Starting phenix.real_space_refine on Mon Feb 19 14:00:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk2_32556/02_2024/7wk2_32556.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk2_32556/02_2024/7wk2_32556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk2_32556/02_2024/7wk2_32556.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk2_32556/02_2024/7wk2_32556.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk2_32556/02_2024/7wk2_32556.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk2_32556/02_2024/7wk2_32556.pdb" } resolution = 3.1 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= 0.030 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 114 5.16 5 C 15921 2.51 5 N 4146 2.21 5 O 4698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24879 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'CIS': 1, 'PTRANS': 54, 'TRANS': 1001} 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': 1, 'PTRANS': 54, 'TRANS': 1001} Chain breaks: 7 Chain: "C" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'CIS': 1, 'PTRANS': 54, 'TRANS': 1001} Chain breaks: 7 Time building chain proxies: 12.22, per 1000 atoms: 0.49 Number of scatterers: 24879 At special positions: 0 Unit cell: (148.648, 144.276, 178.159, 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 114 16.00 O 4698 8.00 N 4146 7.00 C 15921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 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=2.96 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=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.70 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=2.76 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=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.90 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.02 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: 8.64 Conformation dependent library (CDL) restraints added in 4.6 seconds 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5952 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 46 sheets defined 21.6% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 296 through 304 removed outlier: 3.816A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.837A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.867A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.693A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.567A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.842A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.735A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.509A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 4.026A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 removed outlier: 3.539A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 906 removed outlier: 3.668A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.828A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.963A pdb=" N ALA A 924 " --> pdb=" O GLN A 920 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 963 removed outlier: 3.890A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.502A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1032 removed outlier: 3.806A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.868A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.650A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.382A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.844A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.936A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 638 removed outlier: 3.526A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 638' Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.842A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 763 through 783 removed outlier: 3.669A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.738A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.609A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.821A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.644A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 3.540A 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: 3.514A pdb=" N ALA B 924 " --> pdb=" O GLN B 920 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.827A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.524A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1031 removed outlier: 3.644A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B1012 " --> pdb=" O VAL B1008 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.878A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.602A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.509A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.302A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 634 through 638 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.961A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.535A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.581A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 824 removed outlier: 3.824A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.896A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 876 " --> pdb=" O GLN C 872 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY C 880 " --> pdb=" O ALA C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 899 No H-bonds generated for 'chain 'C' and resid 897 through 899' Processing helix chain 'C' and resid 900 through 909 removed outlier: 3.789A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.631A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 3.504A 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: 3.753A pdb=" N ALA C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (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: 3.917A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.671A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.665A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR C1009 " --> pdb=" O GLN C1005 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.883A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 4.287A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.516A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.872A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 3.880A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.580A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 359 removed outlier: 3.793A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.143A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.583A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.713A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.545A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.682A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 removed outlier: 4.185A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.370A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.558A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.673A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.690A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.747A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.519A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.501A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.960A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.879A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.501A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.534A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.201A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.843A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.590A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.506A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.580A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.580A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.474A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.037A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.531A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.953A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.788A 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 728 removed outlier: 3.750A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.729A 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: 3.742A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.978A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 716 hydrogen bonds defined for protein. 1941 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.63 Time building geometry restraints manager: 9.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 4060 1.30 - 1.43: 6814 1.43 - 1.56: 14441 1.56 - 1.70: 2 1.70 - 1.83: 144 Bond restraints: 25461 Sorted by residual: bond pdb=" CA ASN A 317 " pdb=" C ASN A 317 " ideal model delta sigma weight residual 1.524 1.437 0.087 1.21e-02 6.83e+03 5.12e+01 bond pdb=" C THR B 573 " pdb=" O THR B 573 " ideal model delta sigma weight residual 1.234 1.166 0.068 1.35e-02 5.49e+03 2.51e+01 bond pdb=" C LYS A 856 " pdb=" O LYS A 856 " ideal model delta sigma weight residual 1.234 1.162 0.072 1.44e-02 4.82e+03 2.49e+01 bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.449 -0.115 2.34e-02 1.83e+03 2.40e+01 bond pdb=" C GLY A 857 " pdb=" O GLY A 857 " ideal model delta sigma weight residual 1.238 1.167 0.071 1.45e-02 4.76e+03 2.38e+01 ... (remaining 25456 not shown) Histogram of bond angle deviations from ideal: 100.48 - 107.18: 870 107.18 - 113.89: 13704 113.89 - 120.60: 10069 120.60 - 127.31: 9715 127.31 - 134.02: 262 Bond angle restraints: 34620 Sorted by residual: angle pdb=" N GLY A 857 " pdb=" CA GLY A 857 " pdb=" C GLY A 857 " ideal model delta sigma weight residual 115.21 102.90 12.31 1.30e+00 5.92e-01 8.97e+01 angle pdb=" N THR B 573 " pdb=" CA THR B 573 " pdb=" C THR B 573 " ideal model delta sigma weight residual 110.53 121.50 -10.97 1.29e+00 6.01e-01 7.23e+01 angle pdb=" C ASP B 568 " pdb=" N ILE B 569 " pdb=" CA ILE B 569 " ideal model delta sigma weight residual 120.42 129.38 -8.96 1.42e+00 4.96e-01 3.98e+01 angle pdb=" C GLY C 639 " pdb=" N SER C 640 " pdb=" CA SER C 640 " ideal model delta sigma weight residual 121.54 132.87 -11.33 1.91e+00 2.74e-01 3.52e+01 angle pdb=" C ASN C 122 " pdb=" N ALA C 123 " pdb=" CA ALA C 123 " ideal model delta sigma weight residual 121.54 132.46 -10.92 1.91e+00 2.74e-01 3.27e+01 ... (remaining 34615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.07: 14918 22.07 - 44.15: 248 44.15 - 66.22: 29 66.22 - 88.30: 0 88.30 - 110.37: 3 Dihedral angle restraints: 15198 sinusoidal: 5958 harmonic: 9240 Sorted by residual: dihedral pdb=" CA PHE A 157 " pdb=" C PHE A 157 " pdb=" N ARG A 158 " pdb=" CA ARG A 158 " ideal model delta harmonic sigma weight residual 180.00 69.63 110.37 0 5.00e+00 4.00e-02 4.87e+02 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 180.00 71.18 108.82 0 5.00e+00 4.00e-02 4.74e+02 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 180.00 71.66 108.34 0 5.00e+00 4.00e-02 4.70e+02 ... (remaining 15195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3569 0.099 - 0.197: 323 0.197 - 0.296: 22 0.296 - 0.395: 0 0.395 - 0.493: 1 Chirality restraints: 3915 Sorted by residual: chirality pdb=" CA THR B 573 " pdb=" N THR B 573 " pdb=" C THR B 573 " pdb=" CB THR B 573 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.49 2.00e-01 2.50e+01 6.08e+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 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 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 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 3912 not shown) Planarity restraints: 4473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 854 " -0.025 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C LYS A 854 " 0.082 2.00e-02 2.50e+03 pdb=" O LYS A 854 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE A 855 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 317 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C ASN A 317 " 0.070 2.00e-02 2.50e+03 pdb=" O ASN A 317 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE A 318 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 25 " 0.064 5.00e-02 4.00e+02 9.85e-02 1.55e+01 pdb=" N PRO C 26 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO C 26 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 26 " 0.052 5.00e-02 4.00e+02 ... (remaining 4470 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 8 2.20 - 2.88: 8280 2.88 - 3.55: 29620 3.55 - 4.23: 55292 4.23 - 4.90: 90433 Nonbonded interactions: 183633 Sorted by model distance: nonbonded pdb=" NE2 GLN A 14 " pdb=" CZ PHE A 157 " model vdw 1.531 3.420 nonbonded pdb=" NE2 GLN A 14 " pdb=" CE1 PHE A 157 " model vdw 1.665 3.420 nonbonded pdb=" CZ PHE B 759 " pdb=" CD1 PHE C 970 " model vdw 1.667 3.640 nonbonded pdb=" CZ PHE B 759 " pdb=" CE1 PHE C 970 " model vdw 1.862 3.640 nonbonded pdb=" O THR B 761 " pdb=" CG GLN B 762 " model vdw 1.864 3.440 ... (remaining 183628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 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: 10.760 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 61.890 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 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 0.115 25461 Z= 0.399 Angle : 0.837 12.309 34620 Z= 0.490 Chirality : 0.055 0.493 3915 Planarity : 0.007 0.099 4473 Dihedral : 8.836 110.369 9129 Min Nonbonded Distance : 1.531 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.91 % Favored : 95.93 % Rotamer: Outliers : 0.22 % Allowed : 0.65 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.00 (0.12), residues: 3123 helix: -4.95 (0.06), residues: 540 sheet: -0.04 (0.18), residues: 531 loop : -1.76 (0.11), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 633 HIS 0.016 0.002 HIS B 954 PHE 0.038 0.003 PHE A 855 TYR 0.020 0.002 TYR C 904 ARG 0.009 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 790 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6817 (mtt90) cc_final: 0.6493 (mpt180) REVERT: A 191 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7127 (mt-10) REVERT: A 308 VAL cc_start: 0.7832 (t) cc_final: 0.7569 (p) REVERT: A 356 LYS cc_start: 0.7665 (tptt) cc_final: 0.7425 (ttmt) REVERT: A 399 SER cc_start: 0.7897 (t) cc_final: 0.6911 (m) REVERT: A 537 LYS cc_start: 0.8032 (ttmt) cc_final: 0.7707 (mtpp) REVERT: A 595 VAL cc_start: 0.8145 (t) cc_final: 0.7870 (m) REVERT: A 736 VAL cc_start: 0.9048 (t) cc_final: 0.8821 (p) REVERT: A 776 LYS cc_start: 0.7785 (mttt) cc_final: 0.7451 (mttt) REVERT: A 875 SER cc_start: 0.8619 (p) cc_final: 0.8317 (m) REVERT: A 905 ARG cc_start: 0.6711 (mtt180) cc_final: 0.6278 (mtt90) REVERT: A 969 LYS cc_start: 0.8462 (mttt) cc_final: 0.8135 (mttm) REVERT: A 986 PRO cc_start: 0.7590 (Cg_exo) cc_final: 0.7371 (Cg_endo) REVERT: A 988 GLU cc_start: 0.7922 (tp30) cc_final: 0.7132 (tp30) REVERT: A 1028 LYS cc_start: 0.8017 (mttt) cc_final: 0.7265 (mttm) REVERT: A 1040 VAL cc_start: 0.7300 (t) cc_final: 0.7024 (t) REVERT: A 1041 ASP cc_start: 0.7266 (m-30) cc_final: 0.7060 (m-30) REVERT: A 1075 PHE cc_start: 0.6539 (m-10) cc_final: 0.6263 (m-80) REVERT: B 30 ASN cc_start: 0.8058 (m-40) cc_final: 0.7827 (p0) REVERT: B 54 LEU cc_start: 0.8118 (mt) cc_final: 0.7858 (mt) REVERT: B 125 ASN cc_start: 0.7469 (m-40) cc_final: 0.7049 (t0) REVERT: B 129 LYS cc_start: 0.7531 (mttt) cc_final: 0.7299 (mtmt) REVERT: B 177 MET cc_start: 0.1028 (mtt) cc_final: 0.0741 (mtt) REVERT: B 351 TYR cc_start: 0.7184 (p90) cc_final: 0.6510 (p90) REVERT: B 584 ILE cc_start: 0.8116 (mt) cc_final: 0.7905 (tt) REVERT: B 734 THR cc_start: 0.8121 (p) cc_final: 0.7005 (m) REVERT: B 748 GLU cc_start: 0.7332 (tp30) cc_final: 0.7120 (tt0) REVERT: B 768 THR cc_start: 0.8334 (m) cc_final: 0.8044 (p) REVERT: B 797 PHE cc_start: 0.6301 (m-10) cc_final: 0.6076 (m-10) REVERT: B 952 VAL cc_start: 0.8222 (t) cc_final: 0.8005 (m) REVERT: B 979 ASP cc_start: 0.7615 (m-30) cc_final: 0.7331 (m-30) REVERT: B 981 PHE cc_start: 0.6672 (t80) cc_final: 0.6424 (t80) REVERT: B 1073 LYS cc_start: 0.8047 (tttt) cc_final: 0.7773 (mtpp) REVERT: B 1084 ASP cc_start: 0.6391 (p0) cc_final: 0.5250 (p0) REVERT: B 1122 VAL cc_start: 0.8343 (t) cc_final: 0.8100 (p) REVERT: C 195 LYS cc_start: 0.8581 (pttt) cc_final: 0.7926 (pttp) REVERT: C 300 LYS cc_start: 0.7596 (mttt) cc_final: 0.7257 (mttp) REVERT: C 309 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6745 (mt-10) REVERT: C 323 THR cc_start: 0.8240 (m) cc_final: 0.6801 (p) REVERT: C 358 ILE cc_start: 0.7548 (mt) cc_final: 0.7345 (mt) REVERT: C 386 LYS cc_start: 0.7888 (mttt) cc_final: 0.7334 (mttt) REVERT: C 390 LEU cc_start: 0.8290 (mt) cc_final: 0.7883 (mt) REVERT: C 559 PHE cc_start: 0.6161 (m-10) cc_final: 0.5777 (m-10) REVERT: C 595 VAL cc_start: 0.8305 (t) cc_final: 0.7981 (p) REVERT: C 739 THR cc_start: 0.7770 (m) cc_final: 0.7254 (m) REVERT: C 752 LEU cc_start: 0.8992 (mp) cc_final: 0.8790 (mt) REVERT: C 827 THR cc_start: 0.7626 (p) cc_final: 0.7246 (p) REVERT: C 867 ASP cc_start: 0.7376 (m-30) cc_final: 0.7142 (m-30) REVERT: C 868 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6523 (mm-30) REVERT: C 873 TYR cc_start: 0.8062 (m-80) cc_final: 0.7759 (m-10) REVERT: C 875 SER cc_start: 0.8787 (p) cc_final: 0.8497 (m) REVERT: C 884 SER cc_start: 0.7752 (m) cc_final: 0.7510 (t) REVERT: C 969 LYS cc_start: 0.8758 (mttt) cc_final: 0.8519 (mttt) REVERT: C 984 LEU cc_start: 0.7707 (mt) cc_final: 0.7438 (mp) REVERT: C 988 GLU cc_start: 0.7939 (tp30) cc_final: 0.7352 (tp30) REVERT: C 1028 LYS cc_start: 0.8030 (mttt) cc_final: 0.7329 (mttm) REVERT: C 1073 LYS cc_start: 0.7474 (tttt) cc_final: 0.7100 (tttt) REVERT: C 1075 PHE cc_start: 0.7375 (m-10) cc_final: 0.6978 (m-10) REVERT: C 1084 ASP cc_start: 0.6580 (p0) cc_final: 0.6345 (t70) REVERT: C 1116 THR cc_start: 0.7745 (p) cc_final: 0.7362 (m) outliers start: 6 outliers final: 2 residues processed: 796 average time/residue: 0.3861 time to fit residues: 470.5372 Evaluate side-chains 593 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 591 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain B residue 572 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 0.9980 chunk 238 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 246 optimal weight: 0.0870 chunk 95 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 286 optimal weight: 0.9980 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN A 422 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 ASN A 762 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN A 949 GLN A 965 GLN A1054 GLN B 331 ASN B 439 ASN B 505 HIS B 563 GLN B 717 ASN B 895 GLN B 954 HIS B 965 GLN B1002 GLN B1054 GLN B1083 HIS B1119 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 422 ASN C 519 HIS C 563 GLN C 717 ASN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25461 Z= 0.279 Angle : 0.667 10.117 34620 Z= 0.353 Chirality : 0.047 0.294 3915 Planarity : 0.005 0.052 4473 Dihedral : 5.482 63.961 3405 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.44 % Favored : 98.53 % Rotamer: Outliers : 2.34 % Allowed : 8.21 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.96 (0.13), residues: 3123 helix: -2.66 (0.15), residues: 585 sheet: 0.12 (0.18), residues: 627 loop : -1.37 (0.12), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 64 HIS 0.008 0.002 HIS B1064 PHE 0.028 0.002 PHE B 759 TYR 0.021 0.002 TYR C 204 ARG 0.009 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 640 time to evaluate : 2.730 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 269 TYR cc_start: 0.7606 (m-80) cc_final: 0.7063 (m-80) REVERT: A 298 GLU cc_start: 0.8436 (tp30) cc_final: 0.8233 (tp30) REVERT: A 304 LYS cc_start: 0.8393 (mttt) cc_final: 0.8133 (mmmm) REVERT: A 308 VAL cc_start: 0.8082 (t) cc_final: 0.7785 (p) REVERT: A 354 ASN cc_start: 0.6788 (p0) cc_final: 0.6549 (p0) REVERT: A 410 ILE cc_start: 0.6712 (mm) cc_final: 0.6380 (tp) REVERT: A 423 TYR cc_start: 0.6565 (t80) cc_final: 0.6133 (t80) REVERT: A 533 LEU cc_start: 0.9033 (mt) cc_final: 0.8830 (mt) REVERT: A 537 LYS cc_start: 0.8389 (ttmt) cc_final: 0.7918 (mtpp) REVERT: A 780 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6772 (mt-10) REVERT: A 926 GLN cc_start: 0.6694 (OUTLIER) cc_final: 0.6403 (mt0) REVERT: A 950 ASP cc_start: 0.7787 (m-30) cc_final: 0.7411 (m-30) REVERT: A 964 LYS cc_start: 0.8341 (mttt) cc_final: 0.8119 (mmmm) REVERT: A 969 LYS cc_start: 0.8977 (mttt) cc_final: 0.8557 (mttm) REVERT: A 987 PRO cc_start: 0.8964 (Cg_exo) cc_final: 0.8759 (Cg_endo) REVERT: A 988 GLU cc_start: 0.7800 (tp30) cc_final: 0.6955 (tp30) REVERT: A 1002 GLN cc_start: 0.7936 (tp40) cc_final: 0.7401 (tp40) REVERT: A 1019 ARG cc_start: 0.7170 (tpt170) cc_final: 0.6779 (tpt170) REVERT: B 54 LEU cc_start: 0.8349 (mt) cc_final: 0.8125 (mt) REVERT: B 177 MET cc_start: 0.1005 (mtt) cc_final: 0.0656 (mtt) REVERT: B 338 PHE cc_start: 0.6534 (m-80) cc_final: 0.6323 (m-80) REVERT: B 346 ARG cc_start: 0.6958 (mmt-90) cc_final: 0.6751 (mmt-90) REVERT: B 351 TYR cc_start: 0.7432 (p90) cc_final: 0.6756 (p90) REVERT: B 451 TYR cc_start: 0.3936 (m-10) cc_final: 0.3675 (m-10) REVERT: B 515 PHE cc_start: 0.7535 (m-80) cc_final: 0.7049 (m-80) REVERT: B 576 VAL cc_start: 0.8312 (m) cc_final: 0.7993 (t) REVERT: B 586 ASP cc_start: 0.7235 (m-30) cc_final: 0.6968 (m-30) REVERT: B 787 GLN cc_start: 0.7352 (mm-40) cc_final: 0.6826 (mm-40) REVERT: B 797 PHE cc_start: 0.7284 (m-10) cc_final: 0.6955 (m-10) REVERT: B 817 PHE cc_start: 0.8280 (t80) cc_final: 0.7851 (t80) REVERT: B 882 ILE cc_start: 0.7891 (mt) cc_final: 0.7647 (pt) REVERT: B 1002 GLN cc_start: 0.7779 (mm110) cc_final: 0.7133 (mm-40) REVERT: B 1041 ASP cc_start: 0.7697 (m-30) cc_final: 0.7478 (m-30) REVERT: B 1073 LYS cc_start: 0.8254 (tttt) cc_final: 0.8022 (mtpp) REVERT: C 64 TRP cc_start: 0.8256 (t60) cc_final: 0.8047 (t60) REVERT: C 97 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7345 (mmtt) REVERT: C 190 ARG cc_start: 0.7637 (mtm180) cc_final: 0.7178 (mtt180) REVERT: C 191 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7564 (mt-10) REVERT: C 203 ILE cc_start: 0.8380 (mt) cc_final: 0.8147 (mp) REVERT: C 278 LYS cc_start: 0.8324 (tttt) cc_final: 0.8050 (ttmm) REVERT: C 331 ASN cc_start: 0.5125 (OUTLIER) cc_final: 0.4786 (p0) REVERT: C 354 ASN cc_start: 0.7552 (p0) cc_final: 0.7283 (t0) REVERT: C 390 LEU cc_start: 0.8723 (mt) cc_final: 0.8346 (mt) REVERT: C 401 VAL cc_start: 0.7753 (t) cc_final: 0.7504 (m) REVERT: C 421 TYR cc_start: 0.7575 (m-80) cc_final: 0.7347 (m-80) REVERT: C 633 TRP cc_start: 0.7257 (p90) cc_final: 0.6903 (p90) REVERT: C 658 ASN cc_start: 0.8319 (p0) cc_final: 0.7946 (p0) REVERT: C 690 GLN cc_start: 0.7684 (mp10) cc_final: 0.7347 (mp10) REVERT: C 814 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7902 (mmmt) REVERT: C 819 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7127 (mt-10) REVERT: C 868 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6958 (mm-30) REVERT: C 882 ILE cc_start: 0.8474 (mt) cc_final: 0.8253 (mt) REVERT: C 884 SER cc_start: 0.8008 (m) cc_final: 0.7744 (t) REVERT: C 969 LYS cc_start: 0.8837 (mttt) cc_final: 0.8358 (mtmm) REVERT: C 988 GLU cc_start: 0.8054 (tp30) cc_final: 0.7249 (tp30) REVERT: C 1031 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7447 (mm-30) REVERT: C 1084 ASP cc_start: 0.6754 (p0) cc_final: 0.6454 (t70) outliers start: 65 outliers final: 31 residues processed: 669 average time/residue: 0.3613 time to fit residues: 378.6654 Evaluate side-chains 594 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 560 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 158 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 286 optimal weight: 0.2980 chunk 309 optimal weight: 0.0970 chunk 255 optimal weight: 0.5980 chunk 284 optimal weight: 0.0040 chunk 97 optimal weight: 0.9980 chunk 229 optimal weight: 3.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 239 GLN A 658 ASN A 703 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1106 GLN A1119 ASN B 207 HIS B 762 GLN B 895 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25461 Z= 0.166 Angle : 0.554 8.653 34620 Z= 0.287 Chirality : 0.044 0.249 3915 Planarity : 0.004 0.062 4473 Dihedral : 4.783 48.585 3402 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.95 % Favored : 98.01 % Rotamer: Outliers : 2.34 % Allowed : 11.45 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.16 (0.13), residues: 3123 helix: -0.79 (0.20), residues: 600 sheet: 0.40 (0.18), residues: 648 loop : -1.21 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 436 HIS 0.009 0.001 HIS A 207 PHE 0.028 0.001 PHE C 855 TYR 0.026 0.001 TYR C 495 ARG 0.009 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 578 time to evaluate : 2.701 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 40 ASP cc_start: 0.7810 (t0) cc_final: 0.7450 (m-30) REVERT: A 190 ARG cc_start: 0.7561 (mtt90) cc_final: 0.7129 (mtt90) REVERT: A 202 LYS cc_start: 0.7966 (mttp) cc_final: 0.7761 (mttp) REVERT: A 269 TYR cc_start: 0.7789 (m-80) cc_final: 0.6943 (m-80) REVERT: A 304 LYS cc_start: 0.8359 (mttt) cc_final: 0.8061 (mmmm) REVERT: A 308 VAL cc_start: 0.8303 (t) cc_final: 0.8013 (p) REVERT: A 355 ARG cc_start: 0.6461 (ttm-80) cc_final: 0.6158 (ttm-80) REVERT: A 398 ASP cc_start: 0.6322 (m-30) cc_final: 0.5742 (m-30) REVERT: A 537 LYS cc_start: 0.8404 (ttmt) cc_final: 0.7952 (mtpp) REVERT: A 541 PHE cc_start: 0.4387 (m-10) cc_final: 0.3996 (m-10) REVERT: A 552 LEU cc_start: 0.8106 (mt) cc_final: 0.7619 (mm) REVERT: A 583 GLU cc_start: 0.7981 (mp0) cc_final: 0.7630 (mp0) REVERT: A 814 LYS cc_start: 0.8012 (mmmt) cc_final: 0.7610 (mmmt) REVERT: A 969 LYS cc_start: 0.8993 (mttt) cc_final: 0.8744 (mttm) REVERT: A 988 GLU cc_start: 0.7733 (tp30) cc_final: 0.7134 (tp30) REVERT: A 1019 ARG cc_start: 0.7259 (tpt170) cc_final: 0.6878 (tpt170) REVERT: B 54 LEU cc_start: 0.8333 (mt) cc_final: 0.8133 (mt) REVERT: B 99 ASN cc_start: 0.8617 (p0) cc_final: 0.8378 (p0) REVERT: B 177 MET cc_start: 0.0962 (mtt) cc_final: 0.0718 (mtt) REVERT: B 279 TYR cc_start: 0.7724 (m-80) cc_final: 0.7507 (m-80) REVERT: B 281 GLU cc_start: 0.6794 (pp20) cc_final: 0.6547 (pp20) REVERT: B 338 PHE cc_start: 0.6473 (m-80) cc_final: 0.6148 (m-80) REVERT: B 346 ARG cc_start: 0.6860 (mmt-90) cc_final: 0.6651 (mmt-90) REVERT: B 351 TYR cc_start: 0.7409 (p90) cc_final: 0.6638 (p90) REVERT: B 451 TYR cc_start: 0.3796 (m-10) cc_final: 0.3588 (m-10) REVERT: B 586 ASP cc_start: 0.7294 (m-30) cc_final: 0.6975 (m-30) REVERT: B 751 ASN cc_start: 0.7790 (m-40) cc_final: 0.7489 (m-40) REVERT: B 797 PHE cc_start: 0.7601 (m-10) cc_final: 0.7397 (m-10) REVERT: B 988 GLU cc_start: 0.7897 (tp30) cc_final: 0.7670 (tp30) REVERT: B 1002 GLN cc_start: 0.7275 (mm110) cc_final: 0.7063 (mm-40) REVERT: B 1041 ASP cc_start: 0.7648 (m-30) cc_final: 0.7438 (m-30) REVERT: C 97 LYS cc_start: 0.7679 (mmmt) cc_final: 0.7384 (mmtm) REVERT: C 190 ARG cc_start: 0.7634 (mtm180) cc_final: 0.7323 (mtt180) REVERT: C 191 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7516 (mt-10) REVERT: C 203 ILE cc_start: 0.8353 (mt) cc_final: 0.8140 (mp) REVERT: C 206 LYS cc_start: 0.8377 (tppt) cc_final: 0.8012 (tppt) REVERT: C 278 LYS cc_start: 0.8360 (tttt) cc_final: 0.8025 (ttmm) REVERT: C 298 GLU cc_start: 0.8258 (tp30) cc_final: 0.6807 (tp30) REVERT: C 354 ASN cc_start: 0.7579 (p0) cc_final: 0.7292 (t0) REVERT: C 390 LEU cc_start: 0.8713 (mt) cc_final: 0.8378 (mt) REVERT: C 401 VAL cc_start: 0.7677 (t) cc_final: 0.7439 (m) REVERT: C 658 ASN cc_start: 0.8254 (p0) cc_final: 0.7949 (p0) REVERT: C 690 GLN cc_start: 0.7687 (mp10) cc_final: 0.7463 (mp10) REVERT: C 776 LYS cc_start: 0.7790 (ttpp) cc_final: 0.7033 (ttpp) REVERT: C 780 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7046 (mt-10) REVERT: C 811 LYS cc_start: 0.6306 (tptp) cc_final: 0.5861 (tptt) REVERT: C 814 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7878 (mmmt) REVERT: C 819 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7150 (tt0) REVERT: C 859 THR cc_start: 0.8388 (t) cc_final: 0.8090 (p) REVERT: C 868 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6592 (mm-30) REVERT: C 872 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: C 882 ILE cc_start: 0.8423 (mt) cc_final: 0.8217 (mt) REVERT: C 933 LYS cc_start: 0.7933 (mttt) cc_final: 0.7633 (mttm) REVERT: C 955 ASN cc_start: 0.8319 (t0) cc_final: 0.8101 (t0) REVERT: C 969 LYS cc_start: 0.8796 (mttt) cc_final: 0.8222 (mtpp) REVERT: C 988 GLU cc_start: 0.8002 (tp30) cc_final: 0.7075 (tp30) REVERT: C 1002 GLN cc_start: 0.7602 (tp40) cc_final: 0.7335 (tp40) REVERT: C 1031 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7557 (mt-10) REVERT: C 1073 LYS cc_start: 0.7941 (tttt) cc_final: 0.7680 (mtpp) outliers start: 65 outliers final: 30 residues processed: 600 average time/residue: 0.3794 time to fit residues: 350.8326 Evaluate side-chains 573 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 542 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 283 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 287 optimal weight: 0.0670 chunk 304 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 272 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 439 ASN B 613 GLN B 690 GLN B 901 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 580 GLN C 762 GLN C1135 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25461 Z= 0.271 Angle : 0.600 8.428 34620 Z= 0.313 Chirality : 0.046 0.267 3915 Planarity : 0.004 0.057 4473 Dihedral : 4.785 39.841 3402 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.18 % Favored : 97.79 % Rotamer: Outliers : 2.81 % Allowed : 12.67 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3123 helix: -0.09 (0.21), residues: 615 sheet: 0.51 (0.19), residues: 660 loop : -1.11 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 64 HIS 0.032 0.002 HIS A 207 PHE 0.033 0.002 PHE A 133 TYR 0.024 0.002 TYR C 904 ARG 0.012 0.001 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 598 time to evaluate : 2.707 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 83 VAL cc_start: 0.7089 (t) cc_final: 0.6755 (t) REVERT: A 190 ARG cc_start: 0.7642 (mtt90) cc_final: 0.7251 (mtt90) REVERT: A 303 LEU cc_start: 0.8700 (mt) cc_final: 0.8476 (mp) REVERT: A 304 LYS cc_start: 0.8467 (mttt) cc_final: 0.8129 (mmmm) REVERT: A 308 VAL cc_start: 0.8581 (t) cc_final: 0.8280 (p) REVERT: A 390 LEU cc_start: 0.7447 (mt) cc_final: 0.7200 (mp) REVERT: A 410 ILE cc_start: 0.6769 (mm) cc_final: 0.6455 (tp) REVERT: A 534 VAL cc_start: 0.8709 (t) cc_final: 0.8427 (m) REVERT: A 537 LYS cc_start: 0.8522 (ttmt) cc_final: 0.8090 (mtpp) REVERT: A 552 LEU cc_start: 0.8235 (mt) cc_final: 0.7893 (mm) REVERT: A 797 PHE cc_start: 0.8034 (m-10) cc_final: 0.7795 (m-80) REVERT: A 814 LYS cc_start: 0.8142 (mmmt) cc_final: 0.7852 (mmmt) REVERT: A 926 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7304 (mt0) REVERT: A 969 LYS cc_start: 0.9075 (mttt) cc_final: 0.8665 (mttm) REVERT: A 988 GLU cc_start: 0.7764 (tp30) cc_final: 0.7063 (tp30) REVERT: A 1019 ARG cc_start: 0.7259 (tpt170) cc_final: 0.6417 (tpt170) REVERT: B 113 LYS cc_start: 0.7506 (mttt) cc_final: 0.7291 (tppt) REVERT: B 177 MET cc_start: 0.1018 (mtt) cc_final: 0.0741 (mtt) REVERT: B 281 GLU cc_start: 0.6902 (pp20) cc_final: 0.6663 (pp20) REVERT: B 338 PHE cc_start: 0.6460 (m-80) cc_final: 0.6114 (m-80) REVERT: B 351 TYR cc_start: 0.7660 (p90) cc_final: 0.6917 (p90) REVERT: B 586 ASP cc_start: 0.7254 (m-30) cc_final: 0.6912 (m-30) REVERT: B 613 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8085 (mm-40) REVERT: B 751 ASN cc_start: 0.8111 (m-40) cc_final: 0.7843 (m-40) REVERT: B 780 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7118 (mt-10) REVERT: B 797 PHE cc_start: 0.8057 (m-10) cc_final: 0.7832 (m-10) REVERT: B 929 SER cc_start: 0.8391 (m) cc_final: 0.8104 (m) REVERT: B 988 GLU cc_start: 0.8001 (tp30) cc_final: 0.7627 (tp30) REVERT: B 1041 ASP cc_start: 0.7696 (m-30) cc_final: 0.7473 (m-30) REVERT: C 97 LYS cc_start: 0.7759 (mmmt) cc_final: 0.7508 (mptt) REVERT: C 190 ARG cc_start: 0.7839 (mtm180) cc_final: 0.7450 (mtt180) REVERT: C 203 ILE cc_start: 0.8566 (mt) cc_final: 0.8289 (mp) REVERT: C 231 ILE cc_start: 0.8567 (mm) cc_final: 0.8270 (mm) REVERT: C 237 ARG cc_start: 0.7977 (ptp90) cc_final: 0.7396 (ptp90) REVERT: C 278 LYS cc_start: 0.8487 (tttt) cc_final: 0.8140 (ttmm) REVERT: C 304 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8085 (mmmm) REVERT: C 338 PHE cc_start: 0.7132 (m-80) cc_final: 0.6727 (m-80) REVERT: C 390 LEU cc_start: 0.8783 (mt) cc_final: 0.8524 (mt) REVERT: C 401 VAL cc_start: 0.7954 (t) cc_final: 0.7748 (m) REVERT: C 516 GLU cc_start: 0.5789 (tm-30) cc_final: 0.5010 (tm-30) REVERT: C 539 VAL cc_start: 0.8252 (m) cc_final: 0.7551 (p) REVERT: C 691 SER cc_start: 0.8225 (p) cc_final: 0.8017 (m) REVERT: C 698 SER cc_start: 0.8527 (t) cc_final: 0.8286 (p) REVERT: C 773 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6437 (mm-30) REVERT: C 776 LYS cc_start: 0.8021 (ttpp) cc_final: 0.7041 (ttpp) REVERT: C 780 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7242 (mt-10) REVERT: C 811 LYS cc_start: 0.6591 (tptp) cc_final: 0.6150 (tptt) REVERT: C 814 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7912 (mmmt) REVERT: C 859 THR cc_start: 0.8413 (t) cc_final: 0.8173 (p) REVERT: C 900 MET cc_start: 0.7951 (mtt) cc_final: 0.7667 (mtp) REVERT: C 902 MET cc_start: 0.7708 (mmm) cc_final: 0.7226 (mmt) REVERT: C 933 LYS cc_start: 0.8038 (mttt) cc_final: 0.7727 (mttm) REVERT: C 969 LYS cc_start: 0.9075 (mttt) cc_final: 0.8495 (mtpp) REVERT: C 988 GLU cc_start: 0.7868 (tp30) cc_final: 0.7197 (tp30) REVERT: C 993 ILE cc_start: 0.8062 (tt) cc_final: 0.7756 (mt) REVERT: C 1005 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7882 (tp40) outliers start: 78 outliers final: 51 residues processed: 629 average time/residue: 0.3814 time to fit residues: 370.7672 Evaluate side-chains 603 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 549 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1135 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 253 optimal weight: 0.9990 chunk 172 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 226 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 chunk 210 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 273 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 703 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 872 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 52 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 394 ASN C 448 ASN C 580 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.6289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25461 Z= 0.197 Angle : 0.550 7.888 34620 Z= 0.285 Chirality : 0.045 0.270 3915 Planarity : 0.004 0.049 4473 Dihedral : 4.598 33.600 3402 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.17 % Allowed : 13.53 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.58 (0.14), residues: 3123 helix: 0.40 (0.21), residues: 633 sheet: 0.66 (0.19), residues: 675 loop : -1.11 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C1102 HIS 0.005 0.001 HIS B 207 PHE 0.024 0.002 PHE C 855 TYR 0.028 0.002 TYR C 660 ARG 0.008 0.001 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 574 time to evaluate : 2.753 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 83 VAL cc_start: 0.7123 (t) cc_final: 0.6787 (t) REVERT: A 190 ARG cc_start: 0.7597 (mtt90) cc_final: 0.7191 (mtt90) REVERT: A 269 TYR cc_start: 0.7700 (m-80) cc_final: 0.6846 (m-80) REVERT: A 304 LYS cc_start: 0.8469 (mttt) cc_final: 0.8139 (mmmm) REVERT: A 390 LEU cc_start: 0.7567 (mt) cc_final: 0.7276 (mp) REVERT: A 410 ILE cc_start: 0.6922 (mm) cc_final: 0.6632 (tp) REVERT: A 537 LYS cc_start: 0.8440 (ttmt) cc_final: 0.8065 (mtpp) REVERT: A 574 ASP cc_start: 0.7177 (m-30) cc_final: 0.6951 (m-30) REVERT: A 748 GLU cc_start: 0.7651 (pt0) cc_final: 0.7274 (pt0) REVERT: A 814 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7789 (mmmt) REVERT: A 964 LYS cc_start: 0.8461 (mttt) cc_final: 0.8217 (mtpp) REVERT: A 969 LYS cc_start: 0.9079 (mttt) cc_final: 0.8675 (mttm) REVERT: A 988 GLU cc_start: 0.7683 (tp30) cc_final: 0.6974 (tp30) REVERT: B 113 LYS cc_start: 0.7504 (mttt) cc_final: 0.7291 (tppt) REVERT: B 131 CYS cc_start: 0.4141 (t) cc_final: 0.3635 (t) REVERT: B 177 MET cc_start: 0.1014 (mtt) cc_final: 0.0752 (mtt) REVERT: B 281 GLU cc_start: 0.6891 (pp20) cc_final: 0.6641 (pp20) REVERT: B 338 PHE cc_start: 0.6512 (m-80) cc_final: 0.6169 (m-80) REVERT: B 351 TYR cc_start: 0.7725 (p90) cc_final: 0.6822 (p90) REVERT: B 430 THR cc_start: 0.7907 (m) cc_final: 0.7532 (p) REVERT: B 586 ASP cc_start: 0.7271 (m-30) cc_final: 0.6913 (m-30) REVERT: B 646 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7512 (mtm180) REVERT: B 751 ASN cc_start: 0.8167 (m-40) cc_final: 0.7911 (m-40) REVERT: B 780 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7077 (mt-10) REVERT: B 823 PHE cc_start: 0.8240 (t80) cc_final: 0.7833 (t80) REVERT: B 902 MET cc_start: 0.8343 (mmt) cc_final: 0.7925 (mmm) REVERT: B 929 SER cc_start: 0.8405 (m) cc_final: 0.8125 (m) REVERT: B 988 GLU cc_start: 0.7934 (tp30) cc_final: 0.7626 (tp30) REVERT: B 1041 ASP cc_start: 0.7688 (m-30) cc_final: 0.7438 (m-30) REVERT: C 190 ARG cc_start: 0.7867 (mtm180) cc_final: 0.7448 (mtt180) REVERT: C 191 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7701 (mt-10) REVERT: C 203 ILE cc_start: 0.8560 (mt) cc_final: 0.8280 (mp) REVERT: C 231 ILE cc_start: 0.8630 (mm) cc_final: 0.8345 (mm) REVERT: C 237 ARG cc_start: 0.7953 (ptp90) cc_final: 0.7619 (ptp90) REVERT: C 278 LYS cc_start: 0.8491 (tttt) cc_final: 0.8149 (ttmm) REVERT: C 281 GLU cc_start: 0.6600 (pp20) cc_final: 0.6289 (pp20) REVERT: C 304 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8082 (mmmm) REVERT: C 349 SER cc_start: 0.7272 (m) cc_final: 0.6805 (p) REVERT: C 390 LEU cc_start: 0.8795 (mt) cc_final: 0.8546 (mt) REVERT: C 422 ASN cc_start: 0.7412 (m110) cc_final: 0.7198 (m110) REVERT: C 498 ARG cc_start: 0.6597 (mpt-90) cc_final: 0.6260 (mmt90) REVERT: C 568 ASP cc_start: 0.7645 (p0) cc_final: 0.7362 (p0) REVERT: C 572 THR cc_start: 0.7327 (p) cc_final: 0.6856 (p) REVERT: C 608 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8731 (m) REVERT: C 698 SER cc_start: 0.8495 (t) cc_final: 0.8245 (p) REVERT: C 773 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6201 (mm-30) REVERT: C 776 LYS cc_start: 0.7966 (ttpp) cc_final: 0.6946 (ttpp) REVERT: C 780 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7215 (mt-10) REVERT: C 814 LYS cc_start: 0.8286 (mmtt) cc_final: 0.7916 (mmmt) REVERT: C 933 LYS cc_start: 0.8017 (mttt) cc_final: 0.7706 (mttm) REVERT: C 950 ASP cc_start: 0.7660 (m-30) cc_final: 0.7163 (m-30) REVERT: C 969 LYS cc_start: 0.9104 (mttt) cc_final: 0.8666 (mtpp) REVERT: C 988 GLU cc_start: 0.7757 (tp30) cc_final: 0.7134 (tp30) REVERT: C 1005 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7911 (tp40) REVERT: C 1019 ARG cc_start: 0.6760 (tpp80) cc_final: 0.6235 (tpp80) outliers start: 88 outliers final: 63 residues processed: 610 average time/residue: 0.3767 time to fit residues: 355.1697 Evaluate side-chains 606 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 540 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 102 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 304 optimal weight: 0.9980 chunk 253 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A1002 GLN B 422 ASN B 563 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 52 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1135 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.6813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 25461 Z= 0.270 Angle : 0.578 7.609 34620 Z= 0.301 Chirality : 0.046 0.240 3915 Planarity : 0.004 0.059 4473 Dihedral : 4.642 30.041 3402 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.42 % Allowed : 14.25 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.43 (0.14), residues: 3123 helix: 0.71 (0.22), residues: 615 sheet: 0.75 (0.19), residues: 669 loop : -1.07 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C1102 HIS 0.006 0.001 HIS A1064 PHE 0.025 0.002 PHE C 133 TYR 0.033 0.002 TYR C 904 ARG 0.008 0.001 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 563 time to evaluate : 2.758 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 83 VAL cc_start: 0.7255 (OUTLIER) cc_final: 0.6758 (t) REVERT: A 237 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7702 (mtp180) REVERT: A 269 TYR cc_start: 0.7524 (m-80) cc_final: 0.6860 (m-80) REVERT: A 304 LYS cc_start: 0.8517 (mttt) cc_final: 0.8303 (mmmm) REVERT: A 390 LEU cc_start: 0.7524 (mt) cc_final: 0.7247 (mt) REVERT: A 398 ASP cc_start: 0.6616 (m-30) cc_final: 0.6385 (m-30) REVERT: A 410 ILE cc_start: 0.7117 (mm) cc_final: 0.6858 (tp) REVERT: A 421 TYR cc_start: 0.7554 (m-10) cc_final: 0.7096 (m-80) REVERT: A 450 ASN cc_start: 0.8528 (m-40) cc_final: 0.8259 (t0) REVERT: A 537 LYS cc_start: 0.8497 (ttmt) cc_final: 0.8162 (mtpp) REVERT: A 552 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8126 (mm) REVERT: A 574 ASP cc_start: 0.7220 (m-30) cc_final: 0.6940 (m-30) REVERT: A 697 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7915 (ptm) REVERT: A 814 LYS cc_start: 0.8179 (mmmt) cc_final: 0.7852 (mmmt) REVERT: A 896 ILE cc_start: 0.7986 (tp) cc_final: 0.7698 (tt) REVERT: A 964 LYS cc_start: 0.8489 (mttt) cc_final: 0.8219 (mtpp) REVERT: A 969 LYS cc_start: 0.9100 (mttt) cc_final: 0.8709 (mttm) REVERT: A 988 GLU cc_start: 0.7607 (tp30) cc_final: 0.6934 (tp30) REVERT: A 1019 ARG cc_start: 0.7309 (tpp-160) cc_final: 0.6927 (tpm170) REVERT: B 177 MET cc_start: 0.1010 (mtt) cc_final: 0.0730 (mtt) REVERT: B 190 ARG cc_start: 0.8169 (mtm-85) cc_final: 0.7967 (mtm-85) REVERT: B 281 GLU cc_start: 0.6950 (pp20) cc_final: 0.6732 (pp20) REVERT: B 338 PHE cc_start: 0.6673 (m-80) cc_final: 0.6257 (m-80) REVERT: B 351 TYR cc_start: 0.7723 (p90) cc_final: 0.6692 (p90) REVERT: B 430 THR cc_start: 0.8091 (m) cc_final: 0.7758 (p) REVERT: B 586 ASP cc_start: 0.7293 (m-30) cc_final: 0.6923 (m-30) REVERT: B 613 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8430 (tp40) REVERT: B 641 ASN cc_start: 0.6839 (m-40) cc_final: 0.6277 (p0) REVERT: B 642 VAL cc_start: 0.9263 (OUTLIER) cc_final: 0.8857 (t) REVERT: B 719 THR cc_start: 0.8632 (t) cc_final: 0.8381 (p) REVERT: B 751 ASN cc_start: 0.8163 (m-40) cc_final: 0.7851 (m-40) REVERT: B 773 GLU cc_start: 0.7521 (tt0) cc_final: 0.7165 (tt0) REVERT: B 988 GLU cc_start: 0.7932 (tp30) cc_final: 0.7664 (tp30) REVERT: B 1019 ARG cc_start: 0.7456 (ttm-80) cc_final: 0.6710 (ttm-80) REVERT: B 1045 LYS cc_start: 0.8259 (tptt) cc_final: 0.8033 (tptt) REVERT: C 133 PHE cc_start: 0.8025 (m-10) cc_final: 0.7756 (m-10) REVERT: C 190 ARG cc_start: 0.7918 (mtm180) cc_final: 0.7622 (mtt180) REVERT: C 191 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7753 (mt-10) REVERT: C 231 ILE cc_start: 0.8636 (mm) cc_final: 0.8345 (mm) REVERT: C 237 ARG cc_start: 0.7938 (ptp90) cc_final: 0.7715 (ptp90) REVERT: C 278 LYS cc_start: 0.8500 (tttt) cc_final: 0.8042 (ttmm) REVERT: C 281 GLU cc_start: 0.6616 (pp20) cc_final: 0.6291 (pp20) REVERT: C 304 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8166 (mmmm) REVERT: C 340 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7655 (mm-30) REVERT: C 349 SER cc_start: 0.7649 (m) cc_final: 0.7157 (p) REVERT: C 422 ASN cc_start: 0.7446 (m110) cc_final: 0.7233 (m110) REVERT: C 568 ASP cc_start: 0.7706 (p0) cc_final: 0.7389 (p0) REVERT: C 572 THR cc_start: 0.7612 (p) cc_final: 0.7121 (p) REVERT: C 698 SER cc_start: 0.8585 (t) cc_final: 0.8343 (p) REVERT: C 750 SER cc_start: 0.9019 (m) cc_final: 0.8745 (m) REVERT: C 776 LYS cc_start: 0.7925 (ttpp) cc_final: 0.6824 (ttpp) REVERT: C 780 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7179 (mt-10) REVERT: C 814 LYS cc_start: 0.8243 (mmtt) cc_final: 0.7883 (mmmt) REVERT: C 896 ILE cc_start: 0.7902 (tp) cc_final: 0.7693 (tt) REVERT: C 933 LYS cc_start: 0.8072 (mttt) cc_final: 0.7755 (mttm) REVERT: C 950 ASP cc_start: 0.7779 (m-30) cc_final: 0.7341 (m-30) REVERT: C 969 LYS cc_start: 0.9132 (mttt) cc_final: 0.8693 (mtpp) REVERT: C 988 GLU cc_start: 0.7752 (tp30) cc_final: 0.7136 (tp30) REVERT: C 993 ILE cc_start: 0.8031 (tt) cc_final: 0.7755 (mt) REVERT: C 1005 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7913 (tp40) outliers start: 95 outliers final: 64 residues processed: 608 average time/residue: 0.3775 time to fit residues: 351.7655 Evaluate side-chains 603 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 532 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1135 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 293 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 222 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 256 optimal weight: 0.9990 chunk 170 optimal weight: 0.7980 chunk 303 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 613 GLN B 949 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 52 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.7201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25461 Z= 0.238 Angle : 0.576 11.255 34620 Z= 0.297 Chirality : 0.045 0.237 3915 Planarity : 0.004 0.082 4473 Dihedral : 4.620 25.791 3402 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.24 % Allowed : 15.05 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.39 (0.15), residues: 3123 helix: 0.86 (0.22), residues: 615 sheet: 0.65 (0.19), residues: 690 loop : -1.05 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 436 HIS 0.005 0.001 HIS A1064 PHE 0.025 0.002 PHE C 855 TYR 0.019 0.001 TYR C 904 ARG 0.011 0.001 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 554 time to evaluate : 2.782 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 83 VAL cc_start: 0.7365 (OUTLIER) cc_final: 0.6914 (t) REVERT: A 237 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7604 (mtp180) REVERT: A 269 TYR cc_start: 0.7497 (m-80) cc_final: 0.6817 (m-80) REVERT: A 304 LYS cc_start: 0.8513 (mttt) cc_final: 0.8288 (mmmm) REVERT: A 319 ARG cc_start: 0.7620 (mmt-90) cc_final: 0.7397 (tpp-160) REVERT: A 390 LEU cc_start: 0.7539 (mt) cc_final: 0.7181 (mt) REVERT: A 421 TYR cc_start: 0.7559 (m-10) cc_final: 0.7122 (m-80) REVERT: A 450 ASN cc_start: 0.8593 (m-40) cc_final: 0.8331 (t0) REVERT: A 537 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8192 (mtpp) REVERT: A 552 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8126 (mm) REVERT: A 574 ASP cc_start: 0.7272 (m-30) cc_final: 0.6950 (m-30) REVERT: A 576 VAL cc_start: 0.7445 (OUTLIER) cc_final: 0.7106 (t) REVERT: A 697 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7944 (ptm) REVERT: A 814 LYS cc_start: 0.8142 (mmmt) cc_final: 0.7846 (mmmt) REVERT: A 950 ASP cc_start: 0.7724 (m-30) cc_final: 0.7410 (m-30) REVERT: A 964 LYS cc_start: 0.8486 (mttt) cc_final: 0.8218 (mtpp) REVERT: A 969 LYS cc_start: 0.9112 (mttt) cc_final: 0.8718 (mttm) REVERT: A 988 GLU cc_start: 0.7574 (tp30) cc_final: 0.6905 (tp30) REVERT: A 1050 MET cc_start: 0.8287 (ptt) cc_final: 0.7999 (ptm) REVERT: A 1142 GLN cc_start: 0.8386 (pp30) cc_final: 0.8180 (pp30) REVERT: B 177 MET cc_start: 0.0994 (mtt) cc_final: 0.0726 (mtt) REVERT: B 338 PHE cc_start: 0.6649 (m-80) cc_final: 0.6345 (m-80) REVERT: B 351 TYR cc_start: 0.7718 (p90) cc_final: 0.6692 (p90) REVERT: B 430 THR cc_start: 0.8192 (m) cc_final: 0.7884 (p) REVERT: B 586 ASP cc_start: 0.7297 (m-30) cc_final: 0.6916 (m-30) REVERT: B 613 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8514 (tp40) REVERT: B 641 ASN cc_start: 0.6776 (m-40) cc_final: 0.6323 (p0) REVERT: B 642 VAL cc_start: 0.9334 (OUTLIER) cc_final: 0.8934 (t) REVERT: B 719 THR cc_start: 0.8603 (t) cc_final: 0.8394 (p) REVERT: B 751 ASN cc_start: 0.8119 (m-40) cc_final: 0.7779 (m-40) REVERT: B 773 GLU cc_start: 0.7512 (tt0) cc_final: 0.7064 (tt0) REVERT: B 935 GLN cc_start: 0.7626 (tt0) cc_final: 0.7360 (tp-100) REVERT: B 985 ASP cc_start: 0.6782 (m-30) cc_final: 0.6541 (m-30) REVERT: B 988 GLU cc_start: 0.7891 (tp30) cc_final: 0.7635 (tp30) REVERT: B 1019 ARG cc_start: 0.7475 (ttm-80) cc_final: 0.6944 (ttm-80) REVERT: B 1045 LYS cc_start: 0.8275 (tptt) cc_final: 0.8020 (tptt) REVERT: C 133 PHE cc_start: 0.8093 (m-10) cc_final: 0.7838 (m-10) REVERT: C 190 ARG cc_start: 0.7873 (mtm180) cc_final: 0.7551 (mtt180) REVERT: C 231 ILE cc_start: 0.8609 (mm) cc_final: 0.8331 (mm) REVERT: C 278 LYS cc_start: 0.8505 (tttt) cc_final: 0.8037 (ttmm) REVERT: C 304 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8129 (mmmm) REVERT: C 323 THR cc_start: 0.9090 (m) cc_final: 0.8843 (m) REVERT: C 340 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7636 (mm-30) REVERT: C 349 SER cc_start: 0.7799 (m) cc_final: 0.7179 (p) REVERT: C 408 ARG cc_start: 0.8471 (ttp80) cc_final: 0.8245 (ppt170) REVERT: C 422 ASN cc_start: 0.7436 (m110) cc_final: 0.7231 (m110) REVERT: C 508 TYR cc_start: 0.5762 (m-80) cc_final: 0.5416 (m-80) REVERT: C 651 ILE cc_start: 0.8424 (pt) cc_final: 0.8081 (mt) REVERT: C 698 SER cc_start: 0.8585 (t) cc_final: 0.8357 (p) REVERT: C 725 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7070 (tt0) REVERT: C 748 GLU cc_start: 0.8785 (mp0) cc_final: 0.8284 (pt0) REVERT: C 776 LYS cc_start: 0.7892 (ttpp) cc_final: 0.6964 (ttpp) REVERT: C 780 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7027 (mt-10) REVERT: C 814 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7840 (mmmt) REVERT: C 933 LYS cc_start: 0.8108 (mttt) cc_final: 0.7800 (mttm) REVERT: C 950 ASP cc_start: 0.7744 (m-30) cc_final: 0.7236 (m-30) REVERT: C 969 LYS cc_start: 0.9151 (mttt) cc_final: 0.8865 (mttp) REVERT: C 1005 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7928 (tp40) outliers start: 90 outliers final: 66 residues processed: 592 average time/residue: 0.3958 time to fit residues: 359.8197 Evaluate side-chains 612 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 538 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 187 optimal weight: 0.0870 chunk 121 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 150 optimal weight: 0.4980 chunk 28 optimal weight: 0.0570 chunk 238 optimal weight: 0.1980 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 675 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.7364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25461 Z= 0.164 Angle : 0.554 10.705 34620 Z= 0.283 Chirality : 0.044 0.216 3915 Planarity : 0.004 0.091 4473 Dihedral : 4.438 23.036 3402 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.95 % Allowed : 16.20 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.29 (0.15), residues: 3123 helix: 0.99 (0.22), residues: 630 sheet: 0.71 (0.19), residues: 696 loop : -1.02 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 436 HIS 0.003 0.001 HIS B 954 PHE 0.040 0.001 PHE C 855 TYR 0.028 0.001 TYR C 660 ARG 0.010 0.001 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 534 time to evaluate : 3.038 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 40 ASP cc_start: 0.7961 (t0) cc_final: 0.7672 (m-30) REVERT: A 83 VAL cc_start: 0.7275 (OUTLIER) cc_final: 0.6774 (t) REVERT: A 237 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7567 (mtp-110) REVERT: A 269 TYR cc_start: 0.7550 (m-80) cc_final: 0.6805 (m-80) REVERT: A 304 LYS cc_start: 0.8484 (mttt) cc_final: 0.8260 (mmmm) REVERT: A 319 ARG cc_start: 0.7606 (mmt-90) cc_final: 0.7406 (tpp-160) REVERT: A 355 ARG cc_start: 0.6840 (ttm-80) cc_final: 0.6157 (ttm-80) REVERT: A 390 LEU cc_start: 0.7493 (mt) cc_final: 0.7192 (mt) REVERT: A 410 ILE cc_start: 0.7227 (mm) cc_final: 0.6996 (tp) REVERT: A 421 TYR cc_start: 0.7530 (m-10) cc_final: 0.7120 (m-80) REVERT: A 450 ASN cc_start: 0.8608 (m-40) cc_final: 0.8335 (t0) REVERT: A 552 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8214 (mm) REVERT: A 574 ASP cc_start: 0.7256 (m-30) cc_final: 0.6930 (m-30) REVERT: A 576 VAL cc_start: 0.7432 (OUTLIER) cc_final: 0.7084 (t) REVERT: A 632 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7769 (m) REVERT: A 697 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8018 (ptm) REVERT: A 814 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7776 (mmmt) REVERT: A 964 LYS cc_start: 0.8474 (mttt) cc_final: 0.8209 (mtpp) REVERT: A 969 LYS cc_start: 0.9099 (mttt) cc_final: 0.8839 (mttm) REVERT: A 988 GLU cc_start: 0.7448 (tp30) cc_final: 0.6762 (tp30) REVERT: A 1050 MET cc_start: 0.8278 (ptt) cc_final: 0.7995 (ptm) REVERT: B 166 CYS cc_start: 0.3668 (OUTLIER) cc_final: 0.3073 (p) REVERT: B 177 MET cc_start: 0.0982 (mtt) cc_final: 0.0721 (mtt) REVERT: B 338 PHE cc_start: 0.6634 (m-80) cc_final: 0.6408 (m-80) REVERT: B 351 TYR cc_start: 0.7659 (p90) cc_final: 0.6638 (p90) REVERT: B 430 THR cc_start: 0.8238 (m) cc_final: 0.8009 (p) REVERT: B 586 ASP cc_start: 0.7325 (m-30) cc_final: 0.6935 (m-30) REVERT: B 641 ASN cc_start: 0.6706 (m-40) cc_final: 0.6290 (p0) REVERT: B 642 VAL cc_start: 0.9330 (OUTLIER) cc_final: 0.8936 (t) REVERT: B 751 ASN cc_start: 0.8126 (m-40) cc_final: 0.7754 (m-40) REVERT: B 773 GLU cc_start: 0.7506 (tt0) cc_final: 0.7254 (tt0) REVERT: B 823 PHE cc_start: 0.8225 (t80) cc_final: 0.7829 (t80) REVERT: B 935 GLN cc_start: 0.7508 (tt0) cc_final: 0.7165 (tt0) REVERT: B 950 ASP cc_start: 0.7129 (t70) cc_final: 0.6858 (t70) REVERT: B 985 ASP cc_start: 0.6728 (m-30) cc_final: 0.6483 (m-30) REVERT: B 988 GLU cc_start: 0.7813 (tp30) cc_final: 0.7548 (tp30) REVERT: B 1002 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7529 (tp40) REVERT: B 1045 LYS cc_start: 0.8255 (tptt) cc_final: 0.7987 (tptt) REVERT: C 81 ASN cc_start: 0.8503 (m-40) cc_final: 0.7902 (t0) REVERT: C 133 PHE cc_start: 0.8043 (m-10) cc_final: 0.7813 (m-10) REVERT: C 231 ILE cc_start: 0.8532 (mm) cc_final: 0.8285 (mm) REVERT: C 278 LYS cc_start: 0.8524 (tttt) cc_final: 0.8057 (ttmm) REVERT: C 304 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8083 (mmmm) REVERT: C 340 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7608 (mm-30) REVERT: C 349 SER cc_start: 0.7689 (m) cc_final: 0.7106 (p) REVERT: C 408 ARG cc_start: 0.8492 (ttp80) cc_final: 0.8269 (ppt170) REVERT: C 440 LYS cc_start: 0.8749 (ptpt) cc_final: 0.8487 (ptpp) REVERT: C 651 ILE cc_start: 0.8334 (pt) cc_final: 0.7990 (mt) REVERT: C 698 SER cc_start: 0.8567 (t) cc_final: 0.8343 (p) REVERT: C 725 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7184 (tt0) REVERT: C 748 GLU cc_start: 0.8834 (mp0) cc_final: 0.8225 (pt0) REVERT: C 776 LYS cc_start: 0.7955 (ttpp) cc_final: 0.6873 (ttpp) REVERT: C 780 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7147 (mt-10) REVERT: C 814 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7813 (mmmt) REVERT: C 900 MET cc_start: 0.7896 (mtt) cc_final: 0.7666 (mtp) REVERT: C 933 LYS cc_start: 0.8090 (mttt) cc_final: 0.7786 (mttm) REVERT: C 969 LYS cc_start: 0.9155 (mttt) cc_final: 0.8869 (mttp) REVERT: C 988 GLU cc_start: 0.7866 (mp0) cc_final: 0.7562 (mp0) REVERT: C 1005 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7872 (tp40) outliers start: 82 outliers final: 56 residues processed: 569 average time/residue: 0.3776 time to fit residues: 330.9312 Evaluate side-chains 592 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 527 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 276 optimal weight: 0.6980 chunk 290 optimal weight: 0.9990 chunk 265 optimal weight: 2.9990 chunk 282 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 222 optimal weight: 0.5980 chunk 86 optimal weight: 0.3980 chunk 255 optimal weight: 3.9990 chunk 267 optimal weight: 0.0670 chunk 281 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 703 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 370 ASN B 613 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.7555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25461 Z= 0.184 Angle : 0.561 9.948 34620 Z= 0.288 Chirality : 0.045 0.241 3915 Planarity : 0.004 0.088 4473 Dihedral : 4.403 25.133 3402 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.99 % Allowed : 16.56 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.23 (0.15), residues: 3123 helix: 1.12 (0.22), residues: 630 sheet: 0.69 (0.19), residues: 702 loop : -1.00 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 436 HIS 0.003 0.001 HIS B1064 PHE 0.038 0.002 PHE C 855 TYR 0.018 0.001 TYR B 904 ARG 0.010 0.001 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 535 time to evaluate : 2.943 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 40 ASP cc_start: 0.7969 (t0) cc_final: 0.7685 (m-30) REVERT: A 83 VAL cc_start: 0.7283 (OUTLIER) cc_final: 0.6954 (t) REVERT: A 269 TYR cc_start: 0.7542 (m-80) cc_final: 0.6846 (m-80) REVERT: A 304 LYS cc_start: 0.8499 (mttt) cc_final: 0.8252 (mmmm) REVERT: A 355 ARG cc_start: 0.6821 (ttm-80) cc_final: 0.6130 (ttm-80) REVERT: A 390 LEU cc_start: 0.7488 (mt) cc_final: 0.7189 (mt) REVERT: A 410 ILE cc_start: 0.7281 (mm) cc_final: 0.7050 (tp) REVERT: A 421 TYR cc_start: 0.7547 (m-10) cc_final: 0.7153 (m-80) REVERT: A 450 ASN cc_start: 0.8678 (m-40) cc_final: 0.8345 (t0) REVERT: A 554 GLU cc_start: 0.6475 (pm20) cc_final: 0.6109 (pm20) REVERT: A 574 ASP cc_start: 0.7264 (m-30) cc_final: 0.6930 (m-30) REVERT: A 576 VAL cc_start: 0.7496 (OUTLIER) cc_final: 0.7198 (t) REVERT: A 583 GLU cc_start: 0.7755 (mp0) cc_final: 0.6751 (mm-30) REVERT: A 632 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7697 (m) REVERT: A 697 MET cc_start: 0.8425 (ttp) cc_final: 0.8015 (ptm) REVERT: A 814 LYS cc_start: 0.8149 (mmmt) cc_final: 0.7841 (mmmt) REVERT: A 964 LYS cc_start: 0.8475 (mttt) cc_final: 0.8210 (mtpp) REVERT: A 969 LYS cc_start: 0.9103 (mttt) cc_final: 0.8849 (mttm) REVERT: A 988 GLU cc_start: 0.7367 (tp30) cc_final: 0.6740 (tp30) REVERT: A 1050 MET cc_start: 0.8283 (ptt) cc_final: 0.8028 (ptm) REVERT: B 177 MET cc_start: 0.0973 (mtt) cc_final: 0.0723 (mtt) REVERT: B 338 PHE cc_start: 0.6652 (m-80) cc_final: 0.6417 (m-80) REVERT: B 351 TYR cc_start: 0.7657 (p90) cc_final: 0.6647 (p90) REVERT: B 365 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.6792 (t80) REVERT: B 393 THR cc_start: 0.7660 (m) cc_final: 0.7275 (p) REVERT: B 409 GLN cc_start: 0.8761 (mt0) cc_final: 0.8547 (tt0) REVERT: B 430 THR cc_start: 0.8236 (m) cc_final: 0.8008 (p) REVERT: B 586 ASP cc_start: 0.7295 (m-30) cc_final: 0.6920 (m-30) REVERT: B 613 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8461 (tp40) REVERT: B 641 ASN cc_start: 0.6703 (m-40) cc_final: 0.6290 (p0) REVERT: B 642 VAL cc_start: 0.9341 (OUTLIER) cc_final: 0.8951 (t) REVERT: B 751 ASN cc_start: 0.8167 (m-40) cc_final: 0.7793 (m-40) REVERT: B 773 GLU cc_start: 0.7493 (tt0) cc_final: 0.7281 (tt0) REVERT: B 780 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7045 (mt-10) REVERT: B 823 PHE cc_start: 0.8211 (t80) cc_final: 0.7824 (t80) REVERT: B 935 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7394 (tt0) REVERT: B 950 ASP cc_start: 0.7211 (t70) cc_final: 0.6971 (t70) REVERT: B 985 ASP cc_start: 0.6691 (m-30) cc_final: 0.6432 (m-30) REVERT: B 988 GLU cc_start: 0.7771 (tp30) cc_final: 0.7361 (tp30) REVERT: B 1045 LYS cc_start: 0.8266 (tptt) cc_final: 0.7986 (tptt) REVERT: C 231 ILE cc_start: 0.8507 (mm) cc_final: 0.8265 (mm) REVERT: C 278 LYS cc_start: 0.8526 (tttt) cc_final: 0.8058 (ttmm) REVERT: C 298 GLU cc_start: 0.8104 (tp30) cc_final: 0.7900 (tt0) REVERT: C 304 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8110 (mmmm) REVERT: C 340 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7617 (mm-30) REVERT: C 349 SER cc_start: 0.7765 (m) cc_final: 0.7187 (p) REVERT: C 408 ARG cc_start: 0.8506 (ttp80) cc_final: 0.8018 (ppt170) REVERT: C 440 LYS cc_start: 0.8768 (ptpt) cc_final: 0.8490 (ptpp) REVERT: C 516 GLU cc_start: 0.5844 (tm-30) cc_final: 0.4956 (tm-30) REVERT: C 698 SER cc_start: 0.8601 (t) cc_final: 0.8369 (p) REVERT: C 725 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7202 (tt0) REVERT: C 773 GLU cc_start: 0.6781 (mm-30) cc_final: 0.6426 (mm-30) REVERT: C 776 LYS cc_start: 0.8009 (ttpp) cc_final: 0.6966 (ttpp) REVERT: C 780 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7081 (mt-10) REVERT: C 814 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7760 (mmmt) REVERT: C 933 LYS cc_start: 0.8104 (mttt) cc_final: 0.7808 (mttm) REVERT: C 950 ASP cc_start: 0.7699 (m-30) cc_final: 0.7282 (m-30) REVERT: C 969 LYS cc_start: 0.9177 (mttt) cc_final: 0.8823 (mtpp) REVERT: C 988 GLU cc_start: 0.7875 (mp0) cc_final: 0.7549 (mp0) REVERT: C 1002 GLN cc_start: 0.8027 (tp40) cc_final: 0.7761 (tp40) REVERT: C 1005 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7912 (tp40) outliers start: 83 outliers final: 65 residues processed: 573 average time/residue: 0.4196 time to fit residues: 371.7121 Evaluate side-chains 599 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 526 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 185 optimal weight: 0.8980 chunk 299 optimal weight: 0.0070 chunk 182 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 313 optimal weight: 0.9990 chunk 288 optimal weight: 0.5980 chunk 249 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 703 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1002 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 52 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 394 ASN C 580 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1002 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.7730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25461 Z= 0.209 Angle : 0.573 9.921 34620 Z= 0.294 Chirality : 0.045 0.237 3915 Planarity : 0.004 0.088 4473 Dihedral : 4.428 26.480 3402 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.95 % Allowed : 16.70 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.25 (0.15), residues: 3123 helix: 1.17 (0.22), residues: 630 sheet: 0.72 (0.19), residues: 696 loop : -1.05 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 436 HIS 0.026 0.001 HIS B 207 PHE 0.042 0.002 PHE A 133 TYR 0.019 0.001 TYR C 660 ARG 0.010 0.001 ARG C1019 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 539 time to evaluate : 2.650 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 40 ASP cc_start: 0.7981 (t0) cc_final: 0.7663 (m-30) REVERT: A 83 VAL cc_start: 0.7325 (OUTLIER) cc_final: 0.6995 (t) REVERT: A 269 TYR cc_start: 0.7525 (m-80) cc_final: 0.6821 (m-80) REVERT: A 304 LYS cc_start: 0.8519 (mttt) cc_final: 0.8259 (mmmm) REVERT: A 324 GLU cc_start: 0.7413 (pt0) cc_final: 0.7116 (pm20) REVERT: A 340 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7749 (tm-30) REVERT: A 355 ARG cc_start: 0.6795 (ttm-80) cc_final: 0.6085 (ttm-80) REVERT: A 390 LEU cc_start: 0.7488 (mt) cc_final: 0.7232 (mt) REVERT: A 410 ILE cc_start: 0.7386 (mm) cc_final: 0.7152 (tp) REVERT: A 421 TYR cc_start: 0.7543 (m-10) cc_final: 0.7148 (m-80) REVERT: A 450 ASN cc_start: 0.8735 (m-40) cc_final: 0.8401 (t0) REVERT: A 554 GLU cc_start: 0.6507 (pm20) cc_final: 0.6117 (pm20) REVERT: A 574 ASP cc_start: 0.7287 (m-30) cc_final: 0.6941 (m-30) REVERT: A 576 VAL cc_start: 0.7515 (OUTLIER) cc_final: 0.7248 (t) REVERT: A 632 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7762 (m) REVERT: A 697 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7987 (ptm) REVERT: A 804 GLN cc_start: 0.7907 (mt0) cc_final: 0.7620 (mt0) REVERT: A 814 LYS cc_start: 0.8116 (mmmt) cc_final: 0.7820 (mmmt) REVERT: A 964 LYS cc_start: 0.8483 (mttt) cc_final: 0.8219 (mtpp) REVERT: A 969 LYS cc_start: 0.9108 (mttt) cc_final: 0.8857 (mttm) REVERT: A 984 LEU cc_start: 0.7322 (mm) cc_final: 0.7056 (mm) REVERT: A 988 GLU cc_start: 0.7390 (tp30) cc_final: 0.6744 (tp30) REVERT: A 1050 MET cc_start: 0.8286 (ptt) cc_final: 0.8057 (ptm) REVERT: B 177 MET cc_start: 0.0982 (mtt) cc_final: 0.0731 (mtt) REVERT: B 338 PHE cc_start: 0.6715 (m-80) cc_final: 0.6350 (m-80) REVERT: B 351 TYR cc_start: 0.7625 (p90) cc_final: 0.6532 (p90) REVERT: B 365 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.6798 (t80) REVERT: B 409 GLN cc_start: 0.8783 (mt0) cc_final: 0.8552 (mt0) REVERT: B 430 THR cc_start: 0.8256 (m) cc_final: 0.8039 (p) REVERT: B 496 SER cc_start: 0.8691 (m) cc_final: 0.8304 (t) REVERT: B 567 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7569 (mtt-85) REVERT: B 586 ASP cc_start: 0.7290 (m-30) cc_final: 0.6773 (m-30) REVERT: B 641 ASN cc_start: 0.6760 (m-40) cc_final: 0.6392 (p0) REVERT: B 642 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.8967 (t) REVERT: B 751 ASN cc_start: 0.8237 (m-40) cc_final: 0.7841 (m-40) REVERT: B 776 LYS cc_start: 0.8003 (ttpp) cc_final: 0.7721 (ttpp) REVERT: B 780 GLU cc_start: 0.7280 (mt-10) cc_final: 0.7066 (mt-10) REVERT: B 823 PHE cc_start: 0.8213 (t80) cc_final: 0.7852 (t80) REVERT: B 935 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: B 985 ASP cc_start: 0.6647 (m-30) cc_final: 0.6409 (m-30) REVERT: B 988 GLU cc_start: 0.7774 (tp30) cc_final: 0.7466 (tp30) REVERT: B 1002 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7548 (tp40) REVERT: B 1045 LYS cc_start: 0.8268 (tptt) cc_final: 0.7964 (tptt) REVERT: C 81 ASN cc_start: 0.8448 (m-40) cc_final: 0.8039 (t0) REVERT: C 231 ILE cc_start: 0.8526 (mm) cc_final: 0.8279 (mm) REVERT: C 278 LYS cc_start: 0.8518 (tttt) cc_final: 0.8103 (ttmm) REVERT: C 304 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8107 (mmmm) REVERT: C 349 SER cc_start: 0.7674 (m) cc_final: 0.7119 (p) REVERT: C 408 ARG cc_start: 0.8498 (ttp80) cc_final: 0.8026 (ppt170) REVERT: C 454 ARG cc_start: 0.6998 (ptm160) cc_final: 0.6622 (ptm-80) REVERT: C 516 GLU cc_start: 0.5947 (tm-30) cc_final: 0.5089 (tm-30) REVERT: C 607 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8175 (mt0) REVERT: C 698 SER cc_start: 0.8618 (t) cc_final: 0.8385 (p) REVERT: C 725 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7211 (tt0) REVERT: C 773 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6454 (mm-30) REVERT: C 814 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7743 (mmmt) REVERT: C 933 LYS cc_start: 0.8109 (mttt) cc_final: 0.7827 (mttm) REVERT: C 950 ASP cc_start: 0.7711 (m-30) cc_final: 0.7271 (m-30) REVERT: C 969 LYS cc_start: 0.9185 (mttt) cc_final: 0.8751 (mtpp) REVERT: C 988 GLU cc_start: 0.7878 (mp0) cc_final: 0.7616 (mp0) REVERT: C 1005 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7912 (tp40) outliers start: 82 outliers final: 66 residues processed: 576 average time/residue: 0.3919 time to fit residues: 345.1045 Evaluate side-chains 599 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 524 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 198 optimal weight: 1.9990 chunk 266 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 104 optimal weight: 0.0010 chunk 257 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 370 ASN B 563 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 394 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.148294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.120522 restraints weight = 45185.811| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.10 r_work: 0.3548 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.7755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.311 25461 Z= 0.378 Angle : 0.950 59.123 34620 Z= 0.578 Chirality : 0.048 0.582 3915 Planarity : 0.005 0.144 4473 Dihedral : 4.424 26.092 3402 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.88 % Allowed : 17.21 % Favored : 79.91 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.25 (0.15), residues: 3123 helix: 1.16 (0.22), residues: 630 sheet: 0.71 (0.19), residues: 696 loop : -1.06 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 436 HIS 0.015 0.001 HIS B 207 PHE 0.047 0.002 PHE A 981 TYR 0.023 0.001 TYR C 660 ARG 0.008 0.000 ARG C1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7041.20 seconds wall clock time: 127 minutes 12.73 seconds (7632.73 seconds total)