Starting phenix.real_space_refine on Sat Jun 21 18:45:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w92_32359/06_2025/7w92_32359.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w92_32359/06_2025/7w92_32359.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/cci-nas-00/data/ceres_data/7w92_32359/06_2025/7w92_32359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w92_32359/06_2025/7w92_32359.map" model { file = "/net/cci-nas-00/data/ceres_data/7w92_32359/06_2025/7w92_32359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w92_32359/06_2025/7w92_32359.cif" } 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= 0.035 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 15986 2.51 5 N 4211 2.21 5 O 4760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 255 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25071 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8382 Classifications: {'peptide': 1072} Link IDs: {'PTRANS': 53, 'TRANS': 1018} Chain breaks: 6 Chain: "C" Number of atoms: 8296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8296 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 53, 'TRANS': 1007} Chain breaks: 6 Chain: "B" Number of atoms: 8393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8393 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 54, 'TRANS': 1018} Chain breaks: 7 Time building chain proxies: 15.77, per 1000 atoms: 0.63 Number of scatterers: 25071 At special positions: 0 Unit cell: (155.382, 141.987, 201.818, 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 4760 8.00 N 4211 7.00 C 15986 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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 C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.38 Conformation dependent library (CDL) restraints added in 3.3 seconds 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5994 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 55 sheets defined 21.7% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.951A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.049A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.277A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.786A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.762A pdb=" N TYR A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 4.002A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.819A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.502A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.698A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.530A pdb=" N GLY A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 4.098A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.977A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.567A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 944 removed outlier: 4.056A pdb=" N ALA A 944 " --> pdb=" O THR A 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 941 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.013A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.584A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1032 removed outlier: 3.555A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.662A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 389 removed outlier: 4.005A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 389' Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.723A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.554A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.647A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.754A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 3.532A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.549A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 880 " --> pdb=" O ALA C 876 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.760A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.885A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.047A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.722A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 982' Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.568A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG C1014 " --> pdb=" O GLN C1010 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.738A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.765A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.759A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 371' Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.593A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.808A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.592A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 780 removed outlier: 3.933A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.691A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.508A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.687A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.586A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.719A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.215A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.629A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1032 removed outlier: 4.386A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1147 removed outlier: 3.500A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B1147 " --> pdb=" O GLU B1144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1143 through 1147' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.695A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.025A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.517A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.807A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.807A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.699A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 119 through 121 removed outlier: 3.663A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.568A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.705A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 574 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.252A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.942A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.606A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.511A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.387A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.804A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB9, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.503A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC3, first strand: chain 'A' and resid 1122 through 1125 removed outlier: 5.432A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC5, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.538A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.954A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.811A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.141A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.141A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.290A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.937A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.574A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 400 through 402 Processing sheet with id=AD5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.019A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.263A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.719A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 718 through 719 Processing sheet with id=AE1, first strand: chain 'C' and resid 718 through 719 removed outlier: 3.530A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE4, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.241A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.532A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.781A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.907A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.310A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.887A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.544A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.534A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AF6, first strand: chain 'B' and resid 718 through 719 Processing sheet with id=AF7, first strand: chain 'B' and resid 718 through 719 removed outlier: 7.386A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B1047 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AG1, first strand: chain 'B' and resid 1094 through 1097 657 hydrogen bonds defined for protein. 1830 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.27 Time building geometry restraints manager: 6.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8123 1.35 - 1.47: 6422 1.47 - 1.60: 10961 1.60 - 1.72: 0 1.72 - 1.84: 144 Bond restraints: 25650 Sorted by residual: bond pdb=" C GLN C 23 " pdb=" N LEU C 24 " ideal model delta sigma weight residual 1.331 1.373 -0.042 2.07e-02 2.33e+03 4.10e+00 bond pdb=" CA THR B 630 " pdb=" C THR B 630 " ideal model delta sigma weight residual 1.525 1.565 -0.040 2.10e-02 2.27e+03 3.56e+00 bond pdb=" CA GLU B 516 " pdb=" CB GLU B 516 " ideal model delta sigma weight residual 1.526 1.554 -0.028 1.70e-02 3.46e+03 2.64e+00 bond pdb=" C GLN C1142 " pdb=" N PRO C1143 " ideal model delta sigma weight residual 1.334 1.346 -0.013 8.40e-03 1.42e+04 2.35e+00 bond pdb=" CB ASP B 198 " pdb=" CG ASP B 198 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.09e+00 ... (remaining 25645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 34318 2.33 - 4.67: 504 4.67 - 7.00: 51 7.00 - 9.33: 12 9.33 - 11.66: 4 Bond angle restraints: 34889 Sorted by residual: angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 121.54 129.90 -8.36 1.91e+00 2.74e-01 1.92e+01 angle pdb=" N VAL C1128 " pdb=" CA VAL C1128 " pdb=" C VAL C1128 " ideal model delta sigma weight residual 112.96 108.96 4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" C ALA B 570 " pdb=" N ASP B 571 " pdb=" CA ASP B 571 " ideal model delta sigma weight residual 122.46 128.03 -5.57 1.41e+00 5.03e-01 1.56e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 122.08 127.37 -5.29 1.47e+00 4.63e-01 1.30e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.92 -4.22 1.22e+00 6.72e-01 1.20e+01 ... (remaining 34884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 13992 18.00 - 35.99: 1058 35.99 - 53.99: 181 53.99 - 71.99: 39 71.99 - 89.98: 27 Dihedral angle restraints: 15297 sinusoidal: 5979 harmonic: 9318 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -3.44 -82.56 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 175.38 -82.38 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -6.18 -79.82 1 1.00e+01 1.00e-02 7.90e+01 ... (remaining 15294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2911 0.046 - 0.092: 711 0.092 - 0.138: 282 0.138 - 0.183: 30 0.183 - 0.229: 4 Chirality restraints: 3938 Sorted by residual: chirality pdb=" CA ASP B 198 " pdb=" N ASP B 198 " pdb=" C ASP B 198 " pdb=" CB ASP B 198 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE A 434 " pdb=" CA ILE A 434 " pdb=" CG1 ILE A 434 " pdb=" CG2 ILE A 434 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE A 472 " pdb=" CA ILE A 472 " pdb=" CG1 ILE A 472 " pdb=" CG2 ILE A 472 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.05e-01 ... (remaining 3935 not shown) Planarity restraints: 4530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.057 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO C 987 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.052 5.00e-02 4.00e+02 7.70e-02 9.50e+00 pdb=" N PRO B 987 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " -0.048 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO A 987 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " -0.041 5.00e-02 4.00e+02 ... (remaining 4527 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 8060 2.82 - 3.34: 18859 3.34 - 3.86: 39193 3.86 - 4.38: 42873 4.38 - 4.90: 76730 Nonbonded interactions: 185715 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.306 3.040 nonbonded pdb=" O SER B 438 " pdb=" OG SER B 438 " model vdw 2.316 3.040 nonbonded pdb=" O SER B 151 " pdb=" OG SER B 151 " model vdw 2.334 3.040 nonbonded pdb=" O SER C 689 " pdb=" OG SER C 689 " model vdw 2.334 3.040 nonbonded pdb=" OG SER C 591 " pdb=" OE1 GLU C 619 " model vdw 2.336 3.040 ... (remaining 185710 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 621 or resid 641 through 1147)) selection = (chain 'B' and (resid 14 through 621 or resid 641 through 1147)) 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: 4.300 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: 1.160 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 58.770 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25689 Z= 0.150 Angle : 0.667 11.663 34967 Z= 0.363 Chirality : 0.047 0.229 3938 Planarity : 0.006 0.084 4530 Dihedral : 13.050 89.983 9186 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.11 % Allowed : 4.79 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.11), residues: 3163 helix: -4.94 (0.05), residues: 602 sheet: -1.21 (0.19), residues: 597 loop : -2.87 (0.11), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 152 HIS 0.006 0.001 HIS A 519 PHE 0.018 0.001 PHE B 400 TYR 0.014 0.001 TYR C 707 ARG 0.009 0.000 ARG A 408 Details of bonding type rmsd hydrogen bonds : bond 0.35006 ( 645) hydrogen bonds : angle 10.57107 ( 1830) SS BOND : bond 0.00361 ( 39) SS BOND : angle 1.19110 ( 78) covalent geometry : bond 0.00303 (25650) covalent geometry : angle 0.66503 (34889) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 603 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7806 (tm-30) REVERT: A 86 PHE cc_start: 0.7493 (t80) cc_final: 0.7131 (t80) REVERT: A 153 MET cc_start: -0.4908 (tpt) cc_final: -0.5183 (tpt) REVERT: A 296 LEU cc_start: 0.8293 (tp) cc_final: 0.7955 (tp) REVERT: A 515 PHE cc_start: 0.6586 (p90) cc_final: 0.6032 (p90) REVERT: A 539 VAL cc_start: 0.7778 (t) cc_final: 0.7525 (m) REVERT: A 580 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7380 (mm-40) REVERT: A 606 ASN cc_start: 0.8525 (m-40) cc_final: 0.8272 (t0) REVERT: A 790 LYS cc_start: 0.8397 (mttt) cc_final: 0.7689 (mttm) REVERT: C 140 PHE cc_start: 0.7705 (p90) cc_final: 0.7462 (p90) REVERT: C 206 LYS cc_start: 0.8222 (tptt) cc_final: 0.7861 (tppt) REVERT: C 603 ASN cc_start: 0.7866 (p0) cc_final: 0.7533 (p0) REVERT: C 702 GLU cc_start: 0.6734 (tp30) cc_final: 0.6502 (mm-30) REVERT: C 1073 LYS cc_start: 0.8325 (tttt) cc_final: 0.8065 (tttm) REVERT: C 1118 ASP cc_start: 0.6397 (p0) cc_final: 0.6194 (p0) REVERT: B 191 GLU cc_start: 0.5954 (tt0) cc_final: 0.4023 (mt-10) REVERT: B 296 LEU cc_start: 0.8506 (tp) cc_final: 0.8071 (tp) REVERT: B 368 LEU cc_start: 0.8580 (mt) cc_final: 0.8305 (mp) REVERT: B 369 TYR cc_start: 0.4795 (m-80) cc_final: 0.4347 (m-80) REVERT: B 449 TYR cc_start: 0.6887 (m-80) cc_final: 0.6566 (m-80) REVERT: B 453 TYR cc_start: 0.7257 (p90) cc_final: 0.6796 (p90) REVERT: B 455 LEU cc_start: 0.7222 (tp) cc_final: 0.6845 (tp) REVERT: B 826 VAL cc_start: 0.7507 (m) cc_final: 0.7290 (t) REVERT: B 883 THR cc_start: 0.8405 (m) cc_final: 0.8166 (p) REVERT: B 994 ASP cc_start: 0.7445 (t0) cc_final: 0.6946 (t0) outliers start: 3 outliers final: 2 residues processed: 606 average time/residue: 0.4056 time to fit residues: 365.8535 Evaluate side-chains 488 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 486 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain B residue 130 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 5.9990 chunk 242 optimal weight: 1.9990 chunk 134 optimal weight: 0.0070 chunk 82 optimal weight: 0.2980 chunk 163 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 250 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 152 optimal weight: 0.2980 chunk 186 optimal weight: 0.9980 chunk 290 optimal weight: 0.9980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 207 HIS A 239 GLN A 360 ASN A 422 ASN A 487 ASN A 519 HIS A 658 ASN A 762 GLN A 901 GLN A 949 GLN A 955 ASN A1002 GLN A1005 GLN A1071 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 211 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN C 563 GLN C 955 ASN C1071 GLN B 137 ASN B 474 GLN B 493 GLN B 606 ASN B1005 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.183196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.159650 restraints weight = 56101.666| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.26 r_work: 0.3712 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25689 Z= 0.125 Angle : 0.573 10.838 34967 Z= 0.296 Chirality : 0.044 0.200 3938 Planarity : 0.004 0.051 4530 Dihedral : 3.872 20.363 3439 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.22 % Allowed : 11.54 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.12), residues: 3163 helix: -2.36 (0.16), residues: 624 sheet: -0.62 (0.19), residues: 661 loop : -2.45 (0.12), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 353 HIS 0.003 0.001 HIS B1048 PHE 0.026 0.001 PHE B 374 TYR 0.019 0.001 TYR B 369 ARG 0.005 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.06818 ( 645) hydrogen bonds : angle 6.09711 ( 1830) SS BOND : bond 0.00253 ( 39) SS BOND : angle 1.18905 ( 78) covalent geometry : bond 0.00268 (25650) covalent geometry : angle 0.57113 (34889) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 481 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7650 (m-40) cc_final: 0.7450 (m-40) REVERT: A 86 PHE cc_start: 0.7637 (t80) cc_final: 0.7329 (t80) REVERT: A 153 MET cc_start: -0.4622 (tpt) cc_final: -0.4877 (tpt) REVERT: A 177 MET cc_start: 0.0231 (mtt) cc_final: -0.0420 (mtt) REVERT: A 190 ARG cc_start: 0.5671 (ttt180) cc_final: 0.4472 (mmm160) REVERT: A 296 LEU cc_start: 0.8132 (tp) cc_final: 0.7835 (tp) REVERT: A 457 ARG cc_start: 0.5771 (OUTLIER) cc_final: 0.4783 (ttm170) REVERT: A 539 VAL cc_start: 0.7860 (t) cc_final: 0.7615 (m) REVERT: A 580 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7738 (mm-40) REVERT: A 597 VAL cc_start: 0.8652 (t) cc_final: 0.8363 (p) REVERT: A 606 ASN cc_start: 0.8844 (m-40) cc_final: 0.8335 (t0) REVERT: A 690 GLN cc_start: 0.7838 (mt0) cc_final: 0.7563 (mm-40) REVERT: A 790 LYS cc_start: 0.8880 (mttt) cc_final: 0.7985 (mttm) REVERT: A 796 ASP cc_start: 0.8292 (p0) cc_final: 0.7881 (p0) REVERT: A 896 ILE cc_start: 0.7840 (mt) cc_final: 0.7631 (tt) REVERT: A 964 LYS cc_start: 0.9003 (mtpp) cc_final: 0.8732 (ttmm) REVERT: A 995 ARG cc_start: 0.7766 (mtt-85) cc_final: 0.7553 (mtt-85) REVERT: A 1134 ASN cc_start: 0.6772 (m-40) cc_final: 0.6296 (m110) REVERT: C 99 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8380 (p0) REVERT: C 224 GLU cc_start: 0.7191 (mp0) cc_final: 0.6983 (mp0) REVERT: C 290 ASP cc_start: 0.8094 (t0) cc_final: 0.7779 (m-30) REVERT: C 603 ASN cc_start: 0.8362 (p0) cc_final: 0.8065 (p0) REVERT: C 702 GLU cc_start: 0.7175 (tp30) cc_final: 0.6847 (mm-30) REVERT: C 1029 MET cc_start: 0.8949 (tpp) cc_final: 0.8587 (tpp) REVERT: C 1073 LYS cc_start: 0.8684 (tttt) cc_final: 0.8395 (tttm) REVERT: C 1118 ASP cc_start: 0.7234 (p0) cc_final: 0.6912 (p0) REVERT: B 191 GLU cc_start: 0.6107 (tt0) cc_final: 0.3862 (mt-10) REVERT: B 202 LYS cc_start: 0.7696 (tptt) cc_final: 0.7228 (tptt) REVERT: B 225 PRO cc_start: 0.8032 (Cg_exo) cc_final: 0.7585 (Cg_endo) REVERT: B 296 LEU cc_start: 0.8324 (tp) cc_final: 0.8084 (tt) REVERT: B 796 ASP cc_start: 0.7184 (p0) cc_final: 0.6900 (p0) REVERT: B 883 THR cc_start: 0.8679 (m) cc_final: 0.6894 (t) REVERT: B 994 ASP cc_start: 0.7947 (t0) cc_final: 0.7676 (t0) REVERT: B 995 ARG cc_start: 0.8515 (mtp85) cc_final: 0.8212 (mtt-85) outliers start: 34 outliers final: 12 residues processed: 501 average time/residue: 0.4002 time to fit residues: 303.3758 Evaluate side-chains 466 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 452 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 820 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 205 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 310 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 304 optimal weight: 1.9990 chunk 278 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 168 optimal weight: 0.0570 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 536 ASN A1074 ASN A1088 HIS C 23 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 207 HIS C 245 HIS ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 613 GLN C 955 ASN C 978 ASN C1119 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 955 ASN B1106 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.148944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.117004 restraints weight = 47471.779| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 3.27 r_work: 0.3556 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25689 Z= 0.197 Angle : 0.610 12.556 34967 Z= 0.313 Chirality : 0.045 0.172 3938 Planarity : 0.004 0.046 4530 Dihedral : 4.239 21.767 3438 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.18 % Allowed : 13.55 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.13), residues: 3163 helix: -0.83 (0.20), residues: 632 sheet: -0.40 (0.19), residues: 672 loop : -2.26 (0.12), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 353 HIS 0.006 0.001 HIS A1064 PHE 0.037 0.002 PHE A 342 TYR 0.020 0.002 TYR B 396 ARG 0.007 0.001 ARG A 509 Details of bonding type rmsd hydrogen bonds : bond 0.06333 ( 645) hydrogen bonds : angle 5.48933 ( 1830) SS BOND : bond 0.00438 ( 39) SS BOND : angle 1.87019 ( 78) covalent geometry : bond 0.00468 (25650) covalent geometry : angle 0.60418 (34889) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 484 time to evaluate : 2.619 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 52 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8078 (tm-30) REVERT: A 81 ASN cc_start: 0.7806 (m-40) cc_final: 0.7509 (m-40) REVERT: A 86 PHE cc_start: 0.7632 (t80) cc_final: 0.7199 (t80) REVERT: A 153 MET cc_start: -0.4356 (tpt) cc_final: -0.4778 (tpt) REVERT: A 177 MET cc_start: 0.0903 (mtt) cc_final: 0.0544 (mtt) REVERT: A 580 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7868 (mm-40) REVERT: A 690 GLN cc_start: 0.8054 (mt0) cc_final: 0.7516 (mm-40) REVERT: A 790 LYS cc_start: 0.8961 (mttt) cc_final: 0.8715 (mttm) REVERT: A 964 LYS cc_start: 0.8998 (mtpp) cc_final: 0.8785 (ttmm) REVERT: A 995 ARG cc_start: 0.7826 (mtt-85) cc_final: 0.7610 (mtt-85) REVERT: A 1138 TYR cc_start: 0.8271 (t80) cc_final: 0.7985 (t80) REVERT: C 41 LYS cc_start: 0.8013 (mmtm) cc_final: 0.7757 (mmtp) REVERT: C 48 LEU cc_start: 0.8554 (mm) cc_final: 0.8347 (mp) REVERT: C 177 MET cc_start: -0.2951 (mmt) cc_final: -0.3990 (mmt) REVERT: C 224 GLU cc_start: 0.7510 (mp0) cc_final: 0.7300 (mp0) REVERT: C 290 ASP cc_start: 0.8462 (t0) cc_final: 0.8213 (t0) REVERT: C 351 TYR cc_start: 0.4382 (p90) cc_final: 0.4180 (p90) REVERT: C 518 LEU cc_start: 0.5379 (tp) cc_final: 0.5174 (tp) REVERT: C 586 ASP cc_start: 0.8054 (t0) cc_final: 0.7853 (t0) REVERT: C 745 ASP cc_start: 0.6973 (t0) cc_final: 0.6640 (t0) REVERT: C 787 GLN cc_start: 0.7681 (mp10) cc_final: 0.7223 (mt0) REVERT: C 1107 ARG cc_start: 0.8472 (mtm110) cc_final: 0.6355 (tpt90) REVERT: B 41 LYS cc_start: 0.8007 (mttm) cc_final: 0.7537 (mtpt) REVERT: B 140 PHE cc_start: 0.7873 (m-80) cc_final: 0.7458 (m-80) REVERT: B 202 LYS cc_start: 0.7484 (tptt) cc_final: 0.7166 (tptt) REVERT: B 225 PRO cc_start: 0.8130 (Cg_exo) cc_final: 0.7748 (Cg_endo) REVERT: B 298 GLU cc_start: 0.8095 (tp30) cc_final: 0.7857 (tp30) REVERT: B 429 PHE cc_start: 0.8077 (t80) cc_final: 0.7438 (t80) REVERT: B 455 LEU cc_start: 0.8123 (tp) cc_final: 0.7857 (tt) REVERT: B 883 THR cc_start: 0.8486 (m) cc_final: 0.6719 (t) REVERT: B 896 ILE cc_start: 0.7441 (mt) cc_final: 0.7105 (tt) REVERT: B 994 ASP cc_start: 0.7928 (t0) cc_final: 0.7653 (t0) REVERT: B 995 ARG cc_start: 0.8515 (mtp85) cc_final: 0.8150 (mtt-85) outliers start: 61 outliers final: 35 residues processed: 519 average time/residue: 0.4007 time to fit residues: 314.4503 Evaluate side-chains 488 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 453 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 703 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 255 optimal weight: 3.9990 chunk 305 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 171 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 295 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 317 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1074 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 542 ASN C 607 GLN C 955 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 965 GLN B1088 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.149016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.117272 restraints weight = 47962.957| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.35 r_work: 0.3539 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25689 Z= 0.159 Angle : 0.570 11.593 34967 Z= 0.291 Chirality : 0.044 0.205 3938 Planarity : 0.004 0.049 4530 Dihedral : 4.171 22.733 3438 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.36 % Allowed : 15.83 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.91 (0.14), residues: 3163 helix: -0.27 (0.21), residues: 645 sheet: -0.29 (0.19), residues: 678 loop : -2.13 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 353 HIS 0.005 0.001 HIS A1064 PHE 0.026 0.001 PHE B 374 TYR 0.023 0.001 TYR A 351 ARG 0.007 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.05467 ( 645) hydrogen bonds : angle 5.18895 ( 1830) SS BOND : bond 0.00382 ( 39) SS BOND : angle 1.63964 ( 78) covalent geometry : bond 0.00376 (25650) covalent geometry : angle 0.56535 (34889) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 470 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8124 (tm-30) REVERT: A 81 ASN cc_start: 0.7869 (m-40) cc_final: 0.7612 (m-40) REVERT: A 86 PHE cc_start: 0.7671 (t80) cc_final: 0.7260 (t80) REVERT: A 153 MET cc_start: -0.4331 (tpt) cc_final: -0.4734 (tpt) REVERT: A 177 MET cc_start: 0.0769 (mtt) cc_final: -0.2172 (mtt) REVERT: A 190 ARG cc_start: 0.5648 (ttt180) cc_final: 0.4031 (ttt180) REVERT: A 304 LYS cc_start: 0.8849 (tppp) cc_final: 0.8619 (tppp) REVERT: A 457 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6424 (ttp-110) REVERT: A 580 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7884 (mm-40) REVERT: A 690 GLN cc_start: 0.8061 (mt0) cc_final: 0.7655 (tp40) REVERT: A 790 LYS cc_start: 0.9053 (mttt) cc_final: 0.8791 (mttm) REVERT: A 964 LYS cc_start: 0.9013 (mtpp) cc_final: 0.8788 (ttmm) REVERT: A 995 ARG cc_start: 0.7803 (mtt-85) cc_final: 0.7567 (mtt-85) REVERT: A 1138 TYR cc_start: 0.8253 (t80) cc_final: 0.7906 (t80) REVERT: C 52 GLN cc_start: 0.7699 (tm-30) cc_final: 0.7427 (tm-30) REVERT: C 92 PHE cc_start: 0.7102 (t80) cc_final: 0.6875 (t80) REVERT: C 98 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8678 (p) REVERT: C 99 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8491 (p0) REVERT: C 177 MET cc_start: -0.2981 (mmt) cc_final: -0.4002 (mmt) REVERT: C 224 GLU cc_start: 0.7627 (mp0) cc_final: 0.7213 (mp0) REVERT: C 290 ASP cc_start: 0.8491 (t0) cc_final: 0.8273 (t0) REVERT: C 556 ASN cc_start: 0.8775 (t0) cc_final: 0.8563 (t0) REVERT: C 574 ASP cc_start: 0.8191 (p0) cc_final: 0.7372 (t0) REVERT: C 586 ASP cc_start: 0.8003 (t0) cc_final: 0.7568 (t0) REVERT: C 745 ASP cc_start: 0.7171 (t0) cc_final: 0.6849 (t0) REVERT: C 787 GLN cc_start: 0.7666 (mp10) cc_final: 0.7203 (mt0) REVERT: C 1107 ARG cc_start: 0.8507 (mtm110) cc_final: 0.6363 (tpt170) REVERT: B 41 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7589 (mtpt) REVERT: B 140 PHE cc_start: 0.7916 (m-80) cc_final: 0.7484 (m-80) REVERT: B 192 PHE cc_start: 0.7413 (m-80) cc_final: 0.7212 (m-10) REVERT: B 202 LYS cc_start: 0.7622 (tptt) cc_final: 0.7294 (tptt) REVERT: B 203 ILE cc_start: 0.8369 (mt) cc_final: 0.8153 (mp) REVERT: B 298 GLU cc_start: 0.8128 (tp30) cc_final: 0.7879 (tp30) REVERT: B 429 PHE cc_start: 0.8121 (t80) cc_final: 0.7439 (t80) REVERT: B 455 LEU cc_start: 0.8041 (tp) cc_final: 0.7704 (tt) REVERT: B 559 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7505 (t80) REVERT: B 883 THR cc_start: 0.8537 (m) cc_final: 0.7610 (p) REVERT: B 896 ILE cc_start: 0.7684 (mt) cc_final: 0.7344 (tt) REVERT: B 994 ASP cc_start: 0.7854 (t0) cc_final: 0.7582 (t0) REVERT: B 995 ARG cc_start: 0.8511 (mtp85) cc_final: 0.8161 (mtt-85) outliers start: 66 outliers final: 41 residues processed: 504 average time/residue: 0.4059 time to fit residues: 309.9875 Evaluate side-chains 505 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 459 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 299 optimal weight: 0.9990 chunk 57 optimal weight: 0.0010 chunk 261 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 176 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 297 optimal weight: 0.9980 chunk 73 optimal weight: 0.0570 chunk 157 optimal weight: 3.9990 chunk 203 optimal weight: 0.8980 overall best weight: 0.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1074 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 955 ASN B 965 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.150564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.118730 restraints weight = 47905.708| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.36 r_work: 0.3561 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25689 Z= 0.105 Angle : 0.536 11.738 34967 Z= 0.270 Chirality : 0.043 0.191 3938 Planarity : 0.004 0.046 4530 Dihedral : 3.999 22.603 3438 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.18 % Allowed : 16.19 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.14), residues: 3163 helix: 0.24 (0.22), residues: 638 sheet: -0.08 (0.19), residues: 675 loop : -2.02 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 436 HIS 0.003 0.001 HIS A1064 PHE 0.028 0.001 PHE C 43 TYR 0.017 0.001 TYR C 170 ARG 0.007 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 645) hydrogen bonds : angle 4.93532 ( 1830) SS BOND : bond 0.00313 ( 39) SS BOND : angle 1.59563 ( 78) covalent geometry : bond 0.00239 (25650) covalent geometry : angle 0.53101 (34889) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 462 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 86 PHE cc_start: 0.7595 (t80) cc_final: 0.7189 (t80) REVERT: A 153 MET cc_start: -0.4351 (tpt) cc_final: -0.4729 (tpt) REVERT: A 177 MET cc_start: 0.0794 (mtt) cc_final: -0.1211 (mtt) REVERT: A 508 TYR cc_start: 0.7043 (m-80) cc_final: 0.6057 (m-80) REVERT: A 580 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7888 (mm-40) REVERT: A 690 GLN cc_start: 0.8064 (mt0) cc_final: 0.7656 (tp40) REVERT: A 697 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8559 (ptm) REVERT: A 790 LYS cc_start: 0.9076 (mttt) cc_final: 0.8768 (mttm) REVERT: A 935 GLN cc_start: 0.8013 (mt0) cc_final: 0.7659 (mt0) REVERT: A 964 LYS cc_start: 0.8974 (mtpp) cc_final: 0.8722 (ttmm) REVERT: A 1134 ASN cc_start: 0.6451 (m-40) cc_final: 0.6068 (m110) REVERT: A 1138 TYR cc_start: 0.8263 (t80) cc_final: 0.7857 (t80) REVERT: C 52 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7405 (tm-30) REVERT: C 98 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8715 (p) REVERT: C 99 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8444 (p0) REVERT: C 177 MET cc_start: -0.2809 (mmt) cc_final: -0.3916 (mmt) REVERT: C 224 GLU cc_start: 0.7616 (mp0) cc_final: 0.7208 (mp0) REVERT: C 290 ASP cc_start: 0.8487 (t0) cc_final: 0.8272 (t0) REVERT: C 495 TYR cc_start: 0.5676 (m-80) cc_final: 0.5468 (m-80) REVERT: C 537 LYS cc_start: 0.8276 (mmmm) cc_final: 0.8018 (mmtm) REVERT: C 549 THR cc_start: 0.8790 (m) cc_final: 0.8535 (m) REVERT: C 556 ASN cc_start: 0.8751 (t0) cc_final: 0.8548 (t0) REVERT: C 574 ASP cc_start: 0.8075 (p0) cc_final: 0.7404 (t0) REVERT: C 586 ASP cc_start: 0.7984 (t0) cc_final: 0.7530 (t0) REVERT: C 745 ASP cc_start: 0.7181 (t0) cc_final: 0.6856 (t0) REVERT: C 787 GLN cc_start: 0.7638 (mp10) cc_final: 0.7188 (mt0) REVERT: C 790 LYS cc_start: 0.9163 (mtpp) cc_final: 0.8822 (mmtm) REVERT: C 933 LYS cc_start: 0.8192 (ttmt) cc_final: 0.7980 (ttmm) REVERT: C 988 GLU cc_start: 0.8109 (tp30) cc_final: 0.7809 (tp30) REVERT: C 1107 ARG cc_start: 0.8476 (mtm110) cc_final: 0.6337 (tpt170) REVERT: B 41 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7556 (mtpt) REVERT: B 140 PHE cc_start: 0.7907 (m-80) cc_final: 0.7471 (m-80) REVERT: B 202 LYS cc_start: 0.7599 (tptt) cc_final: 0.7168 (tptt) REVERT: B 225 PRO cc_start: 0.8090 (Cg_exo) cc_final: 0.7695 (Cg_endo) REVERT: B 298 GLU cc_start: 0.8072 (tp30) cc_final: 0.7819 (tp30) REVERT: B 429 PHE cc_start: 0.8056 (t80) cc_final: 0.7392 (t80) REVERT: B 455 LEU cc_start: 0.8125 (tp) cc_final: 0.7838 (tt) REVERT: B 654 GLU cc_start: 0.7488 (pm20) cc_final: 0.7263 (pm20) REVERT: B 779 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8157 (mm-40) REVERT: B 883 THR cc_start: 0.8429 (m) cc_final: 0.6724 (t) REVERT: B 896 ILE cc_start: 0.7460 (mt) cc_final: 0.7108 (tt) REVERT: B 995 ARG cc_start: 0.8479 (mtp85) cc_final: 0.8103 (mtt-85) outliers start: 61 outliers final: 38 residues processed: 496 average time/residue: 0.4036 time to fit residues: 304.4408 Evaluate side-chains 487 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 445 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 109 optimal weight: 0.9980 chunk 202 optimal weight: 0.0060 chunk 111 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 249 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 487 ASN C 493 GLN C 607 GLN C 955 ASN B 134 GLN B 498 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.146719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.115465 restraints weight = 48206.953| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.21 r_work: 0.3534 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25689 Z= 0.200 Angle : 0.613 12.034 34967 Z= 0.314 Chirality : 0.045 0.186 3938 Planarity : 0.004 0.050 4530 Dihedral : 4.410 26.169 3438 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.57 % Allowed : 17.19 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.62 (0.14), residues: 3163 helix: 0.28 (0.21), residues: 645 sheet: -0.16 (0.19), residues: 674 loop : -2.04 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 436 HIS 0.006 0.001 HIS C1064 PHE 0.038 0.002 PHE C 374 TYR 0.025 0.002 TYR A 351 ARG 0.008 0.001 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.05770 ( 645) hydrogen bonds : angle 5.12478 ( 1830) SS BOND : bond 0.00511 ( 39) SS BOND : angle 2.02568 ( 78) covalent geometry : bond 0.00478 (25650) covalent geometry : angle 0.60655 (34889) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 477 time to evaluate : 2.659 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 52 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8148 (tm-30) REVERT: A 86 PHE cc_start: 0.7696 (t80) cc_final: 0.7294 (t80) REVERT: A 153 MET cc_start: -0.4249 (tpt) cc_final: -0.4692 (tpt) REVERT: A 177 MET cc_start: 0.0874 (mtt) cc_final: -0.0806 (mtt) REVERT: A 462 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8485 (mmtm) REVERT: A 580 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7959 (mm-40) REVERT: A 790 LYS cc_start: 0.9039 (mttt) cc_final: 0.8822 (mttm) REVERT: A 935 GLN cc_start: 0.7867 (mt0) cc_final: 0.7627 (mt0) REVERT: A 964 LYS cc_start: 0.9026 (mtpp) cc_final: 0.8795 (ttmm) REVERT: A 1017 GLU cc_start: 0.7499 (tp30) cc_final: 0.7023 (tp30) REVERT: A 1138 TYR cc_start: 0.8294 (t80) cc_final: 0.7994 (t80) REVERT: C 99 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8549 (p0) REVERT: C 177 MET cc_start: -0.3075 (mmt) cc_final: -0.4151 (mmt) REVERT: C 224 GLU cc_start: 0.7730 (mp0) cc_final: 0.7325 (mp0) REVERT: C 294 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.7065 (t0) REVERT: C 569 ILE cc_start: 0.9016 (pt) cc_final: 0.8728 (mp) REVERT: C 574 ASP cc_start: 0.8050 (p0) cc_final: 0.7437 (t0) REVERT: C 586 ASP cc_start: 0.7926 (t0) cc_final: 0.7509 (t0) REVERT: C 745 ASP cc_start: 0.7477 (t0) cc_final: 0.7260 (t0) REVERT: C 787 GLN cc_start: 0.7601 (mp10) cc_final: 0.7242 (mt0) REVERT: C 790 LYS cc_start: 0.9106 (mtpp) cc_final: 0.8766 (mmtm) REVERT: C 823 PHE cc_start: 0.8323 (t80) cc_final: 0.7991 (t80) REVERT: C 902 MET cc_start: 0.7986 (mmm) cc_final: 0.7768 (mmt) REVERT: C 933 LYS cc_start: 0.8303 (ttmt) cc_final: 0.8090 (ttmm) REVERT: C 1073 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8491 (mtpp) REVERT: C 1107 ARG cc_start: 0.8589 (mtm110) cc_final: 0.6621 (tpt170) REVERT: B 140 PHE cc_start: 0.8019 (m-80) cc_final: 0.7540 (m-80) REVERT: B 190 ARG cc_start: 0.7293 (mtp180) cc_final: 0.6788 (mtp180) REVERT: B 202 LYS cc_start: 0.7509 (tptt) cc_final: 0.7217 (tptt) REVERT: B 203 ILE cc_start: 0.8370 (mt) cc_final: 0.7983 (mp) REVERT: B 298 GLU cc_start: 0.8209 (tp30) cc_final: 0.7988 (tp30) REVERT: B 429 PHE cc_start: 0.8124 (t80) cc_final: 0.7375 (t80) REVERT: B 462 LYS cc_start: 0.7501 (tptp) cc_final: 0.7295 (tptp) REVERT: B 779 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8172 (mm-40) REVERT: B 896 ILE cc_start: 0.7750 (mt) cc_final: 0.7435 (tt) REVERT: B 1107 ARG cc_start: 0.7538 (mtt180) cc_final: 0.5824 (tpt170) outliers start: 72 outliers final: 48 residues processed: 514 average time/residue: 0.3922 time to fit residues: 307.5989 Evaluate side-chains 511 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 461 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 319 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 208 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 203 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 214 optimal weight: 0.3980 chunk 115 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 268 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 607 GLN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.148182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.116733 restraints weight = 48445.282| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.26 r_work: 0.3552 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25689 Z= 0.131 Angle : 0.575 12.019 34967 Z= 0.293 Chirality : 0.044 0.187 3938 Planarity : 0.004 0.049 4530 Dihedral : 4.250 27.075 3438 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.18 % Allowed : 18.66 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3163 helix: 0.53 (0.22), residues: 645 sheet: -0.09 (0.19), residues: 683 loop : -2.00 (0.13), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 PHE 0.047 0.001 PHE C 374 TYR 0.019 0.001 TYR C 453 ARG 0.010 0.000 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.04882 ( 645) hydrogen bonds : angle 4.90453 ( 1830) SS BOND : bond 0.00369 ( 39) SS BOND : angle 1.85842 ( 78) covalent geometry : bond 0.00306 (25650) covalent geometry : angle 0.56850 (34889) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 455 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: A 52 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8162 (tm-30) REVERT: A 86 PHE cc_start: 0.7675 (t80) cc_final: 0.7319 (t80) REVERT: A 153 MET cc_start: -0.4241 (tpt) cc_final: -0.4605 (tpt) REVERT: A 177 MET cc_start: 0.0890 (mtt) cc_final: -0.0815 (mtt) REVERT: A 462 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8577 (mmtm) REVERT: A 515 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.5739 (p90) REVERT: A 580 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7922 (mm-40) REVERT: A 790 LYS cc_start: 0.9082 (mttt) cc_final: 0.8846 (mttm) REVERT: A 804 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8552 (mm-40) REVERT: A 935 GLN cc_start: 0.7700 (mt0) cc_final: 0.7331 (mt0) REVERT: A 964 LYS cc_start: 0.8980 (mtpp) cc_final: 0.8748 (ttmm) REVERT: A 1017 GLU cc_start: 0.7424 (tp30) cc_final: 0.7046 (tp30) REVERT: A 1138 TYR cc_start: 0.8288 (t80) cc_final: 0.7983 (t80) REVERT: C 52 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7465 (tm-30) REVERT: C 99 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8630 (p0) REVERT: C 177 MET cc_start: -0.3063 (mmt) cc_final: -0.4050 (mmt) REVERT: C 202 LYS cc_start: 0.8548 (mptt) cc_final: 0.7954 (mptt) REVERT: C 224 GLU cc_start: 0.7699 (mp0) cc_final: 0.7295 (mp0) REVERT: C 294 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7048 (t0) REVERT: C 529 LYS cc_start: 0.8349 (tptp) cc_final: 0.8119 (tptp) REVERT: C 564 GLN cc_start: 0.8054 (mp10) cc_final: 0.7698 (mp10) REVERT: C 569 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8745 (mp) REVERT: C 574 ASP cc_start: 0.7986 (p0) cc_final: 0.7438 (t0) REVERT: C 586 ASP cc_start: 0.7969 (t0) cc_final: 0.7566 (t0) REVERT: C 745 ASP cc_start: 0.7458 (t0) cc_final: 0.7242 (t0) REVERT: C 787 GLN cc_start: 0.7602 (mp10) cc_final: 0.7246 (mt0) REVERT: C 790 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8773 (mmtm) REVERT: C 823 PHE cc_start: 0.8317 (t80) cc_final: 0.7991 (t80) REVERT: C 933 LYS cc_start: 0.8329 (ttmt) cc_final: 0.8120 (ttmm) REVERT: C 1073 LYS cc_start: 0.8803 (mtpt) cc_final: 0.8498 (mtpp) REVERT: C 1107 ARG cc_start: 0.8531 (mtm110) cc_final: 0.6479 (tpt170) REVERT: B 41 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7716 (mtpt) REVERT: B 140 PHE cc_start: 0.7974 (m-80) cc_final: 0.7519 (m-80) REVERT: B 190 ARG cc_start: 0.7233 (mtp180) cc_final: 0.6673 (mtp180) REVERT: B 202 LYS cc_start: 0.7507 (tptt) cc_final: 0.7231 (tptt) REVERT: B 203 ILE cc_start: 0.8378 (mt) cc_final: 0.7984 (mp) REVERT: B 298 GLU cc_start: 0.8172 (tp30) cc_final: 0.7951 (tp30) REVERT: B 357 ARG cc_start: 0.7146 (ttm-80) cc_final: 0.6923 (ttm-80) REVERT: B 429 PHE cc_start: 0.7967 (t80) cc_final: 0.7304 (t80) REVERT: B 462 LYS cc_start: 0.7551 (tptp) cc_final: 0.7309 (tptp) REVERT: B 559 PHE cc_start: 0.7126 (t80) cc_final: 0.6917 (t80) REVERT: B 896 ILE cc_start: 0.7649 (mt) cc_final: 0.7344 (tt) REVERT: B 995 ARG cc_start: 0.8363 (mtt-85) cc_final: 0.8127 (mtt-85) REVERT: B 1107 ARG cc_start: 0.7523 (mtt180) cc_final: 0.5828 (tpt170) outliers start: 61 outliers final: 47 residues processed: 490 average time/residue: 0.4014 time to fit residues: 300.7328 Evaluate side-chains 502 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 450 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 8 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 281 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.147998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.116665 restraints weight = 48284.825| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.25 r_work: 0.3545 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25689 Z= 0.145 Angle : 0.597 15.319 34967 Z= 0.302 Chirality : 0.044 0.314 3938 Planarity : 0.004 0.049 4530 Dihedral : 4.245 31.578 3438 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.32 % Allowed : 18.55 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.40 (0.14), residues: 3163 helix: 0.69 (0.22), residues: 645 sheet: -0.06 (0.19), residues: 669 loop : -1.96 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 PHE 0.043 0.001 PHE A 342 TYR 0.021 0.001 TYR A 351 ARG 0.009 0.000 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 645) hydrogen bonds : angle 4.86047 ( 1830) SS BOND : bond 0.00426 ( 39) SS BOND : angle 2.33942 ( 78) covalent geometry : bond 0.00345 (25650) covalent geometry : angle 0.58717 (34889) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 459 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8170 (tm-30) REVERT: A 86 PHE cc_start: 0.7684 (t80) cc_final: 0.7334 (t80) REVERT: A 153 MET cc_start: -0.4239 (tpt) cc_final: -0.4588 (tpt) REVERT: A 177 MET cc_start: 0.0707 (mtt) cc_final: -0.0538 (mtt) REVERT: A 508 TYR cc_start: 0.7079 (m-80) cc_final: 0.6090 (m-80) REVERT: A 515 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.5744 (p90) REVERT: A 544 ASN cc_start: 0.8279 (t0) cc_final: 0.7956 (p0) REVERT: A 564 GLN cc_start: 0.7773 (mp10) cc_final: 0.7428 (mp10) REVERT: A 580 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7933 (mm-40) REVERT: A 690 GLN cc_start: 0.8038 (mt0) cc_final: 0.7545 (mm-40) REVERT: A 790 LYS cc_start: 0.9104 (mttt) cc_final: 0.8860 (mttm) REVERT: A 804 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8500 (mm-40) REVERT: A 935 GLN cc_start: 0.7744 (mt0) cc_final: 0.7356 (mt0) REVERT: A 964 LYS cc_start: 0.8987 (mtpp) cc_final: 0.8741 (ttmm) REVERT: A 1017 GLU cc_start: 0.7449 (tp30) cc_final: 0.7189 (tp30) REVERT: A 1138 TYR cc_start: 0.8301 (t80) cc_final: 0.8000 (t80) REVERT: C 52 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7569 (tm-30) REVERT: C 99 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8653 (p0) REVERT: C 177 MET cc_start: -0.3199 (mmt) cc_final: -0.4256 (mmt) REVERT: C 200 TYR cc_start: 0.7361 (m-10) cc_final: 0.7141 (m-10) REVERT: C 202 LYS cc_start: 0.8557 (mptt) cc_final: 0.7960 (mptt) REVERT: C 224 GLU cc_start: 0.7689 (mp0) cc_final: 0.7282 (mp0) REVERT: C 294 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7131 (t0) REVERT: C 574 ASP cc_start: 0.7974 (p0) cc_final: 0.7483 (t0) REVERT: C 586 ASP cc_start: 0.7991 (t0) cc_final: 0.7589 (t0) REVERT: C 745 ASP cc_start: 0.7511 (t0) cc_final: 0.7291 (t0) REVERT: C 787 GLN cc_start: 0.7611 (mp10) cc_final: 0.7252 (mt0) REVERT: C 790 LYS cc_start: 0.9112 (mtpp) cc_final: 0.8776 (mmtm) REVERT: C 823 PHE cc_start: 0.8310 (t80) cc_final: 0.7987 (t80) REVERT: C 933 LYS cc_start: 0.8329 (ttmt) cc_final: 0.8116 (ttmm) REVERT: C 1073 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8510 (mtpp) REVERT: C 1107 ARG cc_start: 0.8575 (mtm110) cc_final: 0.6535 (tpt170) REVERT: B 41 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7565 (mtpt) REVERT: B 64 TRP cc_start: 0.7288 (t-100) cc_final: 0.6910 (t60) REVERT: B 140 PHE cc_start: 0.7982 (m-80) cc_final: 0.7454 (m-80) REVERT: B 190 ARG cc_start: 0.7224 (mtp180) cc_final: 0.6702 (mtp180) REVERT: B 202 LYS cc_start: 0.7479 (tptt) cc_final: 0.7194 (tptt) REVERT: B 203 ILE cc_start: 0.8361 (mt) cc_final: 0.7971 (mp) REVERT: B 298 GLU cc_start: 0.8196 (tp30) cc_final: 0.7979 (tp30) REVERT: B 429 PHE cc_start: 0.8002 (t80) cc_final: 0.7344 (t80) REVERT: B 462 LYS cc_start: 0.7589 (tptp) cc_final: 0.7344 (tptp) REVERT: B 559 PHE cc_start: 0.7113 (t80) cc_final: 0.6875 (t80) REVERT: B 560 LEU cc_start: 0.8463 (mt) cc_final: 0.8207 (tp) REVERT: B 779 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8141 (mm-40) REVERT: B 896 ILE cc_start: 0.7651 (mt) cc_final: 0.7344 (tt) REVERT: B 995 ARG cc_start: 0.8332 (mtt-85) cc_final: 0.8093 (mtt-85) REVERT: B 1092 GLU cc_start: 0.7316 (pm20) cc_final: 0.7076 (pm20) REVERT: B 1107 ARG cc_start: 0.7529 (mtt180) cc_final: 0.5830 (tpt170) outliers start: 65 outliers final: 54 residues processed: 497 average time/residue: 0.4525 time to fit residues: 348.0694 Evaluate side-chains 512 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 454 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 160 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 309 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 197 optimal weight: 0.7980 chunk 257 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 316 optimal weight: 0.0770 chunk 53 optimal weight: 0.9980 chunk 169 optimal weight: 6.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 607 GLN C 955 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.148229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.116676 restraints weight = 47877.341| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.35 r_work: 0.3529 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25689 Z= 0.126 Angle : 0.584 12.103 34967 Z= 0.295 Chirality : 0.044 0.278 3938 Planarity : 0.004 0.049 4530 Dihedral : 4.148 32.097 3438 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.86 % Allowed : 19.51 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.30 (0.14), residues: 3163 helix: 0.85 (0.22), residues: 649 sheet: -0.06 (0.19), residues: 669 loop : -1.91 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 PHE 0.042 0.001 PHE A 342 TYR 0.015 0.001 TYR B 170 ARG 0.012 0.000 ARG B 408 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 645) hydrogen bonds : angle 4.75880 ( 1830) SS BOND : bond 0.00319 ( 39) SS BOND : angle 2.16634 ( 78) covalent geometry : bond 0.00297 (25650) covalent geometry : angle 0.57542 (34889) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 454 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8188 (tm-30) REVERT: A 86 PHE cc_start: 0.7754 (t80) cc_final: 0.7413 (t80) REVERT: A 153 MET cc_start: -0.4307 (tpt) cc_final: -0.4664 (tpt) REVERT: A 177 MET cc_start: 0.0747 (mtt) cc_final: -0.0385 (mtt) REVERT: A 367 VAL cc_start: 0.8482 (m) cc_final: 0.8235 (p) REVERT: A 508 TYR cc_start: 0.7141 (m-80) cc_final: 0.6057 (m-80) REVERT: A 515 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.5684 (p90) REVERT: A 544 ASN cc_start: 0.8340 (t0) cc_final: 0.8048 (p0) REVERT: A 564 GLN cc_start: 0.7795 (mp10) cc_final: 0.7398 (mp10) REVERT: A 580 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7965 (mm-40) REVERT: A 690 GLN cc_start: 0.8090 (mt0) cc_final: 0.7517 (mm-40) REVERT: A 790 LYS cc_start: 0.9126 (mttt) cc_final: 0.8852 (mttm) REVERT: A 804 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8388 (mt0) REVERT: A 935 GLN cc_start: 0.7832 (mt0) cc_final: 0.6804 (mt0) REVERT: A 964 LYS cc_start: 0.8952 (mtpp) cc_final: 0.8685 (ttmm) REVERT: A 1017 GLU cc_start: 0.7421 (tp30) cc_final: 0.7127 (tp30) REVERT: A 1091 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7898 (ttp-170) REVERT: A 1134 ASN cc_start: 0.6572 (m-40) cc_final: 0.6187 (m110) REVERT: A 1138 TYR cc_start: 0.8342 (t80) cc_final: 0.7972 (t80) REVERT: C 177 MET cc_start: -0.3205 (mmt) cc_final: -0.4363 (mmt) REVERT: C 202 LYS cc_start: 0.8543 (mptt) cc_final: 0.7932 (mptt) REVERT: C 224 GLU cc_start: 0.7671 (mp0) cc_final: 0.7230 (mp0) REVERT: C 294 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7145 (t0) REVERT: C 324 GLU cc_start: 0.7954 (mp0) cc_final: 0.7748 (mp0) REVERT: C 574 ASP cc_start: 0.7955 (p0) cc_final: 0.7447 (t0) REVERT: C 586 ASP cc_start: 0.7974 (t0) cc_final: 0.7520 (t0) REVERT: C 745 ASP cc_start: 0.7544 (t0) cc_final: 0.7331 (t0) REVERT: C 787 GLN cc_start: 0.7706 (mp10) cc_final: 0.7268 (mt0) REVERT: C 790 LYS cc_start: 0.9159 (mtpp) cc_final: 0.8804 (mmtm) REVERT: C 823 PHE cc_start: 0.8271 (t80) cc_final: 0.7950 (t80) REVERT: C 933 LYS cc_start: 0.8205 (ttmt) cc_final: 0.7994 (ttmm) REVERT: C 964 LYS cc_start: 0.8844 (ttpp) cc_final: 0.8593 (ttmm) REVERT: C 1073 LYS cc_start: 0.8824 (mtpt) cc_final: 0.8504 (mtpp) REVERT: C 1107 ARG cc_start: 0.8587 (mtm110) cc_final: 0.6430 (tpt170) REVERT: B 41 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7632 (mtpt) REVERT: B 140 PHE cc_start: 0.8025 (m-80) cc_final: 0.7461 (m-80) REVERT: B 190 ARG cc_start: 0.7198 (mtp180) cc_final: 0.6656 (mtp180) REVERT: B 202 LYS cc_start: 0.7497 (tptt) cc_final: 0.7160 (tptt) REVERT: B 203 ILE cc_start: 0.8259 (mt) cc_final: 0.7879 (mp) REVERT: B 298 GLU cc_start: 0.8214 (tp30) cc_final: 0.7983 (tp30) REVERT: B 317 ASN cc_start: 0.8568 (m-40) cc_final: 0.8276 (m-40) REVERT: B 429 PHE cc_start: 0.8000 (t80) cc_final: 0.7293 (t80) REVERT: B 455 LEU cc_start: 0.8194 (tt) cc_final: 0.7939 (tt) REVERT: B 462 LYS cc_start: 0.7571 (tptp) cc_final: 0.7318 (tptp) REVERT: B 498 GLN cc_start: 0.7681 (pt0) cc_final: 0.7449 (pp30) REVERT: B 559 PHE cc_start: 0.7138 (t80) cc_final: 0.6894 (t80) REVERT: B 560 LEU cc_start: 0.8439 (mt) cc_final: 0.8215 (tp) REVERT: B 779 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8147 (mm-40) REVERT: B 823 PHE cc_start: 0.8618 (t80) cc_final: 0.8403 (t80) REVERT: B 896 ILE cc_start: 0.7588 (mt) cc_final: 0.7247 (tt) REVERT: B 995 ARG cc_start: 0.8404 (mtt-85) cc_final: 0.8137 (mtt-85) REVERT: B 1017 GLU cc_start: 0.7753 (tp30) cc_final: 0.7101 (tp30) REVERT: B 1092 GLU cc_start: 0.7421 (pm20) cc_final: 0.7168 (pm20) REVERT: B 1107 ARG cc_start: 0.7529 (mtt180) cc_final: 0.5757 (tpt170) outliers start: 52 outliers final: 45 residues processed: 482 average time/residue: 0.4816 time to fit residues: 357.7940 Evaluate side-chains 496 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 448 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 8.9990 chunk 310 optimal weight: 1.9990 chunk 207 optimal weight: 0.2980 chunk 180 optimal weight: 0.9980 chunk 311 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 281 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 607 GLN C 955 ASN B 675 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.148134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.116905 restraints weight = 48315.345| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.25 r_work: 0.3528 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25689 Z= 0.141 Angle : 0.594 11.711 34967 Z= 0.301 Chirality : 0.044 0.240 3938 Planarity : 0.004 0.048 4530 Dihedral : 4.182 33.653 3438 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.93 % Allowed : 19.51 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.26 (0.14), residues: 3163 helix: 0.93 (0.22), residues: 648 sheet: -0.03 (0.20), residues: 668 loop : -1.91 (0.13), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 PHE 0.042 0.001 PHE A 342 TYR 0.020 0.001 TYR A 351 ARG 0.009 0.000 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.04679 ( 645) hydrogen bonds : angle 4.75147 ( 1830) SS BOND : bond 0.00347 ( 39) SS BOND : angle 2.14677 ( 78) covalent geometry : bond 0.00338 (25650) covalent geometry : angle 0.58606 (34889) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 451 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8224 (tm-30) REVERT: A 86 PHE cc_start: 0.7773 (t80) cc_final: 0.7468 (t80) REVERT: A 153 MET cc_start: -0.4361 (tpt) cc_final: -0.4763 (tpt) REVERT: A 177 MET cc_start: 0.0650 (mtt) cc_final: -0.0466 (mtt) REVERT: A 367 VAL cc_start: 0.8388 (m) cc_final: 0.8166 (p) REVERT: A 508 TYR cc_start: 0.6992 (m-80) cc_final: 0.5975 (m-80) REVERT: A 515 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.5984 (p90) REVERT: A 544 ASN cc_start: 0.8288 (t0) cc_final: 0.8019 (p0) REVERT: A 564 GLN cc_start: 0.7814 (mp10) cc_final: 0.7395 (mp10) REVERT: A 580 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7984 (mm-40) REVERT: A 690 GLN cc_start: 0.8054 (mt0) cc_final: 0.7556 (mm-40) REVERT: A 790 LYS cc_start: 0.9113 (mttt) cc_final: 0.8862 (mttm) REVERT: A 804 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8396 (mt0) REVERT: A 935 GLN cc_start: 0.7770 (mt0) cc_final: 0.6583 (mt0) REVERT: A 964 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8713 (ttmm) REVERT: A 1017 GLU cc_start: 0.7431 (tp30) cc_final: 0.7191 (tp30) REVERT: A 1091 ARG cc_start: 0.8101 (mtm-85) cc_final: 0.7838 (ttp-170) REVERT: A 1134 ASN cc_start: 0.6615 (m-40) cc_final: 0.6259 (m110) REVERT: A 1138 TYR cc_start: 0.8373 (t80) cc_final: 0.8043 (t80) REVERT: C 138 ASP cc_start: 0.8588 (t0) cc_final: 0.8350 (t0) REVERT: C 177 MET cc_start: -0.3193 (mmt) cc_final: -0.4373 (mmt) REVERT: C 202 LYS cc_start: 0.8491 (mptt) cc_final: 0.7896 (mptt) REVERT: C 224 GLU cc_start: 0.7685 (mp0) cc_final: 0.7265 (mp0) REVERT: C 294 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7208 (t0) REVERT: C 324 GLU cc_start: 0.7910 (mp0) cc_final: 0.7708 (mp0) REVERT: C 574 ASP cc_start: 0.7925 (p0) cc_final: 0.7497 (t0) REVERT: C 586 ASP cc_start: 0.7965 (t0) cc_final: 0.7546 (t0) REVERT: C 591 SER cc_start: 0.9020 (p) cc_final: 0.8812 (m) REVERT: C 787 GLN cc_start: 0.7652 (mp10) cc_final: 0.7281 (mt0) REVERT: C 790 LYS cc_start: 0.9133 (mtpp) cc_final: 0.8782 (mmtm) REVERT: C 823 PHE cc_start: 0.8278 (t80) cc_final: 0.7966 (t80) REVERT: C 902 MET cc_start: 0.7976 (mmm) cc_final: 0.7770 (mmt) REVERT: C 933 LYS cc_start: 0.8299 (ttmt) cc_final: 0.8082 (ttmm) REVERT: C 964 LYS cc_start: 0.8880 (ttpp) cc_final: 0.8633 (ttmm) REVERT: C 1073 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8495 (mtpp) REVERT: C 1107 ARG cc_start: 0.8546 (mtm110) cc_final: 0.6470 (tpt170) REVERT: B 41 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7622 (mtpt) REVERT: B 64 TRP cc_start: 0.7257 (t-100) cc_final: 0.6904 (t60) REVERT: B 140 PHE cc_start: 0.7989 (m-80) cc_final: 0.7441 (m-80) REVERT: B 190 ARG cc_start: 0.7193 (mtp180) cc_final: 0.6612 (mtp180) REVERT: B 202 LYS cc_start: 0.7469 (tptt) cc_final: 0.7169 (tptt) REVERT: B 203 ILE cc_start: 0.8317 (mt) cc_final: 0.7922 (mp) REVERT: B 298 GLU cc_start: 0.8200 (tp30) cc_final: 0.7978 (tp30) REVERT: B 317 ASN cc_start: 0.8503 (m-40) cc_final: 0.8213 (m-40) REVERT: B 429 PHE cc_start: 0.8053 (t80) cc_final: 0.7346 (t80) REVERT: B 455 LEU cc_start: 0.8185 (tt) cc_final: 0.7906 (tt) REVERT: B 462 LYS cc_start: 0.7637 (tptp) cc_final: 0.7388 (tptp) REVERT: B 559 PHE cc_start: 0.7188 (t80) cc_final: 0.6977 (t80) REVERT: B 779 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8148 (mm-40) REVERT: B 823 PHE cc_start: 0.8673 (t80) cc_final: 0.8460 (t80) REVERT: B 896 ILE cc_start: 0.7647 (mt) cc_final: 0.7343 (tt) REVERT: B 985 ASP cc_start: 0.7402 (p0) cc_final: 0.6881 (p0) REVERT: B 995 ARG cc_start: 0.8314 (mtt-85) cc_final: 0.8101 (mtt-85) REVERT: B 1017 GLU cc_start: 0.7799 (tp30) cc_final: 0.7164 (tp30) REVERT: B 1092 GLU cc_start: 0.7321 (pm20) cc_final: 0.7085 (pm20) REVERT: B 1107 ARG cc_start: 0.7519 (mtt180) cc_final: 0.5816 (tpt170) outliers start: 54 outliers final: 49 residues processed: 482 average time/residue: 0.4191 time to fit residues: 312.2112 Evaluate side-chains 499 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 447 time to evaluate : 3.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 23 optimal weight: 2.9990 chunk 151 optimal weight: 0.3980 chunk 169 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 147 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 250 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 158 optimal weight: 0.4980 chunk 242 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.148271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.116784 restraints weight = 47819.151| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.35 r_work: 0.3531 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25689 Z= 0.127 Angle : 0.587 11.778 34967 Z= 0.298 Chirality : 0.044 0.230 3938 Planarity : 0.004 0.050 4530 Dihedral : 4.120 33.940 3438 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.14 % Allowed : 19.51 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.19 (0.15), residues: 3163 helix: 1.03 (0.22), residues: 649 sheet: 0.02 (0.20), residues: 670 loop : -1.87 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 PHE 0.042 0.001 PHE A 342 TYR 0.015 0.001 TYR B 170 ARG 0.009 0.000 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.04469 ( 645) hydrogen bonds : angle 4.68973 ( 1830) SS BOND : bond 0.00332 ( 39) SS BOND : angle 2.02326 ( 78) covalent geometry : bond 0.00302 (25650) covalent geometry : angle 0.58022 (34889) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15587.11 seconds wall clock time: 272 minutes 51.81 seconds (16371.81 seconds total)