Starting phenix.real_space_refine on Tue Mar 19 04:12:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvo_32855/03_2024/7wvo_32855.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvo_32855/03_2024/7wvo_32855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvo_32855/03_2024/7wvo_32855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvo_32855/03_2024/7wvo_32855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvo_32855/03_2024/7wvo_32855.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvo_32855/03_2024/7wvo_32855.pdb" } resolution = 3.41 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= 0.002 sd= 0.029 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 106 5.16 5 C 14829 2.51 5 N 3860 2.21 5 O 4393 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "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: 23188 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "B" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'CIS': 2, 'PTRANS': 54, 'TRANS': 1000} Chain breaks: 7 Chain: "C" Number of atoms: 6676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 856, 6676 Classifications: {'peptide': 856} Link IDs: {'CIS': 2, 'PTRANS': 41, 'TRANS': 812} Chain breaks: 8 Time building chain proxies: 11.87, per 1000 atoms: 0.51 Number of scatterers: 23188 At special positions: 0 Unit cell: (147.555, 144.276, 197.833, 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 106 16.00 O 4393 8.00 N 3860 7.00 C 14829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, 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=2.03 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 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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: 7.45 Conformation dependent library (CDL) restraints added in 4.2 seconds 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5558 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 47 sheets defined 22.1% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.545A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.664A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.583A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.912A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.700A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.610A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 825 removed outlier: 3.787A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 removed outlier: 3.754A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.751A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.723A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 919' Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.690A pdb=" N ALA A 924 " --> pdb=" O GLN A 920 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 960 removed outlier: 3.720A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 965 removed outlier: 3.769A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.599A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 977 through 982' Processing helix chain 'A' and resid 985 through 1031 removed outlier: 3.939A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.514A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.171A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.569A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 410' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.602A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 639' Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.653A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 752 removed outlier: 3.577A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 759 removed outlier: 3.859A pdb=" N PHE B 759 " --> pdb=" O TYR B 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 756 through 759' Processing helix chain 'B' and resid 760 through 782 removed outlier: 3.737A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 4.036A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.503A pdb=" N ALA B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.888A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.621A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.767A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 919' Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.093A pdb=" N ALA B 924 " --> pdb=" O GLN B 920 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 926 " --> pdb=" O LEU B 922 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 963 removed outlier: 3.890A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.681A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.861A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.778A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.682A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 304 " --> pdb=" O LYS C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.773A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.760A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.794A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.793A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 4.005A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.526A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C 876 " --> pdb=" O GLN C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.738A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.783A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 919' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.768A pdb=" N ALA C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 963 removed outlier: 3.868A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.567A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.727A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR C1009 " --> pdb=" O GLN C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 3.882A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.761A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.686A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.568A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327 removed outlier: 4.990A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.691A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.691A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.278A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 454 removed outlier: 8.012A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR A 495 " --> pdb=" O TYR A 451 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.934A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.942A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.646A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.658A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.936A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.713A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASN B 188 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR B 208 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG B 190 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS B 206 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE B 192 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TYR B 204 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N PHE B 194 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LYS B 202 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN B 196 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TYR B 200 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.570A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.947A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 244 through 245 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.805A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.923A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 355 through 359 removed outlier: 3.659A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.670A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.745A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.727A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.363A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.895A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.052A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.862A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.773A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.773A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.648A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.565A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.307A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.811A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.701A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.700A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 706 hydrogen bonds defined for protein. 1935 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: 11.22 Time building geometry restraints manager: 8.31 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: 7394 1.35 - 1.47: 5833 1.47 - 1.59: 10353 1.59 - 1.71: 0 1.71 - 1.83: 136 Bond restraints: 23716 Sorted by residual: bond pdb=" C CYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.432 -0.098 2.34e-02 1.83e+03 1.75e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.424 -0.090 2.34e-02 1.83e+03 1.49e+01 bond pdb=" C VAL A 620 " pdb=" N PRO A 631 " ideal model delta sigma weight residual 1.341 1.384 -0.043 1.60e-02 3.91e+03 7.21e+00 bond pdb=" C GLN C1142 " pdb=" N PRO C1143 " ideal model delta sigma weight residual 1.336 1.363 -0.027 1.25e-02 6.40e+03 4.83e+00 bond pdb=" CA PHE C 157 " pdb=" CB PHE C 157 " ideal model delta sigma weight residual 1.530 1.571 -0.041 2.00e-02 2.50e+03 4.29e+00 ... (remaining 23711 not shown) Histogram of bond angle deviations from ideal: 99.99 - 107.17: 794 107.17 - 114.36: 13319 114.36 - 121.55: 12062 121.55 - 128.74: 5953 128.74 - 135.93: 114 Bond angle restraints: 32242 Sorted by residual: angle pdb=" C PHE B 157 " pdb=" N ARG B 158 " pdb=" CA ARG B 158 " ideal model delta sigma weight residual 121.70 133.40 -11.70 1.80e+00 3.09e-01 4.22e+01 angle pdb=" C ASN B 122 " pdb=" N ALA B 123 " pdb=" CA ALA B 123 " ideal model delta sigma weight residual 121.54 133.23 -11.69 1.91e+00 2.74e-01 3.75e+01 angle pdb=" C ASN A 122 " pdb=" N ALA A 123 " pdb=" CA ALA A 123 " ideal model delta sigma weight residual 121.54 132.95 -11.41 1.91e+00 2.74e-01 3.57e+01 angle pdb=" C GLY C 639 " pdb=" N SER C 640 " pdb=" CA SER C 640 " ideal model delta sigma weight residual 121.54 132.18 -10.64 1.91e+00 2.74e-01 3.10e+01 angle pdb=" C GLY B 639 " pdb=" N SER B 640 " pdb=" CA SER B 640 " ideal model delta sigma weight residual 121.54 131.95 -10.41 1.91e+00 2.74e-01 2.97e+01 ... (remaining 32237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 13750 15.96 - 31.92: 320 31.92 - 47.88: 84 47.88 - 63.84: 14 63.84 - 79.80: 1 Dihedral angle restraints: 14169 sinusoidal: 5550 harmonic: 8619 Sorted by residual: dihedral pdb=" CA PHE C 157 " pdb=" C PHE C 157 " pdb=" N ARG C 158 " pdb=" CA ARG C 158 " ideal model delta harmonic sigma weight residual 0.00 33.70 -33.70 0 5.00e+00 4.00e-02 4.54e+01 dihedral pdb=" CA PHE B 157 " pdb=" C PHE B 157 " pdb=" N ARG B 158 " pdb=" CA ARG B 158 " ideal model delta harmonic sigma weight residual 0.00 33.40 -33.40 0 5.00e+00 4.00e-02 4.46e+01 dihedral pdb=" CA PHE C 86 " pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta harmonic sigma weight residual -180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 14166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2881 0.061 - 0.122: 665 0.122 - 0.184: 92 0.184 - 0.245: 22 0.245 - 0.306: 7 Chirality restraints: 3667 Sorted by residual: chirality pdb=" CB ILE B 312 " pdb=" CA ILE B 312 " pdb=" CG1 ILE B 312 " pdb=" CG2 ILE B 312 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB ILE C 312 " pdb=" CA ILE C 312 " pdb=" CG1 ILE C 312 " pdb=" CG2 ILE C 312 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB ILE A 312 " pdb=" CA ILE A 312 " pdb=" CG1 ILE A 312 " pdb=" CG2 ILE A 312 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 3664 not shown) Planarity restraints: 4164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 25 " 0.065 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO B 26 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 26 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 26 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.058 5.00e-02 4.00e+02 8.79e-02 1.24e+01 pdb=" N PRO A 295 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 25 " 0.053 5.00e-02 4.00e+02 8.16e-02 1.06e+01 pdb=" N PRO A 26 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " 0.044 5.00e-02 4.00e+02 ... (remaining 4161 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 7370 2.86 - 3.37: 17247 3.37 - 3.88: 37117 3.88 - 4.39: 38676 4.39 - 4.90: 69531 Nonbonded interactions: 169941 Sorted by model distance: nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.354 2.440 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.367 2.440 nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.368 2.440 nonbonded pdb=" O GLY A1093 " pdb=" OH TYR C 904 " model vdw 2.369 2.440 nonbonded pdb=" O ASN A 978 " pdb=" OG SER A 982 " model vdw 2.373 2.440 ... (remaining 169936 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' and (resid 14 through 631 or resid 641 through 1147)) } 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: 4.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.600 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 61.110 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.110 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 23716 Z= 0.372 Angle : 0.833 11.698 32242 Z= 0.485 Chirality : 0.055 0.306 3667 Planarity : 0.007 0.101 4164 Dihedral : 8.312 79.801 8506 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.15 % Rotamer: Outliers : 0.08 % Allowed : 0.46 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.17 (0.12), residues: 2911 helix: -4.98 (0.05), residues: 561 sheet: -0.28 (0.18), residues: 543 loop : -1.76 (0.12), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 64 HIS 0.013 0.002 HIS C1048 PHE 0.025 0.003 PHE A 32 TYR 0.022 0.002 TYR A 873 ARG 0.007 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 779 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7159 (mtt-85) cc_final: 0.6399 (ttp80) REVERT: A 133 PHE cc_start: 0.5809 (m-10) cc_final: 0.5558 (m-10) REVERT: A 141 LEU cc_start: 0.5705 (mt) cc_final: 0.5462 (tt) REVERT: A 191 GLU cc_start: 0.7645 (mt-10) cc_final: 0.6747 (mt-10) REVERT: A 298 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6580 (mt-10) REVERT: A 305 SER cc_start: 0.8342 (t) cc_final: 0.8045 (t) REVERT: A 309 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7502 (mt-10) REVERT: A 321 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7623 (pm20) REVERT: A 536 ASN cc_start: 0.8375 (m-40) cc_final: 0.8151 (m-40) REVERT: A 591 SER cc_start: 0.8796 (t) cc_final: 0.8345 (p) REVERT: A 663 ASP cc_start: 0.7296 (m-30) cc_final: 0.7033 (m-30) REVERT: A 752 LEU cc_start: 0.8377 (mt) cc_final: 0.8062 (tt) REVERT: A 764 LYS cc_start: 0.8358 (mttt) cc_final: 0.8059 (ttmm) REVERT: A 773 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6947 (mm-30) REVERT: A 776 LYS cc_start: 0.8075 (mttt) cc_final: 0.7857 (mttt) REVERT: A 917 TYR cc_start: 0.6942 (m-80) cc_final: 0.5874 (m-80) REVERT: A 947 LYS cc_start: 0.7927 (mmtt) cc_final: 0.7463 (mtpp) REVERT: A 969 LYS cc_start: 0.8578 (mttt) cc_final: 0.8217 (mttt) REVERT: A 976 VAL cc_start: 0.8187 (t) cc_final: 0.7942 (t) REVERT: A 1028 LYS cc_start: 0.8278 (mttt) cc_final: 0.7781 (mmtp) REVERT: A 1116 THR cc_start: 0.7594 (p) cc_final: 0.7300 (p) REVERT: B 101 ILE cc_start: 0.8833 (mm) cc_final: 0.8521 (mm) REVERT: B 132 GLU cc_start: 0.5330 (mt-10) cc_final: 0.4321 (tt0) REVERT: B 195 LYS cc_start: 0.7702 (pttt) cc_final: 0.7270 (tppt) REVERT: B 206 LYS cc_start: 0.8185 (tptt) cc_final: 0.7831 (tptm) REVERT: B 315 THR cc_start: 0.9006 (m) cc_final: 0.8691 (p) REVERT: B 425 LEU cc_start: 0.8013 (mt) cc_final: 0.7727 (mm) REVERT: B 524 VAL cc_start: 0.7403 (t) cc_final: 0.7144 (m) REVERT: B 537 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8075 (mtpp) REVERT: B 599 THR cc_start: 0.7052 (t) cc_final: 0.6843 (t) REVERT: B 654 GLU cc_start: 0.7814 (tt0) cc_final: 0.7561 (tt0) REVERT: B 725 GLU cc_start: 0.7574 (tt0) cc_final: 0.7354 (tt0) REVERT: B 737 ASP cc_start: 0.7137 (t0) cc_final: 0.6924 (t0) REVERT: B 759 PHE cc_start: 0.7540 (t80) cc_final: 0.7285 (t80) REVERT: B 776 LYS cc_start: 0.8116 (mttt) cc_final: 0.7742 (mttt) REVERT: B 780 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6967 (mt-10) REVERT: B 884 SER cc_start: 0.8247 (m) cc_final: 0.7769 (t) REVERT: B 898 PHE cc_start: 0.6487 (t80) cc_final: 0.5915 (t80) REVERT: B 953 ASN cc_start: 0.8405 (m-40) cc_final: 0.7938 (m-40) REVERT: B 1004 LEU cc_start: 0.8083 (tp) cc_final: 0.7795 (mt) REVERT: B 1073 LYS cc_start: 0.7810 (tttt) cc_final: 0.7226 (ttmm) REVERT: B 1122 VAL cc_start: 0.7767 (t) cc_final: 0.7550 (p) REVERT: C 49 HIS cc_start: 0.7450 (t70) cc_final: 0.6901 (t70) REVERT: C 62 VAL cc_start: 0.7481 (m) cc_final: 0.7233 (p) REVERT: C 195 LYS cc_start: 0.7358 (pttt) cc_final: 0.6457 (tppt) REVERT: C 294 ASP cc_start: 0.7189 (m-30) cc_final: 0.6960 (t70) REVERT: C 296 LEU cc_start: 0.8423 (tp) cc_final: 0.8196 (tp) REVERT: C 299 THR cc_start: 0.8272 (m) cc_final: 0.7795 (p) REVERT: C 697 MET cc_start: 0.7834 (ttm) cc_final: 0.7616 (ttm) REVERT: C 721 SER cc_start: 0.7988 (t) cc_final: 0.7581 (p) REVERT: C 736 VAL cc_start: 0.9050 (t) cc_final: 0.8656 (m) REVERT: C 737 ASP cc_start: 0.7924 (t0) cc_final: 0.7477 (t0) REVERT: C 821 LEU cc_start: 0.8959 (mt) cc_final: 0.8669 (mt) REVERT: C 884 SER cc_start: 0.8889 (m) cc_final: 0.8414 (t) REVERT: C 898 PHE cc_start: 0.6387 (t80) cc_final: 0.4736 (t80) REVERT: C 935 GLN cc_start: 0.8073 (tt0) cc_final: 0.7363 (tt0) REVERT: C 947 LYS cc_start: 0.7615 (mttt) cc_final: 0.7378 (ttmm) REVERT: C 1141 LEU cc_start: 0.8111 (mt) cc_final: 0.7867 (mt) outliers start: 2 outliers final: 0 residues processed: 780 average time/residue: 0.3671 time to fit residues: 430.7849 Evaluate side-chains 589 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 589 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 2.9990 chunk 222 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 230 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 266 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 414 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 564 GLN A 613 GLN A 641 ASN A 762 GLN A 895 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN A 955 ASN A 965 GLN A1119 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 409 GLN B 519 HIS B 544 ASN B 717 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 914 ASN B 935 GLN B 955 ASN B1083 HIS C 66 HIS C 188 ASN C 239 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 717 ASN C 895 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 23716 Z= 0.317 Angle : 0.686 12.524 32242 Z= 0.359 Chirality : 0.047 0.253 3667 Planarity : 0.005 0.053 4164 Dihedral : 4.974 25.493 3163 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.78 % Allowed : 8.87 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -1.99 (0.13), residues: 2911 helix: -2.78 (0.15), residues: 586 sheet: 0.16 (0.19), residues: 586 loop : -1.33 (0.12), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 886 HIS 0.009 0.002 HIS C1064 PHE 0.028 0.002 PHE A 559 TYR 0.020 0.002 TYR B 501 ARG 0.008 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 612 time to evaluate : 2.460 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 66 HIS cc_start: 0.6399 (t-170) cc_final: 0.6061 (t70) REVERT: A 226 LEU cc_start: 0.8086 (tp) cc_final: 0.7822 (tp) REVERT: A 290 ASP cc_start: 0.7908 (t0) cc_final: 0.7679 (t0) REVERT: A 305 SER cc_start: 0.8888 (t) cc_final: 0.8654 (m) REVERT: A 321 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7843 (pm20) REVERT: A 592 PHE cc_start: 0.7973 (p90) cc_final: 0.7704 (p90) REVERT: A 702 GLU cc_start: 0.6399 (tt0) cc_final: 0.6129 (tt0) REVERT: A 752 LEU cc_start: 0.8792 (mt) cc_final: 0.8517 (tt) REVERT: A 773 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7032 (mm-30) REVERT: A 780 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7250 (mt-10) REVERT: A 886 TRP cc_start: 0.8850 (p90) cc_final: 0.8125 (p90) REVERT: A 964 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8602 (mtpp) REVERT: A 969 LYS cc_start: 0.8859 (mttt) cc_final: 0.8537 (mttt) REVERT: A 984 LEU cc_start: 0.8014 (mp) cc_final: 0.7645 (tp) REVERT: A 1029 MET cc_start: 0.8130 (tpp) cc_final: 0.7904 (tpp) REVERT: A 1038 LYS cc_start: 0.8529 (mttt) cc_final: 0.8195 (mmmm) REVERT: A 1086 LYS cc_start: 0.8630 (pttt) cc_final: 0.8255 (pttp) REVERT: B 52 GLN cc_start: 0.6587 (tp-100) cc_final: 0.6364 (tp40) REVERT: B 191 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7356 (mt-10) REVERT: B 195 LYS cc_start: 0.8194 (pttt) cc_final: 0.7403 (tppt) REVERT: B 206 LYS cc_start: 0.8770 (tptt) cc_final: 0.8330 (tptp) REVERT: B 271 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7800 (mm-40) REVERT: B 309 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6547 (mt-10) REVERT: B 315 THR cc_start: 0.8729 (m) cc_final: 0.8349 (p) REVERT: B 351 TYR cc_start: 0.6797 (p90) cc_final: 0.6363 (p90) REVERT: B 386 LYS cc_start: 0.8298 (mttt) cc_final: 0.8016 (mmtm) REVERT: B 425 LEU cc_start: 0.8168 (mt) cc_final: 0.7793 (mm) REVERT: B 493 ARG cc_start: 0.7427 (mtp85) cc_final: 0.7062 (mpt180) REVERT: B 528 LYS cc_start: 0.6817 (ttpt) cc_final: 0.5927 (ttpt) REVERT: B 537 LYS cc_start: 0.8162 (ttmt) cc_final: 0.7835 (mtpp) REVERT: B 556 ASN cc_start: 0.7998 (p0) cc_final: 0.7688 (p0) REVERT: B 581 THR cc_start: 0.7869 (m) cc_final: 0.7452 (m) REVERT: B 721 SER cc_start: 0.8392 (t) cc_final: 0.8183 (t) REVERT: B 752 LEU cc_start: 0.9090 (mt) cc_final: 0.8480 (mp) REVERT: B 796 TYR cc_start: 0.7484 (t80) cc_final: 0.7238 (t80) REVERT: B 825 LYS cc_start: 0.8423 (mtpp) cc_final: 0.7857 (mtpt) REVERT: B 884 SER cc_start: 0.8560 (m) cc_final: 0.8211 (t) REVERT: B 900 MET cc_start: 0.7757 (mmm) cc_final: 0.7315 (mtt) REVERT: B 933 LYS cc_start: 0.8701 (mttt) cc_final: 0.8069 (mtmm) REVERT: B 935 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: B 960 ASN cc_start: 0.8813 (m-40) cc_final: 0.8573 (t0) REVERT: B 1010 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7925 (mm-40) REVERT: B 1073 LYS cc_start: 0.8216 (tttt) cc_final: 0.7971 (mttp) REVERT: B 1084 ASP cc_start: 0.7597 (p0) cc_final: 0.7226 (p0) REVERT: B 1125 ASN cc_start: 0.8502 (p0) cc_final: 0.8291 (p0) REVERT: C 42 VAL cc_start: 0.8563 (t) cc_final: 0.8350 (m) REVERT: C 49 HIS cc_start: 0.7568 (t70) cc_final: 0.7015 (t70) REVERT: C 62 VAL cc_start: 0.7922 (m) cc_final: 0.7482 (p) REVERT: C 170 TYR cc_start: 0.8314 (t80) cc_final: 0.7974 (t80) REVERT: C 195 LYS cc_start: 0.8096 (pttt) cc_final: 0.7179 (tppt) REVERT: C 206 LYS cc_start: 0.8541 (tptt) cc_final: 0.8232 (tptp) REVERT: C 267 VAL cc_start: 0.8095 (p) cc_final: 0.7847 (p) REVERT: C 289 VAL cc_start: 0.8482 (t) cc_final: 0.8187 (p) REVERT: C 299 THR cc_start: 0.8476 (m) cc_final: 0.8152 (p) REVERT: C 583 GLU cc_start: 0.7816 (pm20) cc_final: 0.6966 (pm20) REVERT: C 697 MET cc_start: 0.7967 (ttm) cc_final: 0.7661 (ttm) REVERT: C 710 ASN cc_start: 0.8771 (p0) cc_final: 0.8473 (p0) REVERT: C 736 VAL cc_start: 0.9146 (t) cc_final: 0.8919 (m) REVERT: C 737 ASP cc_start: 0.8059 (t0) cc_final: 0.7715 (t0) REVERT: C 779 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7922 (mm-40) REVERT: C 790 LYS cc_start: 0.8347 (mttt) cc_final: 0.7573 (mttt) REVERT: C 804 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7287 (mm-40) REVERT: C 821 LEU cc_start: 0.8955 (mt) cc_final: 0.8693 (mt) REVERT: C 884 SER cc_start: 0.8995 (m) cc_final: 0.8548 (t) REVERT: C 905 ARG cc_start: 0.8262 (mtt180) cc_final: 0.8045 (mtt180) REVERT: C 986 PRO cc_start: 0.8389 (Cg_exo) cc_final: 0.8050 (Cg_endo) REVERT: C 1006 THR cc_start: 0.8631 (m) cc_final: 0.8300 (p) REVERT: C 1019 ARG cc_start: 0.7473 (tpt170) cc_final: 0.6712 (tpt170) REVERT: C 1073 LYS cc_start: 0.8229 (tttt) cc_final: 0.7906 (mtpp) REVERT: C 1086 LYS cc_start: 0.7138 (mtmm) cc_final: 0.6708 (mtmm) outliers start: 72 outliers final: 45 residues processed: 658 average time/residue: 0.3652 time to fit residues: 363.2306 Evaluate side-chains 586 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 540 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 chunk 181 optimal weight: 0.0270 chunk 73 optimal weight: 3.9990 chunk 267 optimal weight: 0.7980 chunk 288 optimal weight: 0.7980 chunk 238 optimal weight: 6.9990 chunk 265 optimal weight: 0.0060 chunk 91 optimal weight: 0.6980 chunk 214 optimal weight: 1.9990 overall best weight: 0.4654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 506 GLN A 563 GLN A 613 GLN A 872 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1083 HIS ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 239 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN C1083 HIS C1113 GLN C1119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23716 Z= 0.174 Angle : 0.580 11.490 32242 Z= 0.294 Chirality : 0.044 0.193 3667 Planarity : 0.004 0.058 4164 Dihedral : 4.546 20.967 3163 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.66 % Allowed : 13.45 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -1.09 (0.14), residues: 2911 helix: -0.75 (0.20), residues: 586 sheet: 0.37 (0.19), residues: 616 loop : -1.14 (0.13), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 104 HIS 0.006 0.001 HIS B 505 PHE 0.040 0.002 PHE B 342 TYR 0.021 0.001 TYR B 501 ARG 0.008 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 543 time to evaluate : 2.310 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 62 VAL cc_start: 0.8203 (m) cc_final: 0.7948 (p) REVERT: A 141 LEU cc_start: 0.6183 (mm) cc_final: 0.5440 (tt) REVERT: A 194 PHE cc_start: 0.7298 (m-10) cc_final: 0.6842 (m-10) REVERT: A 202 LYS cc_start: 0.8365 (mttp) cc_final: 0.8142 (mttp) REVERT: A 290 ASP cc_start: 0.7950 (t0) cc_final: 0.7714 (t0) REVERT: A 304 LYS cc_start: 0.8620 (mmmt) cc_final: 0.8325 (mmmt) REVERT: A 305 SER cc_start: 0.8957 (t) cc_final: 0.8717 (m) REVERT: A 321 GLN cc_start: 0.8454 (mm-40) cc_final: 0.7786 (pm20) REVERT: A 539 VAL cc_start: 0.8160 (m) cc_final: 0.7884 (p) REVERT: A 644 GLN cc_start: 0.7224 (tp40) cc_final: 0.6859 (tp40) REVERT: A 702 GLU cc_start: 0.6393 (tt0) cc_final: 0.6113 (tt0) REVERT: A 752 LEU cc_start: 0.8756 (mt) cc_final: 0.8464 (tp) REVERT: A 773 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7136 (mm-30) REVERT: A 776 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7943 (ttpp) REVERT: A 780 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6949 (mt-10) REVERT: A 886 TRP cc_start: 0.8965 (p90) cc_final: 0.8217 (p90) REVERT: A 953 ASN cc_start: 0.8158 (m-40) cc_final: 0.7927 (m-40) REVERT: A 969 LYS cc_start: 0.8866 (mttt) cc_final: 0.8540 (mttt) REVERT: A 977 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8538 (mt) REVERT: A 984 LEU cc_start: 0.8109 (mp) cc_final: 0.7549 (tp) REVERT: A 1019 ARG cc_start: 0.8177 (tpp-160) cc_final: 0.7871 (tpp-160) REVERT: A 1038 LYS cc_start: 0.8608 (mttt) cc_final: 0.8254 (mmmm) REVERT: A 1086 LYS cc_start: 0.8546 (pttt) cc_final: 0.8194 (pttp) REVERT: A 1111 GLU cc_start: 0.8096 (pm20) cc_final: 0.7800 (pm20) REVERT: B 191 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7180 (mt-10) REVERT: B 195 LYS cc_start: 0.8245 (pttt) cc_final: 0.7553 (tppt) REVERT: B 206 LYS cc_start: 0.8834 (tptt) cc_final: 0.8302 (tptm) REVERT: B 315 THR cc_start: 0.8595 (m) cc_final: 0.8120 (p) REVERT: B 351 TYR cc_start: 0.6760 (p90) cc_final: 0.6297 (p90) REVERT: B 386 LYS cc_start: 0.8317 (mttt) cc_final: 0.7968 (mttt) REVERT: B 425 LEU cc_start: 0.8158 (mt) cc_final: 0.7756 (mm) REVERT: B 516 GLU cc_start: 0.5391 (tm-30) cc_final: 0.3001 (tt0) REVERT: B 528 LYS cc_start: 0.6885 (ttpt) cc_final: 0.5652 (ttmm) REVERT: B 556 ASN cc_start: 0.8106 (p0) cc_final: 0.7709 (p0) REVERT: B 721 SER cc_start: 0.8517 (t) cc_final: 0.7919 (p) REVERT: B 796 TYR cc_start: 0.7559 (t80) cc_final: 0.7214 (t80) REVERT: B 804 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8103 (mt0) REVERT: B 825 LYS cc_start: 0.8408 (mtpp) cc_final: 0.7783 (mtpt) REVERT: B 884 SER cc_start: 0.8537 (m) cc_final: 0.8192 (t) REVERT: B 900 MET cc_start: 0.7528 (mmm) cc_final: 0.7174 (mtt) REVERT: B 933 LYS cc_start: 0.8661 (mttt) cc_final: 0.8088 (mtmm) REVERT: B 935 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: B 1005 GLN cc_start: 0.8339 (mm-40) cc_final: 0.8026 (tp40) REVERT: B 1073 LYS cc_start: 0.8254 (tttt) cc_final: 0.7950 (mtpp) REVERT: B 1076 THR cc_start: 0.8816 (m) cc_final: 0.8467 (t) REVERT: B 1084 ASP cc_start: 0.7476 (p0) cc_final: 0.6804 (p0) REVERT: B 1086 LYS cc_start: 0.7334 (mttt) cc_final: 0.7033 (mttt) REVERT: C 41 LYS cc_start: 0.5444 (tptt) cc_final: 0.5069 (tptt) REVERT: C 42 VAL cc_start: 0.8514 (t) cc_final: 0.8284 (m) REVERT: C 62 VAL cc_start: 0.7904 (m) cc_final: 0.7462 (p) REVERT: C 104 TRP cc_start: 0.6889 (m-90) cc_final: 0.6661 (m-90) REVERT: C 191 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7397 (mt-10) REVERT: C 195 LYS cc_start: 0.8028 (pttt) cc_final: 0.7263 (tppt) REVERT: C 267 VAL cc_start: 0.8074 (p) cc_final: 0.7798 (p) REVERT: C 289 VAL cc_start: 0.8543 (t) cc_final: 0.8266 (p) REVERT: C 299 THR cc_start: 0.8469 (m) cc_final: 0.8073 (p) REVERT: C 304 LYS cc_start: 0.8688 (mttt) cc_final: 0.8438 (mttt) REVERT: C 583 GLU cc_start: 0.7668 (pm20) cc_final: 0.7441 (pm20) REVERT: C 643 PHE cc_start: 0.8302 (t80) cc_final: 0.7997 (t80) REVERT: C 697 MET cc_start: 0.7971 (ttm) cc_final: 0.7710 (ttm) REVERT: C 710 ASN cc_start: 0.8849 (p0) cc_final: 0.8533 (p0) REVERT: C 736 VAL cc_start: 0.9174 (t) cc_final: 0.8820 (m) REVERT: C 737 ASP cc_start: 0.8075 (t0) cc_final: 0.7793 (t0) REVERT: C 779 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7814 (mm-40) REVERT: C 790 LYS cc_start: 0.8310 (mttt) cc_final: 0.7621 (mttt) REVERT: C 804 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7755 (mm-40) REVERT: C 825 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8314 (mtpp) REVERT: C 884 SER cc_start: 0.8949 (m) cc_final: 0.8564 (t) REVERT: C 905 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7901 (mtt90) REVERT: C 1006 THR cc_start: 0.8534 (m) cc_final: 0.8265 (p) REVERT: C 1031 GLU cc_start: 0.7309 (mt-10) cc_final: 0.7075 (mt-10) REVERT: C 1073 LYS cc_start: 0.8141 (tttt) cc_final: 0.7827 (mtpp) REVERT: C 1086 LYS cc_start: 0.7188 (mtmm) cc_final: 0.6921 (mtmm) outliers start: 69 outliers final: 49 residues processed: 584 average time/residue: 0.3767 time to fit residues: 332.9239 Evaluate side-chains 575 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 523 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 268 optimal weight: 2.9990 chunk 284 optimal weight: 0.0040 chunk 140 optimal weight: 0.2980 chunk 254 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1142 GLN C 901 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN C1071 GLN C1083 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23716 Z= 0.181 Angle : 0.562 13.570 32242 Z= 0.281 Chirality : 0.043 0.173 3667 Planarity : 0.004 0.068 4164 Dihedral : 4.323 19.567 3163 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.24 % Allowed : 13.76 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.60 (0.14), residues: 2911 helix: 0.36 (0.21), residues: 604 sheet: 0.52 (0.20), residues: 593 loop : -1.02 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 104 HIS 0.004 0.001 HIS B 505 PHE 0.050 0.001 PHE B 342 TYR 0.016 0.001 TYR C 796 ARG 0.010 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 536 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8103 (mt) cc_final: 0.7737 (mm) REVERT: A 141 LEU cc_start: 0.6362 (mm) cc_final: 0.5564 (tp) REVERT: A 191 GLU cc_start: 0.4990 (tp30) cc_final: 0.4203 (mm-30) REVERT: A 202 LYS cc_start: 0.8448 (mttp) cc_final: 0.8152 (mttp) REVERT: A 224 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: A 281 GLU cc_start: 0.7906 (pm20) cc_final: 0.7404 (pm20) REVERT: A 290 ASP cc_start: 0.7993 (t0) cc_final: 0.7784 (t0) REVERT: A 321 GLN cc_start: 0.8508 (mm-40) cc_final: 0.7891 (pm20) REVERT: A 539 VAL cc_start: 0.8089 (m) cc_final: 0.7884 (p) REVERT: A 654 GLU cc_start: 0.7805 (tt0) cc_final: 0.7480 (tt0) REVERT: A 752 LEU cc_start: 0.8772 (mt) cc_final: 0.8480 (tp) REVERT: A 776 LYS cc_start: 0.8135 (ttpp) cc_final: 0.7476 (ttpp) REVERT: A 817 PHE cc_start: 0.8476 (t80) cc_final: 0.8171 (t80) REVERT: A 869 MET cc_start: 0.8200 (mtm) cc_final: 0.7984 (mtp) REVERT: A 902 MET cc_start: 0.8436 (mmm) cc_final: 0.8178 (tpp) REVERT: A 933 LYS cc_start: 0.8573 (mttm) cc_final: 0.8216 (mttp) REVERT: A 953 ASN cc_start: 0.8119 (m-40) cc_final: 0.7867 (m-40) REVERT: A 969 LYS cc_start: 0.8964 (mttt) cc_final: 0.8582 (mttt) REVERT: A 984 LEU cc_start: 0.8117 (mp) cc_final: 0.7797 (tp) REVERT: A 1038 LYS cc_start: 0.8735 (mttt) cc_final: 0.8388 (mmmm) REVERT: A 1045 LYS cc_start: 0.8490 (tmtt) cc_final: 0.8133 (tptt) REVERT: A 1111 GLU cc_start: 0.7952 (pm20) cc_final: 0.7622 (pm20) REVERT: B 191 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7225 (mt-10) REVERT: B 206 LYS cc_start: 0.8859 (tptt) cc_final: 0.8464 (tptm) REVERT: B 271 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7741 (mm-40) REVERT: B 338 PHE cc_start: 0.7258 (m-10) cc_final: 0.6565 (m-10) REVERT: B 351 TYR cc_start: 0.6829 (p90) cc_final: 0.6328 (p90) REVERT: B 528 LYS cc_start: 0.7012 (ttpt) cc_final: 0.5754 (ttmm) REVERT: B 556 ASN cc_start: 0.8201 (p0) cc_final: 0.7792 (p0) REVERT: B 560 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5954 (tt) REVERT: B 721 SER cc_start: 0.8543 (t) cc_final: 0.7981 (p) REVERT: B 796 TYR cc_start: 0.7594 (t80) cc_final: 0.7368 (t80) REVERT: B 825 LYS cc_start: 0.8493 (mtpp) cc_final: 0.8021 (mtpp) REVERT: B 884 SER cc_start: 0.8457 (m) cc_final: 0.8114 (t) REVERT: B 900 MET cc_start: 0.7444 (mmm) cc_final: 0.7133 (mtm) REVERT: B 921 LYS cc_start: 0.8205 (mmmt) cc_final: 0.7818 (tptm) REVERT: B 933 LYS cc_start: 0.8633 (mttt) cc_final: 0.8142 (mtmm) REVERT: B 935 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: B 992 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8352 (mp10) REVERT: B 1005 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7984 (tp40) REVERT: B 1073 LYS cc_start: 0.8253 (tttt) cc_final: 0.8034 (mttm) REVERT: B 1084 ASP cc_start: 0.7547 (p0) cc_final: 0.6941 (p0) REVERT: B 1086 LYS cc_start: 0.7422 (mttt) cc_final: 0.7116 (mttt) REVERT: C 41 LYS cc_start: 0.5857 (tptt) cc_final: 0.5339 (tptt) REVERT: C 44 ARG cc_start: 0.7997 (mtt-85) cc_final: 0.7759 (mtt180) REVERT: C 119 ILE cc_start: 0.5608 (mm) cc_final: 0.5354 (mm) REVERT: C 191 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7443 (mt-10) REVERT: C 289 VAL cc_start: 0.8547 (t) cc_final: 0.8186 (p) REVERT: C 299 THR cc_start: 0.8498 (m) cc_final: 0.8105 (p) REVERT: C 304 LYS cc_start: 0.8791 (mttt) cc_final: 0.8567 (mttt) REVERT: C 534 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.8992 (m) REVERT: C 583 GLU cc_start: 0.7606 (pm20) cc_final: 0.7346 (pm20) REVERT: C 697 MET cc_start: 0.8018 (ttm) cc_final: 0.7754 (ttm) REVERT: C 710 ASN cc_start: 0.8923 (p0) cc_final: 0.8641 (p0) REVERT: C 737 ASP cc_start: 0.8103 (t0) cc_final: 0.7820 (t0) REVERT: C 751 ASN cc_start: 0.8622 (m-40) cc_final: 0.8239 (m-40) REVERT: C 790 LYS cc_start: 0.8325 (mttt) cc_final: 0.7764 (mttt) REVERT: C 804 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7782 (mm-40) REVERT: C 825 LYS cc_start: 0.8634 (mtpp) cc_final: 0.8244 (mtpp) REVERT: C 859 THR cc_start: 0.7601 (t) cc_final: 0.7368 (p) REVERT: C 884 SER cc_start: 0.8813 (m) cc_final: 0.8451 (t) REVERT: C 905 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7903 (mtt90) REVERT: C 957 GLN cc_start: 0.7941 (tt0) cc_final: 0.7607 (tm-30) REVERT: C 969 LYS cc_start: 0.8737 (mttt) cc_final: 0.8417 (mmmm) REVERT: C 984 LEU cc_start: 0.7561 (mt) cc_final: 0.6941 (tp) REVERT: C 1006 THR cc_start: 0.8462 (m) cc_final: 0.8251 (p) REVERT: C 1031 GLU cc_start: 0.7302 (mt-10) cc_final: 0.7048 (mt-10) REVERT: C 1073 LYS cc_start: 0.8053 (tttt) cc_final: 0.7827 (mtpp) REVERT: C 1081 ILE cc_start: 0.7866 (pt) cc_final: 0.7636 (mt) outliers start: 84 outliers final: 58 residues processed: 580 average time/residue: 0.3708 time to fit residues: 322.6337 Evaluate side-chains 559 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 497 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 255 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 439 ASN A 613 GLN A 895 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 343 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.6854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 23716 Z= 0.402 Angle : 0.695 10.346 32242 Z= 0.363 Chirality : 0.048 0.241 3667 Planarity : 0.005 0.075 4164 Dihedral : 4.951 21.375 3163 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.47 % Allowed : 13.53 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.76 (0.15), residues: 2911 helix: 0.36 (0.21), residues: 625 sheet: 0.20 (0.19), residues: 631 loop : -1.15 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP A 104 HIS 0.012 0.002 HIS B 505 PHE 0.034 0.003 PHE C 168 TYR 0.039 0.002 TYR A 91 ARG 0.011 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 567 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.9000 (t) cc_final: 0.8754 (p) REVERT: A 52 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7799 (tm-30) REVERT: A 141 LEU cc_start: 0.6914 (mm) cc_final: 0.6085 (tp) REVERT: A 191 GLU cc_start: 0.4254 (tp30) cc_final: 0.2514 (mm-30) REVERT: A 192 PHE cc_start: 0.8009 (m-80) cc_final: 0.7434 (m-10) REVERT: A 202 LYS cc_start: 0.8526 (mttp) cc_final: 0.8272 (mttp) REVERT: A 298 GLU cc_start: 0.7984 (tp30) cc_final: 0.7768 (tp30) REVERT: A 304 LYS cc_start: 0.8821 (mmmm) cc_final: 0.8619 (mmmm) REVERT: A 321 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8274 (pm20) REVERT: A 591 SER cc_start: 0.8639 (t) cc_final: 0.8203 (p) REVERT: A 654 GLU cc_start: 0.7861 (tt0) cc_final: 0.7588 (tt0) REVERT: A 745 ASP cc_start: 0.6660 (t0) cc_final: 0.6269 (t0) REVERT: A 752 LEU cc_start: 0.8944 (mt) cc_final: 0.8577 (tp) REVERT: A 776 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7752 (ttpp) REVERT: A 790 LYS cc_start: 0.8600 (mttt) cc_final: 0.8374 (mttt) REVERT: A 969 LYS cc_start: 0.8991 (mttt) cc_final: 0.8698 (mttt) REVERT: A 984 LEU cc_start: 0.8210 (mp) cc_final: 0.7929 (tp) REVERT: A 988 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6360 (mt-10) REVERT: A 1038 LYS cc_start: 0.8929 (mttt) cc_final: 0.8584 (mmmm) REVERT: A 1111 GLU cc_start: 0.7989 (pm20) cc_final: 0.7761 (pm20) REVERT: B 125 ASN cc_start: 0.3219 (OUTLIER) cc_final: 0.2034 (m-40) REVERT: B 191 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7231 (mt-10) REVERT: B 206 LYS cc_start: 0.8704 (tptt) cc_final: 0.8363 (tptm) REVERT: B 231 ILE cc_start: 0.9031 (mp) cc_final: 0.8774 (mp) REVERT: B 309 GLU cc_start: 0.6957 (mp0) cc_final: 0.6501 (mp0) REVERT: B 329 PHE cc_start: 0.6270 (t80) cc_final: 0.5870 (t80) REVERT: B 351 TYR cc_start: 0.7107 (p90) cc_final: 0.6576 (p90) REVERT: B 392 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.6935 (m-10) REVERT: B 528 LYS cc_start: 0.7311 (ttpt) cc_final: 0.6572 (mtpt) REVERT: B 537 LYS cc_start: 0.8518 (ttpp) cc_final: 0.8264 (tttm) REVERT: B 556 ASN cc_start: 0.8505 (p0) cc_final: 0.8246 (p0) REVERT: B 674 TYR cc_start: 0.8300 (t80) cc_final: 0.8094 (t80) REVERT: B 814 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7855 (mmtt) REVERT: B 867 ASP cc_start: 0.7449 (p0) cc_final: 0.7128 (t0) REVERT: B 884 SER cc_start: 0.8665 (m) cc_final: 0.8161 (t) REVERT: B 900 MET cc_start: 0.7645 (mmm) cc_final: 0.7055 (mtm) REVERT: B 921 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8040 (tptm) REVERT: B 931 ILE cc_start: 0.8768 (tp) cc_final: 0.8420 (mt) REVERT: B 1005 GLN cc_start: 0.8297 (mm-40) cc_final: 0.8041 (tp40) REVERT: B 1073 LYS cc_start: 0.8195 (tttt) cc_final: 0.7931 (mttm) REVERT: B 1084 ASP cc_start: 0.7823 (p0) cc_final: 0.6677 (p0) REVERT: B 1086 LYS cc_start: 0.7721 (mttt) cc_final: 0.7153 (mttt) REVERT: B 1111 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: C 31 SER cc_start: 0.8414 (t) cc_final: 0.8139 (p) REVERT: C 41 LYS cc_start: 0.6059 (tptt) cc_final: 0.5560 (tptt) REVERT: C 44 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.7665 (mtt-85) REVERT: C 49 HIS cc_start: 0.7519 (t70) cc_final: 0.6859 (t-90) REVERT: C 54 LEU cc_start: 0.8937 (mt) cc_final: 0.8726 (mm) REVERT: C 55 PHE cc_start: 0.8514 (m-10) cc_final: 0.8167 (m-80) REVERT: C 170 TYR cc_start: 0.8325 (t80) cc_final: 0.7757 (t80) REVERT: C 191 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7709 (mt-10) REVERT: C 281 GLU cc_start: 0.7005 (pp20) cc_final: 0.6600 (pp20) REVERT: C 289 VAL cc_start: 0.8743 (t) cc_final: 0.8362 (p) REVERT: C 317 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.7360 (m-40) REVERT: C 613 GLN cc_start: 0.7680 (tp40) cc_final: 0.7227 (mt0) REVERT: C 646 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7765 (mpp80) REVERT: C 725 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7110 (mt-10) REVERT: C 737 ASP cc_start: 0.8320 (t0) cc_final: 0.7992 (t0) REVERT: C 739 THR cc_start: 0.8662 (m) cc_final: 0.8328 (p) REVERT: C 751 ASN cc_start: 0.8866 (m-40) cc_final: 0.8524 (m-40) REVERT: C 814 LYS cc_start: 0.8277 (mmmt) cc_final: 0.7872 (mmmt) REVERT: C 859 THR cc_start: 0.7987 (t) cc_final: 0.7749 (p) REVERT: C 868 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7483 (mm-30) REVERT: C 884 SER cc_start: 0.8821 (m) cc_final: 0.8432 (t) REVERT: C 955 ASN cc_start: 0.7998 (m-40) cc_final: 0.7463 (t0) REVERT: C 957 GLN cc_start: 0.8042 (tt0) cc_final: 0.7759 (tm-30) REVERT: C 984 LEU cc_start: 0.7907 (mt) cc_final: 0.7559 (tp) REVERT: C 1006 THR cc_start: 0.8584 (m) cc_final: 0.8362 (p) REVERT: C 1017 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: C 1031 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7192 (mt-10) REVERT: C 1081 ILE cc_start: 0.8142 (pt) cc_final: 0.7909 (mt) REVERT: C 1103 PHE cc_start: 0.8371 (m-10) cc_final: 0.8161 (m-10) REVERT: C 1107 ARG cc_start: 0.7843 (tpt170) cc_final: 0.7632 (tpt170) REVERT: C 1119 ASN cc_start: 0.7708 (t160) cc_final: 0.7298 (t0) REVERT: C 1127 ASP cc_start: 0.8078 (p0) cc_final: 0.7729 (p0) outliers start: 116 outliers final: 79 residues processed: 623 average time/residue: 0.3660 time to fit residues: 345.0899 Evaluate side-chains 609 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 524 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 2.9990 chunk 255 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 166 optimal weight: 0.0170 chunk 70 optimal weight: 0.0770 chunk 284 optimal weight: 0.5980 chunk 236 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 394 ASN A 613 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 755 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23716 Z= 0.180 Angle : 0.580 10.473 32242 Z= 0.293 Chirality : 0.044 0.173 3667 Planarity : 0.004 0.051 4164 Dihedral : 4.556 22.350 3163 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.78 % Allowed : 16.65 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.49 (0.15), residues: 2911 helix: 0.84 (0.22), residues: 621 sheet: 0.42 (0.20), residues: 592 loop : -1.08 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 104 HIS 0.006 0.001 HIS B 505 PHE 0.022 0.002 PHE A 565 TYR 0.020 0.001 TYR A 91 ARG 0.006 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 539 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.9023 (t) cc_final: 0.8797 (p) REVERT: A 52 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7745 (tm-30) REVERT: A 104 TRP cc_start: 0.7818 (m-90) cc_final: 0.7413 (m-10) REVERT: A 105 ILE cc_start: 0.8137 (mt) cc_final: 0.7806 (mm) REVERT: A 191 GLU cc_start: 0.3977 (tp30) cc_final: 0.2849 (mm-30) REVERT: A 192 PHE cc_start: 0.8016 (m-80) cc_final: 0.7573 (m-80) REVERT: A 194 PHE cc_start: 0.7828 (m-10) cc_final: 0.7153 (m-10) REVERT: A 202 LYS cc_start: 0.8519 (mttp) cc_final: 0.8256 (mttp) REVERT: A 239 GLN cc_start: 0.8178 (tt0) cc_final: 0.7635 (tm-30) REVERT: A 304 LYS cc_start: 0.8790 (mmmm) cc_final: 0.8557 (mmmm) REVERT: A 321 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8337 (pm20) REVERT: A 591 SER cc_start: 0.8560 (t) cc_final: 0.8127 (p) REVERT: A 654 GLU cc_start: 0.7796 (tt0) cc_final: 0.7527 (tt0) REVERT: A 745 ASP cc_start: 0.6642 (t0) cc_final: 0.6360 (t0) REVERT: A 752 LEU cc_start: 0.8833 (mt) cc_final: 0.8464 (tp) REVERT: A 776 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7874 (ttpp) REVERT: A 790 LYS cc_start: 0.8488 (mttt) cc_final: 0.8212 (mttt) REVERT: A 902 MET cc_start: 0.8313 (tpp) cc_final: 0.7744 (tpt) REVERT: A 969 LYS cc_start: 0.8969 (mttt) cc_final: 0.8659 (mttt) REVERT: A 973 ILE cc_start: 0.8756 (pt) cc_final: 0.8412 (pt) REVERT: A 984 LEU cc_start: 0.8162 (mp) cc_final: 0.7848 (tp) REVERT: A 1038 LYS cc_start: 0.8875 (mttt) cc_final: 0.8510 (mmmm) REVERT: A 1045 LYS cc_start: 0.8503 (tmtt) cc_final: 0.8151 (tptt) REVERT: A 1111 GLU cc_start: 0.8029 (pm20) cc_final: 0.7728 (pm20) REVERT: B 191 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6989 (mt-10) REVERT: B 202 LYS cc_start: 0.7223 (mptt) cc_final: 0.6757 (mptt) REVERT: B 206 LYS cc_start: 0.8761 (tptt) cc_final: 0.8416 (tptm) REVERT: B 231 ILE cc_start: 0.9008 (mp) cc_final: 0.8805 (mp) REVERT: B 271 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7793 (mm-40) REVERT: B 309 GLU cc_start: 0.7073 (mp0) cc_final: 0.6589 (mp0) REVERT: B 351 TYR cc_start: 0.7044 (p90) cc_final: 0.6487 (p90) REVERT: B 528 LYS cc_start: 0.7212 (ttpt) cc_final: 0.6405 (mtmt) REVERT: B 556 ASN cc_start: 0.8393 (p0) cc_final: 0.8152 (p0) REVERT: B 558 LYS cc_start: 0.7185 (mttt) cc_final: 0.6872 (pttt) REVERT: B 559 PHE cc_start: 0.6028 (m-80) cc_final: 0.5492 (m-10) REVERT: B 762 GLN cc_start: 0.8220 (pp30) cc_final: 0.7949 (pp30) REVERT: B 814 LYS cc_start: 0.8199 (mmtt) cc_final: 0.7814 (mmtt) REVERT: B 817 PHE cc_start: 0.8652 (t80) cc_final: 0.8287 (t80) REVERT: B 884 SER cc_start: 0.8575 (m) cc_final: 0.8341 (t) REVERT: B 900 MET cc_start: 0.7302 (mmm) cc_final: 0.6700 (mtp) REVERT: B 921 LYS cc_start: 0.8279 (mmmt) cc_final: 0.7993 (tptm) REVERT: B 949 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7112 (mm-40) REVERT: B 969 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8388 (mmmm) REVERT: B 1005 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7943 (tp40) REVERT: B 1073 LYS cc_start: 0.8076 (tttt) cc_final: 0.7856 (mttm) REVERT: B 1111 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: C 31 SER cc_start: 0.8394 (t) cc_final: 0.8099 (p) REVERT: C 44 ARG cc_start: 0.8202 (mtt-85) cc_final: 0.7860 (mtt-85) REVERT: C 49 HIS cc_start: 0.7488 (t70) cc_final: 0.7134 (t-90) REVERT: C 55 PHE cc_start: 0.8500 (m-10) cc_final: 0.8128 (m-10) REVERT: C 191 GLU cc_start: 0.7475 (mt-10) cc_final: 0.6984 (mm-30) REVERT: C 203 ILE cc_start: 0.8414 (mt) cc_final: 0.8140 (mm) REVERT: C 224 GLU cc_start: 0.7349 (mp0) cc_final: 0.7002 (mp0) REVERT: C 281 GLU cc_start: 0.6940 (pp20) cc_final: 0.6595 (pp20) REVERT: C 289 VAL cc_start: 0.8680 (t) cc_final: 0.8279 (p) REVERT: C 613 GLN cc_start: 0.7557 (tp40) cc_final: 0.7140 (mt0) REVERT: C 710 ASN cc_start: 0.9040 (p0) cc_final: 0.8732 (p0) REVERT: C 737 ASP cc_start: 0.8241 (t0) cc_final: 0.7956 (t0) REVERT: C 739 THR cc_start: 0.8539 (m) cc_final: 0.8266 (p) REVERT: C 751 ASN cc_start: 0.8874 (m-40) cc_final: 0.8522 (m-40) REVERT: C 817 PHE cc_start: 0.8378 (t80) cc_final: 0.7811 (t80) REVERT: C 859 THR cc_start: 0.7969 (t) cc_final: 0.7705 (p) REVERT: C 884 SER cc_start: 0.8747 (m) cc_final: 0.8356 (t) REVERT: C 955 ASN cc_start: 0.7865 (m-40) cc_final: 0.7478 (t0) REVERT: C 957 GLN cc_start: 0.7950 (tt0) cc_final: 0.7689 (tm-30) REVERT: C 984 LEU cc_start: 0.7932 (mt) cc_final: 0.7528 (tp) REVERT: C 1006 THR cc_start: 0.8596 (m) cc_final: 0.8329 (p) REVERT: C 1031 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7128 (mt-10) REVERT: C 1119 ASN cc_start: 0.7655 (t160) cc_final: 0.7292 (t0) REVERT: C 1127 ASP cc_start: 0.8031 (p0) cc_final: 0.7673 (p0) outliers start: 72 outliers final: 53 residues processed: 579 average time/residue: 0.3706 time to fit residues: 323.1185 Evaluate side-chains 576 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 522 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 0.0670 chunk 32 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 239 optimal weight: 0.4980 chunk 158 optimal weight: 0.5980 chunk 283 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 613 GLN A 751 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN B 52 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1119 ASN C 755 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.7312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23716 Z= 0.226 Angle : 0.578 9.461 32242 Z= 0.295 Chirality : 0.044 0.165 3667 Planarity : 0.004 0.051 4164 Dihedral : 4.470 22.509 3163 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.16 % Allowed : 16.92 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.38 (0.15), residues: 2911 helix: 1.07 (0.22), residues: 616 sheet: 0.39 (0.20), residues: 610 loop : -1.03 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 104 HIS 0.006 0.001 HIS B 505 PHE 0.020 0.002 PHE A 592 TYR 0.025 0.001 TYR A 91 ARG 0.007 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 530 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.9006 (t) cc_final: 0.8781 (p) REVERT: A 104 TRP cc_start: 0.7724 (m-90) cc_final: 0.7159 (m-10) REVERT: A 191 GLU cc_start: 0.4049 (tp30) cc_final: 0.2528 (mm-30) REVERT: A 192 PHE cc_start: 0.8015 (m-80) cc_final: 0.7570 (m-80) REVERT: A 202 LYS cc_start: 0.8537 (mttp) cc_final: 0.8243 (mttp) REVERT: A 239 GLN cc_start: 0.8175 (tt0) cc_final: 0.7640 (tm-30) REVERT: A 290 ASP cc_start: 0.8227 (t0) cc_final: 0.7879 (t70) REVERT: A 304 LYS cc_start: 0.8777 (mmmm) cc_final: 0.8362 (mmmm) REVERT: A 321 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8356 (pm20) REVERT: A 591 SER cc_start: 0.8515 (t) cc_final: 0.8038 (p) REVERT: A 745 ASP cc_start: 0.6750 (t0) cc_final: 0.6261 (t0) REVERT: A 752 LEU cc_start: 0.8802 (mt) cc_final: 0.8486 (tp) REVERT: A 776 LYS cc_start: 0.8270 (ttpp) cc_final: 0.7825 (ttpp) REVERT: A 790 LYS cc_start: 0.8461 (mttt) cc_final: 0.8202 (mttt) REVERT: A 859 THR cc_start: 0.8377 (m) cc_final: 0.8088 (p) REVERT: A 902 MET cc_start: 0.8323 (tpp) cc_final: 0.7975 (tpt) REVERT: A 969 LYS cc_start: 0.8991 (mttt) cc_final: 0.8659 (mttt) REVERT: A 973 ILE cc_start: 0.8771 (pt) cc_final: 0.8423 (pt) REVERT: A 984 LEU cc_start: 0.8245 (mp) cc_final: 0.7931 (tp) REVERT: A 1038 LYS cc_start: 0.8892 (mttt) cc_final: 0.8536 (mmmm) REVERT: A 1084 ASP cc_start: 0.7923 (p0) cc_final: 0.7385 (p0) REVERT: A 1111 GLU cc_start: 0.8039 (pm20) cc_final: 0.7728 (pm20) REVERT: B 191 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7076 (mt-10) REVERT: B 202 LYS cc_start: 0.7259 (mptt) cc_final: 0.6770 (mptt) REVERT: B 206 LYS cc_start: 0.8820 (tptt) cc_final: 0.8465 (tptm) REVERT: B 231 ILE cc_start: 0.9010 (mp) cc_final: 0.8792 (mp) REVERT: B 309 GLU cc_start: 0.7175 (mp0) cc_final: 0.6662 (mp0) REVERT: B 324 GLU cc_start: 0.8257 (pm20) cc_final: 0.7995 (pm20) REVERT: B 351 TYR cc_start: 0.7041 (p90) cc_final: 0.6478 (p90) REVERT: B 444 LYS cc_start: 0.6537 (pttt) cc_final: 0.6324 (pttp) REVERT: B 528 LYS cc_start: 0.7094 (ttpt) cc_final: 0.6451 (mtmt) REVERT: B 556 ASN cc_start: 0.8429 (p0) cc_final: 0.8212 (p0) REVERT: B 558 LYS cc_start: 0.7229 (mttt) cc_final: 0.6909 (pttt) REVERT: B 559 PHE cc_start: 0.6102 (m-80) cc_final: 0.5625 (m-10) REVERT: B 592 PHE cc_start: 0.4638 (OUTLIER) cc_final: 0.4291 (p90) REVERT: B 762 GLN cc_start: 0.8223 (pp30) cc_final: 0.7918 (pp30) REVERT: B 814 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7758 (mmtt) REVERT: B 884 SER cc_start: 0.8517 (m) cc_final: 0.8317 (t) REVERT: B 921 LYS cc_start: 0.8265 (mmmt) cc_final: 0.7883 (tptm) REVERT: B 933 LYS cc_start: 0.8512 (mttt) cc_final: 0.8266 (ttmm) REVERT: B 935 GLN cc_start: 0.8358 (tt0) cc_final: 0.8153 (tm-30) REVERT: B 949 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7186 (mm-40) REVERT: B 969 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8401 (mmmm) REVERT: B 1005 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7967 (tp40) REVERT: B 1073 LYS cc_start: 0.8070 (tttt) cc_final: 0.7824 (mttm) REVERT: B 1111 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: C 31 SER cc_start: 0.8382 (t) cc_final: 0.8106 (p) REVERT: C 44 ARG cc_start: 0.8179 (mtt-85) cc_final: 0.7828 (mtt-85) REVERT: C 49 HIS cc_start: 0.7557 (t70) cc_final: 0.7119 (t-90) REVERT: C 55 PHE cc_start: 0.8485 (m-10) cc_final: 0.8062 (m-10) REVERT: C 170 TYR cc_start: 0.8325 (t80) cc_final: 0.7698 (t80) REVERT: C 191 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7066 (mm-30) REVERT: C 203 ILE cc_start: 0.8404 (mt) cc_final: 0.8160 (mm) REVERT: C 224 GLU cc_start: 0.7274 (mp0) cc_final: 0.6870 (mp0) REVERT: C 281 GLU cc_start: 0.7037 (pp20) cc_final: 0.6610 (pp20) REVERT: C 289 VAL cc_start: 0.8769 (t) cc_final: 0.8423 (p) REVERT: C 613 GLN cc_start: 0.7563 (tp40) cc_final: 0.7257 (mt0) REVERT: C 710 ASN cc_start: 0.9048 (p0) cc_final: 0.8722 (p0) REVERT: C 737 ASP cc_start: 0.8278 (t0) cc_final: 0.8005 (t0) REVERT: C 739 THR cc_start: 0.8572 (m) cc_final: 0.8318 (p) REVERT: C 751 ASN cc_start: 0.8895 (m-40) cc_final: 0.8530 (m-40) REVERT: C 814 LYS cc_start: 0.8284 (mmtt) cc_final: 0.7927 (mmmt) REVERT: C 817 PHE cc_start: 0.8397 (t80) cc_final: 0.7966 (t80) REVERT: C 859 THR cc_start: 0.8014 (t) cc_final: 0.7742 (p) REVERT: C 884 SER cc_start: 0.8798 (m) cc_final: 0.8421 (t) REVERT: C 955 ASN cc_start: 0.7882 (m-40) cc_final: 0.7507 (t0) REVERT: C 957 GLN cc_start: 0.7982 (tt0) cc_final: 0.7715 (tm-30) REVERT: C 969 LYS cc_start: 0.8838 (mttt) cc_final: 0.8513 (mtpp) REVERT: C 984 LEU cc_start: 0.8203 (mt) cc_final: 0.7692 (tp) REVERT: C 1006 THR cc_start: 0.8610 (m) cc_final: 0.8336 (p) REVERT: C 1031 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7134 (mt-10) REVERT: C 1119 ASN cc_start: 0.7745 (t160) cc_final: 0.7314 (t0) REVERT: C 1127 ASP cc_start: 0.8067 (p0) cc_final: 0.7707 (p0) outliers start: 82 outliers final: 59 residues processed: 571 average time/residue: 0.3653 time to fit residues: 315.0216 Evaluate side-chains 579 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 518 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 222 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 613 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN B 52 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.7568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23716 Z= 0.233 Angle : 0.590 9.273 32242 Z= 0.300 Chirality : 0.044 0.162 3667 Planarity : 0.004 0.092 4164 Dihedral : 4.490 20.955 3163 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.05 % Allowed : 17.42 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.31 (0.15), residues: 2911 helix: 1.19 (0.22), residues: 615 sheet: 0.37 (0.20), residues: 625 loop : -1.00 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 104 HIS 0.005 0.001 HIS B 505 PHE 0.040 0.002 PHE C 559 TYR 0.022 0.001 TYR C 655 ARG 0.007 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 530 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8988 (t) cc_final: 0.8750 (p) REVERT: A 141 LEU cc_start: 0.7172 (mm) cc_final: 0.6464 (tt) REVERT: A 191 GLU cc_start: 0.4077 (tp30) cc_final: 0.2569 (mm-30) REVERT: A 192 PHE cc_start: 0.8028 (m-80) cc_final: 0.7649 (m-80) REVERT: A 202 LYS cc_start: 0.8554 (mttp) cc_final: 0.8223 (mttp) REVERT: A 239 GLN cc_start: 0.8145 (tt0) cc_final: 0.7633 (tm-30) REVERT: A 304 LYS cc_start: 0.8765 (mmmm) cc_final: 0.8339 (mmmm) REVERT: A 591 SER cc_start: 0.8501 (t) cc_final: 0.7965 (p) REVERT: A 745 ASP cc_start: 0.6922 (t0) cc_final: 0.6420 (t0) REVERT: A 752 LEU cc_start: 0.8848 (mt) cc_final: 0.8522 (tp) REVERT: A 776 LYS cc_start: 0.8282 (ttpp) cc_final: 0.7797 (ttpp) REVERT: A 790 LYS cc_start: 0.8443 (mttt) cc_final: 0.8206 (mttt) REVERT: A 859 THR cc_start: 0.8418 (m) cc_final: 0.8134 (p) REVERT: A 902 MET cc_start: 0.8347 (tpp) cc_final: 0.7984 (tpt) REVERT: A 969 LYS cc_start: 0.9002 (mttt) cc_final: 0.8690 (mttt) REVERT: A 973 ILE cc_start: 0.8808 (pt) cc_final: 0.8439 (pt) REVERT: A 984 LEU cc_start: 0.8202 (mp) cc_final: 0.7941 (tp) REVERT: A 1038 LYS cc_start: 0.8904 (mttt) cc_final: 0.8541 (mmmm) REVERT: A 1045 LYS cc_start: 0.8536 (tmtt) cc_final: 0.8216 (tptp) REVERT: A 1084 ASP cc_start: 0.7893 (p0) cc_final: 0.7351 (p0) REVERT: A 1111 GLU cc_start: 0.8017 (pm20) cc_final: 0.7737 (pm20) REVERT: B 191 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7090 (mt-10) REVERT: B 206 LYS cc_start: 0.8784 (tptt) cc_final: 0.8438 (tptm) REVERT: B 231 ILE cc_start: 0.9018 (mp) cc_final: 0.8787 (mp) REVERT: B 309 GLU cc_start: 0.7260 (mp0) cc_final: 0.6723 (mp0) REVERT: B 351 TYR cc_start: 0.7052 (p90) cc_final: 0.6396 (p90) REVERT: B 444 LYS cc_start: 0.6447 (pttt) cc_final: 0.6227 (pttp) REVERT: B 528 LYS cc_start: 0.7295 (ttpt) cc_final: 0.6771 (mtpt) REVERT: B 556 ASN cc_start: 0.8481 (p0) cc_final: 0.8276 (p0) REVERT: B 558 LYS cc_start: 0.7379 (mttt) cc_final: 0.7005 (pttt) REVERT: B 559 PHE cc_start: 0.6279 (m-80) cc_final: 0.5798 (m-10) REVERT: B 592 PHE cc_start: 0.4916 (OUTLIER) cc_final: 0.4705 (p90) REVERT: B 698 SER cc_start: 0.8312 (t) cc_final: 0.7516 (p) REVERT: B 762 GLN cc_start: 0.8266 (pp30) cc_final: 0.7915 (pp30) REVERT: B 814 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7286 (mmtt) REVERT: B 868 GLU cc_start: 0.7511 (tp30) cc_final: 0.6964 (tp30) REVERT: B 884 SER cc_start: 0.8551 (m) cc_final: 0.8312 (t) REVERT: B 921 LYS cc_start: 0.8316 (mmmt) cc_final: 0.7933 (tptm) REVERT: B 949 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7199 (mm-40) REVERT: B 960 ASN cc_start: 0.8977 (t0) cc_final: 0.8678 (t0) REVERT: B 969 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8404 (mmmm) REVERT: B 1005 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7973 (tp40) REVERT: B 1073 LYS cc_start: 0.8022 (tttt) cc_final: 0.7816 (mttm) REVERT: C 31 SER cc_start: 0.8355 (t) cc_final: 0.8079 (p) REVERT: C 44 ARG cc_start: 0.8184 (mtt-85) cc_final: 0.7739 (mtt180) REVERT: C 49 HIS cc_start: 0.7572 (t70) cc_final: 0.6785 (t-90) REVERT: C 55 PHE cc_start: 0.8509 (m-10) cc_final: 0.8108 (m-10) REVERT: C 170 TYR cc_start: 0.8379 (t80) cc_final: 0.7766 (t80) REVERT: C 191 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7163 (mm-30) REVERT: C 203 ILE cc_start: 0.8367 (mt) cc_final: 0.8153 (mm) REVERT: C 224 GLU cc_start: 0.7282 (mp0) cc_final: 0.6829 (mp0) REVERT: C 281 GLU cc_start: 0.7035 (pp20) cc_final: 0.6466 (pp20) REVERT: C 289 VAL cc_start: 0.8789 (t) cc_final: 0.8434 (p) REVERT: C 304 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8574 (mmmt) REVERT: C 583 GLU cc_start: 0.7572 (pm20) cc_final: 0.7296 (pm20) REVERT: C 613 GLN cc_start: 0.7588 (tp40) cc_final: 0.7288 (mt0) REVERT: C 646 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7744 (mpp80) REVERT: C 710 ASN cc_start: 0.9056 (p0) cc_final: 0.8721 (p0) REVERT: C 736 VAL cc_start: 0.9191 (t) cc_final: 0.8811 (p) REVERT: C 737 ASP cc_start: 0.8270 (t0) cc_final: 0.8031 (t0) REVERT: C 739 THR cc_start: 0.8593 (m) cc_final: 0.8348 (p) REVERT: C 751 ASN cc_start: 0.8902 (m-40) cc_final: 0.8563 (m-40) REVERT: C 814 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8042 (mmmt) REVERT: C 817 PHE cc_start: 0.8411 (t80) cc_final: 0.8050 (t80) REVERT: C 859 THR cc_start: 0.8027 (t) cc_final: 0.7753 (p) REVERT: C 884 SER cc_start: 0.8803 (m) cc_final: 0.8415 (t) REVERT: C 935 GLN cc_start: 0.8585 (tp40) cc_final: 0.8215 (tp40) REVERT: C 955 ASN cc_start: 0.7885 (m-40) cc_final: 0.7539 (t0) REVERT: C 957 GLN cc_start: 0.7948 (tt0) cc_final: 0.7719 (tm-30) REVERT: C 984 LEU cc_start: 0.8215 (mt) cc_final: 0.7700 (tp) REVERT: C 1006 THR cc_start: 0.8631 (m) cc_final: 0.8378 (p) REVERT: C 1031 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7151 (mt-10) REVERT: C 1119 ASN cc_start: 0.7813 (t160) cc_final: 0.7429 (t0) REVERT: C 1127 ASP cc_start: 0.8120 (p0) cc_final: 0.7738 (p0) outliers start: 79 outliers final: 65 residues processed: 570 average time/residue: 0.3689 time to fit residues: 318.0975 Evaluate side-chains 594 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 527 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 264 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 263 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 613 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 99 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.7852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23716 Z= 0.301 Angle : 0.627 9.615 32242 Z= 0.322 Chirality : 0.045 0.170 3667 Planarity : 0.004 0.045 4164 Dihedral : 4.614 21.888 3163 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.20 % Allowed : 17.73 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.38 (0.15), residues: 2911 helix: 1.20 (0.22), residues: 610 sheet: 0.34 (0.20), residues: 607 loop : -1.05 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 104 HIS 0.006 0.001 HIS B 505 PHE 0.042 0.002 PHE C 133 TYR 0.029 0.002 TYR C 655 ARG 0.008 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 522 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.8563 (mttp) cc_final: 0.8192 (mttp) REVERT: A 239 GLN cc_start: 0.8229 (tt0) cc_final: 0.7749 (tm-30) REVERT: A 304 LYS cc_start: 0.8780 (mmmm) cc_final: 0.8383 (mmmm) REVERT: A 307 THR cc_start: 0.8555 (m) cc_final: 0.8072 (t) REVERT: A 309 GLU cc_start: 0.7820 (tp30) cc_final: 0.7614 (tp30) REVERT: A 591 SER cc_start: 0.8504 (t) cc_final: 0.7871 (p) REVERT: A 654 GLU cc_start: 0.7819 (tt0) cc_final: 0.7552 (tt0) REVERT: A 745 ASP cc_start: 0.6907 (t0) cc_final: 0.6467 (t0) REVERT: A 752 LEU cc_start: 0.8872 (mt) cc_final: 0.8556 (tp) REVERT: A 776 LYS cc_start: 0.8272 (ttpp) cc_final: 0.7891 (ttpp) REVERT: A 787 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7545 (mm-40) REVERT: A 790 LYS cc_start: 0.8453 (mttt) cc_final: 0.8194 (mttt) REVERT: A 859 THR cc_start: 0.8457 (m) cc_final: 0.8166 (p) REVERT: A 902 MET cc_start: 0.8355 (tpp) cc_final: 0.7978 (tpt) REVERT: A 969 LYS cc_start: 0.9004 (mttt) cc_final: 0.8712 (mttt) REVERT: A 973 ILE cc_start: 0.8850 (pt) cc_final: 0.8516 (pt) REVERT: A 984 LEU cc_start: 0.8206 (mp) cc_final: 0.7944 (tp) REVERT: A 1038 LYS cc_start: 0.8938 (mttt) cc_final: 0.8578 (mmmm) REVERT: A 1084 ASP cc_start: 0.7908 (p0) cc_final: 0.7383 (p0) REVERT: A 1111 GLU cc_start: 0.8002 (pm20) cc_final: 0.7717 (pm20) REVERT: B 83 VAL cc_start: 0.8216 (t) cc_final: 0.7869 (p) REVERT: B 191 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7073 (mt-10) REVERT: B 206 LYS cc_start: 0.8781 (tptt) cc_final: 0.8451 (tptm) REVERT: B 231 ILE cc_start: 0.9032 (mp) cc_final: 0.8803 (mp) REVERT: B 309 GLU cc_start: 0.7361 (mp0) cc_final: 0.6869 (mp0) REVERT: B 351 TYR cc_start: 0.7124 (p90) cc_final: 0.6481 (p90) REVERT: B 444 LYS cc_start: 0.6462 (pttt) cc_final: 0.6245 (pttp) REVERT: B 558 LYS cc_start: 0.7458 (mttt) cc_final: 0.6828 (pttt) REVERT: B 698 SER cc_start: 0.8347 (t) cc_final: 0.7491 (p) REVERT: B 762 GLN cc_start: 0.8333 (pp30) cc_final: 0.8008 (pp30) REVERT: B 814 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7687 (mmtt) REVERT: B 884 SER cc_start: 0.8577 (m) cc_final: 0.8343 (t) REVERT: B 921 LYS cc_start: 0.8343 (mmmt) cc_final: 0.7956 (tptm) REVERT: B 933 LYS cc_start: 0.8466 (mttt) cc_final: 0.8102 (ttmm) REVERT: B 949 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7235 (tm-30) REVERT: B 960 ASN cc_start: 0.8961 (t0) cc_final: 0.8653 (t0) REVERT: B 969 LYS cc_start: 0.8756 (mmtt) cc_final: 0.8344 (mmmm) REVERT: B 1005 GLN cc_start: 0.8209 (mm-40) cc_final: 0.8005 (tp40) REVERT: B 1073 LYS cc_start: 0.8071 (tttt) cc_final: 0.7851 (mttm) REVERT: B 1111 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: C 31 SER cc_start: 0.8395 (t) cc_final: 0.8093 (p) REVERT: C 44 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7826 (mtt-85) REVERT: C 49 HIS cc_start: 0.7566 (t70) cc_final: 0.7170 (t-90) REVERT: C 55 PHE cc_start: 0.8486 (m-10) cc_final: 0.8083 (m-10) REVERT: C 170 TYR cc_start: 0.8431 (t80) cc_final: 0.7846 (t80) REVERT: C 281 GLU cc_start: 0.7138 (pp20) cc_final: 0.6521 (pp20) REVERT: C 289 VAL cc_start: 0.8784 (t) cc_final: 0.8425 (p) REVERT: C 304 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8579 (mmmt) REVERT: C 613 GLN cc_start: 0.7671 (tp40) cc_final: 0.7404 (mt0) REVERT: C 644 GLN cc_start: 0.7824 (tp40) cc_final: 0.7383 (tp-100) REVERT: C 646 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7907 (mpp80) REVERT: C 736 VAL cc_start: 0.9202 (t) cc_final: 0.8818 (p) REVERT: C 737 ASP cc_start: 0.8337 (t0) cc_final: 0.8103 (t0) REVERT: C 739 THR cc_start: 0.8621 (m) cc_final: 0.8412 (p) REVERT: C 751 ASN cc_start: 0.8970 (m-40) cc_final: 0.8564 (m-40) REVERT: C 790 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7810 (mmmt) REVERT: C 814 LYS cc_start: 0.8439 (mmtt) cc_final: 0.8183 (mmmt) REVERT: C 817 PHE cc_start: 0.8496 (t80) cc_final: 0.8014 (t80) REVERT: C 884 SER cc_start: 0.8847 (m) cc_final: 0.8437 (t) REVERT: C 935 GLN cc_start: 0.8575 (tp40) cc_final: 0.8247 (tp40) REVERT: C 955 ASN cc_start: 0.7930 (m-40) cc_final: 0.7574 (t0) REVERT: C 984 LEU cc_start: 0.8235 (mt) cc_final: 0.7654 (tp) REVERT: C 1006 THR cc_start: 0.8601 (m) cc_final: 0.8346 (p) REVERT: C 1017 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: C 1031 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7217 (mt-10) REVERT: C 1119 ASN cc_start: 0.7901 (t160) cc_final: 0.7469 (t0) REVERT: C 1127 ASP cc_start: 0.8183 (p0) cc_final: 0.7773 (p0) outliers start: 83 outliers final: 71 residues processed: 563 average time/residue: 0.4060 time to fit residues: 350.2292 Evaluate side-chains 591 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 517 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 0.5980 chunk 279 optimal weight: 0.5980 chunk 170 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 292 optimal weight: 0.7980 chunk 269 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.7979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23716 Z= 0.230 Angle : 0.616 9.475 32242 Z= 0.314 Chirality : 0.045 0.206 3667 Planarity : 0.004 0.045 4164 Dihedral : 4.589 27.951 3163 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.93 % Allowed : 18.47 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.33 (0.15), residues: 2911 helix: 1.33 (0.22), residues: 606 sheet: 0.30 (0.20), residues: 617 loop : -1.03 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 104 HIS 0.005 0.001 HIS B 505 PHE 0.035 0.002 PHE B1109 TYR 0.022 0.001 TYR A 91 ARG 0.010 0.000 ARG B 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 518 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.8537 (mttp) cc_final: 0.8166 (mttp) REVERT: A 239 GLN cc_start: 0.8275 (tt0) cc_final: 0.7722 (tm-30) REVERT: A 304 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8334 (mmmm) REVERT: A 307 THR cc_start: 0.8547 (m) cc_final: 0.8068 (t) REVERT: A 591 SER cc_start: 0.8429 (t) cc_final: 0.7848 (p) REVERT: A 654 GLU cc_start: 0.7815 (tt0) cc_final: 0.7545 (tt0) REVERT: A 745 ASP cc_start: 0.6921 (t0) cc_final: 0.6473 (t0) REVERT: A 752 LEU cc_start: 0.8847 (mt) cc_final: 0.8544 (tp) REVERT: A 776 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7856 (ttpp) REVERT: A 787 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7534 (mm-40) REVERT: A 790 LYS cc_start: 0.8451 (mttt) cc_final: 0.8105 (mttt) REVERT: A 859 THR cc_start: 0.8463 (m) cc_final: 0.8177 (p) REVERT: A 902 MET cc_start: 0.8342 (tpp) cc_final: 0.7951 (tpt) REVERT: A 969 LYS cc_start: 0.8985 (mttt) cc_final: 0.8690 (mttt) REVERT: A 973 ILE cc_start: 0.8838 (pt) cc_final: 0.8479 (pt) REVERT: A 984 LEU cc_start: 0.8172 (mp) cc_final: 0.7951 (tp) REVERT: A 1038 LYS cc_start: 0.8915 (mttt) cc_final: 0.8529 (mmmm) REVERT: A 1084 ASP cc_start: 0.7878 (p0) cc_final: 0.7358 (p0) REVERT: A 1111 GLU cc_start: 0.7992 (pm20) cc_final: 0.7691 (pm20) REVERT: B 83 VAL cc_start: 0.8230 (t) cc_final: 0.7960 (p) REVERT: B 170 TYR cc_start: 0.7788 (t80) cc_final: 0.7350 (t80) REVERT: B 191 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7038 (mt-10) REVERT: B 206 LYS cc_start: 0.8771 (tptt) cc_final: 0.8541 (tppt) REVERT: B 237 ARG cc_start: 0.6363 (mtm-85) cc_final: 0.5857 (ptt90) REVERT: B 309 GLU cc_start: 0.7297 (mp0) cc_final: 0.6825 (mp0) REVERT: B 351 TYR cc_start: 0.7085 (p90) cc_final: 0.6441 (p90) REVERT: B 444 LYS cc_start: 0.6448 (pttt) cc_final: 0.6247 (pttp) REVERT: B 528 LYS cc_start: 0.7164 (pttp) cc_final: 0.6754 (pttp) REVERT: B 558 LYS cc_start: 0.7580 (mttt) cc_final: 0.7248 (pttt) REVERT: B 698 SER cc_start: 0.8266 (t) cc_final: 0.7312 (m) REVERT: B 748 GLU cc_start: 0.8132 (pt0) cc_final: 0.7827 (pt0) REVERT: B 762 GLN cc_start: 0.8283 (pp30) cc_final: 0.7959 (pp30) REVERT: B 814 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7563 (mmtt) REVERT: B 867 ASP cc_start: 0.7623 (m-30) cc_final: 0.7124 (t0) REVERT: B 884 SER cc_start: 0.8581 (m) cc_final: 0.8329 (t) REVERT: B 921 LYS cc_start: 0.8351 (mmmt) cc_final: 0.7983 (tptm) REVERT: B 933 LYS cc_start: 0.8402 (mttt) cc_final: 0.8075 (ttmm) REVERT: B 949 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7222 (tm-30) REVERT: B 960 ASN cc_start: 0.8959 (t0) cc_final: 0.8642 (t0) REVERT: B 969 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8308 (mmmm) REVERT: B 988 GLU cc_start: 0.7257 (mp0) cc_final: 0.6855 (pm20) REVERT: B 1073 LYS cc_start: 0.7987 (tttt) cc_final: 0.7779 (mttm) REVERT: C 31 SER cc_start: 0.8325 (t) cc_final: 0.8025 (p) REVERT: C 41 LYS cc_start: 0.6322 (tptt) cc_final: 0.5803 (tttt) REVERT: C 44 ARG cc_start: 0.8131 (mtt-85) cc_final: 0.7686 (mtt180) REVERT: C 49 HIS cc_start: 0.7547 (t70) cc_final: 0.6814 (t-90) REVERT: C 55 PHE cc_start: 0.8515 (m-10) cc_final: 0.8106 (m-10) REVERT: C 170 TYR cc_start: 0.8420 (t80) cc_final: 0.7848 (t80) REVERT: C 191 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7133 (mm-30) REVERT: C 281 GLU cc_start: 0.7067 (pp20) cc_final: 0.6466 (pp20) REVERT: C 289 VAL cc_start: 0.8811 (t) cc_final: 0.8463 (p) REVERT: C 304 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8609 (mmmt) REVERT: C 613 GLN cc_start: 0.7626 (tp40) cc_final: 0.7389 (mt0) REVERT: C 644 GLN cc_start: 0.7770 (tp40) cc_final: 0.7394 (tp-100) REVERT: C 646 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7879 (mpp80) REVERT: C 660 TYR cc_start: 0.8533 (m-10) cc_final: 0.8270 (m-10) REVERT: C 736 VAL cc_start: 0.9177 (t) cc_final: 0.8817 (p) REVERT: C 737 ASP cc_start: 0.8307 (t0) cc_final: 0.8101 (t0) REVERT: C 790 LYS cc_start: 0.8189 (mmmt) cc_final: 0.7799 (mmmt) REVERT: C 814 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8267 (mmmt) REVERT: C 817 PHE cc_start: 0.8440 (t80) cc_final: 0.8090 (t80) REVERT: C 884 SER cc_start: 0.8812 (m) cc_final: 0.8411 (t) REVERT: C 955 ASN cc_start: 0.7892 (m-40) cc_final: 0.7569 (t0) REVERT: C 984 LEU cc_start: 0.8178 (mt) cc_final: 0.7942 (mt) REVERT: C 1006 THR cc_start: 0.8623 (m) cc_final: 0.8359 (p) REVERT: C 1017 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: C 1031 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7170 (mt-10) REVERT: C 1119 ASN cc_start: 0.7915 (t160) cc_final: 0.7505 (t0) REVERT: C 1127 ASP cc_start: 0.8151 (p0) cc_final: 0.7772 (p0) outliers start: 76 outliers final: 63 residues processed: 553 average time/residue: 0.3649 time to fit residues: 304.5402 Evaluate side-chains 572 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 507 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.6980 chunk 248 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 239 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.144210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.112753 restraints weight = 46826.406| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.36 r_work: 0.3475 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.8175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23716 Z= 0.242 Angle : 0.613 10.061 32242 Z= 0.313 Chirality : 0.045 0.190 3667 Planarity : 0.004 0.043 4164 Dihedral : 4.566 29.914 3163 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.01 % Allowed : 18.35 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.35 (0.15), residues: 2911 helix: 1.30 (0.22), residues: 607 sheet: 0.39 (0.20), residues: 605 loop : -1.08 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 104 HIS 0.005 0.001 HIS B 505 PHE 0.031 0.002 PHE C 565 TYR 0.022 0.001 TYR A 91 ARG 0.008 0.001 ARG B 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6686.76 seconds wall clock time: 119 minutes 43.79 seconds (7183.79 seconds total)