6638 (tt0) REVERT: B 745 ASP cc_start: 0.7571 (m-30) cc_final: 0.7087 (p0) REVERT: B 790 LYS cc_start: 0.7436 (pttt) cc_final: 0.6948 (ptmm) REVERT: B 814 LYS cc_start: 0.7677 (mttt) cc_final: 0.7306 (mptp) REVERT: B 969 ASN cc_start: 0.6644 (m110) cc_final: 0.6167 (m-40) REVERT: B 1092 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6630 (mp0) REVERT: B 1142 GLN cc_start: 0.7313 (tp40) cc_final: 0.7070 (tp-100) REVERT: C 305 SER cc_start: 0.8012 (t) cc_final: 0.7783 (t) REVERT: C 351 TYR cc_start: 0.6924 (p90) cc_final: 0.6438 (p90) REVERT: C 360 ASN cc_start: 0.7502 (m-40) cc_final: 0.7232 (t0) REVERT: C 529 LYS cc_start: 0.8166 (mttt) cc_final: 0.7487 (tmtt) REVERT: C 556 ASN cc_start: 0.7476 (p0) cc_final: 0.7101 (p0) REVERT: C 574 ASP cc_start: 0.5881 (t70) cc_final: 0.5402 (t0) REVERT: C 614 ASP cc_start: 0.7343 (t0) cc_final: 0.6922 (m-30) REVERT: C 661 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6379 (mm-30) REVERT: C 780 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6342 (mm-30) REVERT: C 790 LYS cc_start: 0.7556 (pttt) cc_final: 0.7282 (ptmt) REVERT: C 791 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7849 (p) REVERT: C 794 ILE cc_start: 0.7704 (mt) cc_final: 0.7042 (pp) REVERT: C 814 LYS cc_start: 0.7706 (mttt) cc_final: 0.7226 (mptp) REVERT: C 1092 GLU cc_start: 0.7549 (mt-10) cc_final: 0.6733 (mp0) outliers start: 43 outliers final: 25 residues processed: 259 average time/residue: 0.9559 time to fit residues: 297.6535 Evaluate side-chains 251 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 223 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 0.9990 chunk 268 optimal weight: 2.9990 chunk 245 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 247 optimal weight: 7.9990 chunk 260 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A1005 GLN A1142 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5623 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 23310 Z= 0.372 Angle : 0.591 12.450 31707 Z= 0.301 Chirality : 0.047 0.187 3633 Planarity : 0.004 0.051 4098 Dihedral : 4.750 52.065 3101 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.60 % Allowed : 13.73 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.78 (0.15), residues: 2844 helix: 1.02 (0.21), residues: 666 sheet: -0.73 (0.19), residues: 669 loop : -1.11 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 353 HIS 0.006 0.001 HIS C1058 PHE 0.036 0.002 PHE B 194 TYR 0.029 0.002 TYR A 265 ARG 0.010 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 223 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.5913 (tt) cc_final: 0.5279 (mt) REVERT: A 351 TYR cc_start: 0.7252 (p90) cc_final: 0.6551 (p90) REVERT: A 353 TRP cc_start: 0.5881 (p-90) cc_final: 0.5542 (p-90) REVERT: A 400 PHE cc_start: 0.7258 (p90) cc_final: 0.6964 (p90) REVERT: A 422 ASN cc_start: 0.6359 (OUTLIER) cc_final: 0.5996 (p0) REVERT: A 529 LYS cc_start: 0.8463 (mttt) cc_final: 0.7861 (tmtt) REVERT: A 532 ASN cc_start: 0.7372 (t0) cc_final: 0.6851 (t0) REVERT: A 574 ASP cc_start: 0.6065 (t70) cc_final: 0.5632 (t0) REVERT: A 614 ASP cc_start: 0.7384 (t0) cc_final: 0.7034 (m-30) REVERT: A 661 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6729 (tt0) REVERT: A 702 GLU cc_start: 0.8062 (tt0) cc_final: 0.7696 (tp30) REVERT: A 745 ASP cc_start: 0.7604 (m-30) cc_final: 0.7013 (p0) REVERT: A 780 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6138 (mm-30) REVERT: A 790 LYS cc_start: 0.7157 (pttt) cc_final: 0.6806 (ptmm) REVERT: A 814 LYS cc_start: 0.7440 (mttt) cc_final: 0.7112 (mptp) REVERT: A 912 THR cc_start: 0.7453 (OUTLIER) cc_final: 0.6925 (p) REVERT: A 1045 LYS cc_start: 0.6949 (ttpp) cc_final: 0.6580 (mtpm) REVERT: A 1092 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6885 (mp0) REVERT: B 190 ARG cc_start: 0.6095 (mtm180) cc_final: 0.5780 (mtt-85) REVERT: B 314 GLN cc_start: 0.7586 (tt0) cc_final: 0.7336 (tt0) REVERT: B 351 TYR cc_start: 0.7101 (p90) cc_final: 0.6215 (p90) REVERT: B 357 ARG cc_start: 0.7460 (mmm-85) cc_final: 0.7214 (mmm-85) REVERT: B 529 LYS cc_start: 0.8456 (mttt) cc_final: 0.7844 (tmtt) REVERT: B 537 LYS cc_start: 0.6486 (ttpt) cc_final: 0.6240 (tttt) REVERT: B 556 ASN cc_start: 0.7868 (p0) cc_final: 0.7336 (p0) REVERT: B 574 ASP cc_start: 0.5758 (t70) cc_final: 0.5345 (t0) REVERT: B 661 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6697 (tt0) REVERT: B 745 ASP cc_start: 0.7670 (m-30) cc_final: 0.7141 (p0) REVERT: B 790 LYS cc_start: 0.7247 (pttt) cc_final: 0.6966 (pttt) REVERT: B 814 LYS cc_start: 0.7597 (mttt) cc_final: 0.7274 (mptp) REVERT: B 1092 GLU cc_start: 0.7476 (mt-10) cc_final: 0.6532 (mp0) REVERT: B 1142 GLN cc_start: 0.7363 (tp40) cc_final: 0.7100 (tp-100) REVERT: C 305 SER cc_start: 0.7942 (t) cc_final: 0.7689 (t) REVERT: C 351 TYR cc_start: 0.6974 (p90) cc_final: 0.6495 (p90) REVERT: C 360 ASN cc_start: 0.7542 (m-40) cc_final: 0.7252 (t0) REVERT: C 529 LYS cc_start: 0.8311 (mttt) cc_final: 0.7701 (tmtt) REVERT: C 556 ASN cc_start: 0.7433 (p0) cc_final: 0.7002 (p0) REVERT: C 574 ASP cc_start: 0.5841 (t70) cc_final: 0.5392 (t0) REVERT: C 614 ASP cc_start: 0.7290 (t0) cc_final: 0.6907 (m-30) REVERT: C 661 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6477 (mm-30) REVERT: C 780 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6362 (mm-30) REVERT: C 790 LYS cc_start: 0.7447 (pttt) cc_final: 0.7066 (ptmm) REVERT: C 794 ILE cc_start: 0.7639 (mt) cc_final: 0.6991 (pp) REVERT: C 814 LYS cc_start: 0.7558 (mttt) cc_final: 0.7139 (mptp) REVERT: C 912 THR cc_start: 0.7459 (OUTLIER) cc_final: 0.7060 (p) REVERT: C 1092 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6799 (mp0) outliers start: 41 outliers final: 27 residues processed: 250 average time/residue: 0.9636 time to fit residues: 294.3991 Evaluate side-chains 241 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 211 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 0.9990 chunk 276 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 chunk 131 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 266 optimal weight: 0.6980 chunk 230 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 178 optimal weight: 0.0030 chunk 141 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A1005 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5600 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23310 Z= 0.162 Angle : 0.511 11.554 31707 Z= 0.257 Chirality : 0.043 0.177 3633 Planarity : 0.004 0.050 4098 Dihedral : 4.428 50.883 3101 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.13 % Allowed : 14.05 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.45 (0.16), residues: 2844 helix: 1.57 (0.21), residues: 666 sheet: -0.68 (0.19), residues: 666 loop : -0.96 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 353 HIS 0.002 0.001 HIS B 655 PHE 0.036 0.001 PHE B 194 TYR 0.029 0.001 TYR A 265 ARG 0.008 0.000 ARG B 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 227 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.5948 (tt) cc_final: 0.5308 (mt) REVERT: A 351 TYR cc_start: 0.7235 (p90) cc_final: 0.6484 (p90) REVERT: A 400 PHE cc_start: 0.7296 (p90) cc_final: 0.7085 (p90) REVERT: A 529 LYS cc_start: 0.8435 (mttt) cc_final: 0.7843 (tmtt) REVERT: A 532 ASN cc_start: 0.7397 (t0) cc_final: 0.6869 (t0) REVERT: A 556 ASN cc_start: 0.7860 (p0) cc_final: 0.7160 (p0) REVERT: A 574 ASP cc_start: 0.5991 (t70) cc_final: 0.5588 (t0) REVERT: A 614 ASP cc_start: 0.7186 (t0) cc_final: 0.6907 (m-30) REVERT: A 661 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6686 (tt0) REVERT: A 702 GLU cc_start: 0.8081 (tt0) cc_final: 0.7709 (tp30) REVERT: A 740 MET cc_start: 0.7052 (ttt) cc_final: 0.6759 (tmm) REVERT: A 745 ASP cc_start: 0.7568 (m-30) cc_final: 0.7013 (p0) REVERT: A 780 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6120 (mm-30) REVERT: A 790 LYS cc_start: 0.7159 (pttt) cc_final: 0.6788 (ptmm) REVERT: A 811 LYS cc_start: 0.5544 (mmtp) cc_final: 0.5070 (tttm) REVERT: A 814 LYS cc_start: 0.7424 (mttt) cc_final: 0.7069 (mptp) REVERT: A 912 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.6994 (p) REVERT: A 988 GLU cc_start: 0.7462 (mp0) cc_final: 0.6728 (mp0) REVERT: A 1045 LYS cc_start: 0.6820 (ttpp) cc_final: 0.6439 (mtpm) REVERT: A 1092 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6832 (mp0) REVERT: B 190 ARG cc_start: 0.6198 (mtm180) cc_final: 0.5846 (mtt-85) REVERT: B 314 GLN cc_start: 0.7585 (tt0) cc_final: 0.7324 (tt0) REVERT: B 351 TYR cc_start: 0.6998 (p90) cc_final: 0.6066 (p90) REVERT: B 529 LYS cc_start: 0.8429 (mttt) cc_final: 0.7813 (tmtt) REVERT: B 537 LYS cc_start: 0.6472 (ttpt) cc_final: 0.6244 (tttt) REVERT: B 556 ASN cc_start: 0.7671 (p0) cc_final: 0.7127 (p0) REVERT: B 574 ASP cc_start: 0.5681 (t70) cc_final: 0.5275 (t0) REVERT: B 661 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6359 (mm-30) REVERT: B 745 ASP cc_start: 0.7551 (m-30) cc_final: 0.7013 (p0) REVERT: B 790 LYS cc_start: 0.7331 (pttt) cc_final: 0.7059 (pttt) REVERT: B 814 LYS cc_start: 0.7648 (mttt) cc_final: 0.7261 (mptp) REVERT: B 969 ASN cc_start: 0.6672 (m110) cc_final: 0.6248 (m-40) REVERT: B 1092 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6566 (mp0) REVERT: B 1142 GLN cc_start: 0.7372 (tp40) cc_final: 0.7120 (tp-100) REVERT: C 305 SER cc_start: 0.7927 (t) cc_final: 0.7687 (t) REVERT: C 351 TYR cc_start: 0.6918 (p90) cc_final: 0.6459 (p90) REVERT: C 360 ASN cc_start: 0.7496 (m-40) cc_final: 0.7213 (t0) REVERT: C 529 LYS cc_start: 0.8246 (mttt) cc_final: 0.7576 (tmtt) REVERT: C 574 ASP cc_start: 0.5793 (t70) cc_final: 0.5328 (t0) REVERT: C 614 ASP cc_start: 0.7298 (t0) cc_final: 0.6950 (m-30) REVERT: C 661 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6394 (mm-30) REVERT: C 740 MET cc_start: 0.6840 (ttt) cc_final: 0.6499 (tmm) REVERT: C 780 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6275 (mm-30) REVERT: C 790 LYS cc_start: 0.7458 (pttt) cc_final: 0.7044 (ptmm) REVERT: C 794 ILE cc_start: 0.7676 (mt) cc_final: 0.7002 (pp) REVERT: C 814 LYS cc_start: 0.7657 (mttt) cc_final: 0.7131 (mptp) REVERT: C 912 THR cc_start: 0.7430 (OUTLIER) cc_final: 0.7066 (p) REVERT: C 1092 GLU cc_start: 0.7532 (mt-10) cc_final: 0.6758 (mp0) outliers start: 29 outliers final: 23 residues processed: 247 average time/residue: 0.9068 time to fit residues: 272.1248 Evaluate side-chains 247 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 2.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 1.9990 chunk 245 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 212 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 231 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A1005 GLN A1142 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 394 ASN C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.178866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.115374 restraints weight = 29451.799| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.20 r_work: 0.3614 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 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 : 0.003 0.032 23310 Z= 0.204 Angle : 0.519 11.473 31707 Z= 0.263 Chirality : 0.044 0.186 3633 Planarity : 0.004 0.051 4098 Dihedral : 4.428 50.162 3101 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.37 % Allowed : 14.08 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.48 (0.16), residues: 2844 helix: 1.55 (0.21), residues: 684 sheet: -0.65 (0.19), residues: 666 loop : -1.03 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 353 HIS 0.003 0.001 HIS B 655 PHE 0.032 0.002 PHE B 194 TYR 0.027 0.001 TYR A 265 ARG 0.011 0.001 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7198.09 seconds wall clock time: 128 minutes 29.03 seconds (7709.03 seconds total)