Starting phenix.real_space_refine on Fri Jun 27 10:07:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wka_32564/06_2025/7wka_32564.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wka_32564/06_2025/7wka_32564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wka_32564/06_2025/7wka_32564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wka_32564/06_2025/7wka_32564.map" model { file = "/net/cci-nas-00/data/ceres_data/7wka_32564/06_2025/7wka_32564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wka_32564/06_2025/7wka_32564.cif" } resolution = 3.64 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= 0.033 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 139 5.16 5 C 20002 2.51 5 N 5231 2.21 5 O 5981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 1.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31353 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8239 Classifications: {'peptide': 1051} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 996} Chain breaks: 7 Chain: "C" Number of atoms: 8239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8239 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 54, 'TRANS': 996} Chain breaks: 7 Chain: "c" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1662 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "d" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1656 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Chain: "B" Number of atoms: 8239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8239 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 54, 'TRANS': 996} Chain breaks: 7 Chain: "a" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1662 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "b" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1656 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 18.38, per 1000 atoms: 0.59 Number of scatterers: 31353 At special positions: 0 Unit cell: (218.6, 137.718, 178.159, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 139 16.00 O 5981 8.00 N 5231 7.00 C 20002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 96 " distance=2.03 Simple disulfide: pdb=" SG CYS c 147 " - pdb=" SG CYS c 202 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 92 " distance=2.04 Simple disulfide: pdb=" SG CYS d 138 " - pdb=" SG CYS d 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 96 " distance=2.03 Simple disulfide: pdb=" SG CYS a 147 " - pdb=" SG CYS a 202 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 92 " distance=2.03 Simple disulfide: pdb=" SG CYS b 138 " - pdb=" SG CYS b 198 " 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: 6.98 Conformation dependent library (CDL) restraints added in 4.1 seconds 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7540 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 68 sheets defined 18.4% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.74 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.516A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.779A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 removed outlier: 3.640A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.819A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.667A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.831A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.691A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.539A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 899 No H-bonds generated for 'chain 'A' and resid 897 through 899' Processing helix chain 'A' and resid 900 through 909 removed outlier: 3.643A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.704A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 931 removed outlier: 3.594A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 939 removed outlier: 3.525A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.866A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.752A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.981A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.872A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.538A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.947A 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 384 through 389 removed outlier: 3.815A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.731A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 4.079A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.686A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.659A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 746 through 752' Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.646A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.953A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 4.076A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.636A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.648A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.711A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.815A pdb=" N ALA C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 963 removed outlier: 3.888A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.642A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1032 removed outlier: 4.012A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.798A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'd' and resid 83 through 87 removed outlier: 4.124A pdb=" N ALA d 87 " --> pdb=" O GLU d 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 125 through 132 removed outlier: 3.668A pdb=" N LEU d 129 " --> pdb=" O SER d 125 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER d 131 " --> pdb=" O GLU d 127 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 192 removed outlier: 3.590A pdb=" N ARG d 192 " --> pdb=" O ASP d 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.668A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.323A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.861A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.420A 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 406 through 410 removed outlier: 3.737A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.691A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.883A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.709A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.869A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 824 removed outlier: 3.882A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.603A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.628A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.689A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.749A pdb=" N ALA B 924 " --> pdb=" O GLN B 920 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 963 removed outlier: 3.802A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.607A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.892A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET B1029 " --> pdb=" O ALA B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.914A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 32 removed outlier: 3.574A pdb=" N ARG a 31 " --> pdb=" O SER a 28 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE a 32 " --> pdb=" O PHE a 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 28 through 32' Processing helix chain 'a' and resid 87 through 91 removed outlier: 3.896A pdb=" N SER a 91 " --> pdb=" O SER a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 193 through 198 removed outlier: 4.010A pdb=" N SER a 197 " --> pdb=" O SER a 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 87 removed outlier: 4.223A pdb=" N ALA b 87 " --> pdb=" O GLU b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 132 removed outlier: 3.612A pdb=" N LEU b 129 " --> pdb=" O SER b 125 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER b 131 " --> pdb=" O GLU b 127 " (cutoff:3.500A) Processing helix chain 'b' and resid 187 through 192 removed outlier: 3.894A pdb=" N ARG b 192 " --> pdb=" O ASP b 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.920A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.968A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.664A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.937A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 245 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.422A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.602A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 357 removed outlier: 4.380A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.670A pdb=" N TYR A 453 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.503A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.294A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.720A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.044A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.553A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.522A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.743A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AC3, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.030A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.563A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY C 566 " --> pdb=" O ALA C 575 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.888A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.835A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.591A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AD1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.817A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.567A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C1061 " --> pdb=" O GLN C1054 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.347A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.975A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'c' and resid 9 through 12 removed outlier: 6.565A pdb=" N GLU c 10 " --> pdb=" O THR c 117 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR c 95 " --> pdb=" O VAL c 37 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL c 37 " --> pdb=" O TYR c 95 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN c 35 " --> pdb=" O ALA c 97 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N MET c 34 " --> pdb=" O MET c 50 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N MET c 50 " --> pdb=" O MET c 34 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP c 36 " --> pdb=" O ILE c 48 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG c 40 " --> pdb=" O GLY c 44 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY c 44 " --> pdb=" O ARG c 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU c 57 " --> pdb=" O HIS c 52 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'c' and resid 9 through 12 removed outlier: 6.565A pdb=" N GLU c 10 " --> pdb=" O THR c 117 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS c 96 " --> pdb=" O TRP c 110 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TRP c 110 " --> pdb=" O CYS c 96 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG c 98 " --> pdb=" O ALA c 108 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'c' and resid 17 through 23 removed outlier: 3.620A pdb=" N LEU c 20 " --> pdb=" O MET c 81 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET c 81 " --> pdb=" O LEU c 20 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR c 71 " --> pdb=" O TYR c 80 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'c' and resid 127 through 131 removed outlier: 3.576A pdb=" N GLY c 146 " --> pdb=" O LEU c 131 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER c 187 " --> pdb=" O HIS c 171 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 127 through 131 removed outlier: 3.576A pdb=" N GLY c 146 " --> pdb=" O LEU c 131 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR c 152 " --> pdb=" O TYR c 182 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'c' and resid 158 through 161 removed outlier: 3.789A pdb=" N THR c 158 " --> pdb=" O ALA c 205 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 4 through 7 removed outlier: 3.893A pdb=" N SER d 7 " --> pdb=" O SER d 22 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER d 22 " --> pdb=" O SER d 7 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS d 23 " --> pdb=" O PHE d 75 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE d 75 " --> pdb=" O CYS d 23 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP d 74 " --> pdb=" O SER d 71 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 10 through 14 removed outlier: 6.594A pdb=" N LEU d 11 " --> pdb=" O GLU d 109 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS d 111 " --> pdb=" O LEU d 11 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL d 13 " --> pdb=" O LYS d 111 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP d 39 " --> pdb=" O LEU d 51 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'd' and resid 30 through 31 Processing sheet with id=AE6, first strand: chain 'd' and resid 118 through 122 removed outlier: 3.672A pdb=" N VAL d 137 " --> pdb=" O PHE d 122 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR d 177 " --> pdb=" O ASN d 142 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'd' and resid 157 through 158 removed outlier: 3.941A pdb=" N TYR d 196 " --> pdb=" O PHE d 213 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE d 213 " --> pdb=" O TYR d 196 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.102A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.644A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.816A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.403A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.524A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.771A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.857A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.752A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.519A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.689A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AG2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.876A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AG4, first strand: chain 'a' and resid 9 through 12 removed outlier: 3.657A pdb=" N VAL a 12 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA a 92 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS a 99 " --> pdb=" O TRP a 33 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TRP a 33 " --> pdb=" O LYS a 99 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET a 34 " --> pdb=" O MET a 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N MET a 50 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TRP a 36 " --> pdb=" O ILE a 48 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG a 40 " --> pdb=" O GLY a 44 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 9 through 12 removed outlier: 3.657A pdb=" N VAL a 12 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA a 92 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG a 98 " --> pdb=" O TYR a 109 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR a 109 " --> pdb=" O ARG a 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 17 through 23 removed outlier: 3.752A pdb=" N THR a 71 " --> pdb=" O TYR a 80 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'a' and resid 127 through 131 removed outlier: 3.548A pdb=" N SER a 186 " --> pdb=" O CYS a 147 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR a 182 " --> pdb=" O GLY a 151 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER a 187 " --> pdb=" O HIS a 171 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'a' and resid 127 through 131 removed outlier: 3.548A pdb=" N SER a 186 " --> pdb=" O CYS a 147 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR a 182 " --> pdb=" O GLY a 151 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR a 183 " --> pdb=" O VAL a 176 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'a' and resid 158 through 161 removed outlier: 3.508A pdb=" N THR a 211 " --> pdb=" O HIS a 206 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 5 through 7 removed outlier: 3.795A pdb=" N SER b 7 " --> pdb=" O SER b 22 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER b 22 " --> pdb=" O SER b 7 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE b 21 " --> pdb=" O LEU b 77 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS b 23 " --> pdb=" O PHE b 75 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE b 75 " --> pdb=" O CYS b 23 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP b 74 " --> pdb=" O SER b 71 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 10 through 14 removed outlier: 6.296A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS b 111 " --> pdb=" O LEU b 11 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL b 13 " --> pdb=" O LYS b 111 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP b 39 " --> pdb=" O LEU b 51 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN b 41 " --> pdb=" O LYS b 49 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 10 through 14 removed outlier: 6.296A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS b 111 " --> pdb=" O LEU b 11 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL b 13 " --> pdb=" O LYS b 111 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N HIS b 94 " --> pdb=" O ALA b 101 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA b 101 " --> pdb=" O HIS b 94 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 118 through 122 removed outlier: 3.551A pdb=" N VAL b 137 " --> pdb=" O PHE b 122 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR b 177 " --> pdb=" O ASN b 142 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 157 through 158 removed outlier: 3.758A pdb=" N TYR b 196 " --> pdb=" O PHE b 213 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE b 213 " --> pdb=" O TYR b 196 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA b 200 " --> pdb=" O ILE b 209 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE b 209 " --> pdb=" O ALA b 200 " (cutoff:3.500A) 929 hydrogen bonds defined for protein. 2469 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: 15.31 Time building geometry restraints manager: 8.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6953 1.33 - 1.45: 7717 1.45 - 1.58: 17260 1.58 - 1.70: 0 1.70 - 1.83: 178 Bond restraints: 32108 Sorted by residual: bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.436 -0.102 2.34e-02 1.83e+03 1.91e+01 bond pdb=" N GLN C 271 " pdb=" CA GLN C 271 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.65e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.416 -0.082 2.34e-02 1.83e+03 1.23e+01 bond pdb=" N VAL A 367 " pdb=" CA VAL A 367 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N VAL d 33 " pdb=" CA VAL d 33 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.89e+00 ... (remaining 32103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 42699 2.31 - 4.62: 875 4.62 - 6.93: 91 6.93 - 9.23: 22 9.23 - 11.54: 9 Bond angle restraints: 43696 Sorted by residual: angle pdb=" C VAL C 524 " pdb=" N CYS C 525 " pdb=" CA CYS C 525 " ideal model delta sigma weight residual 121.54 133.08 -11.54 1.91e+00 2.74e-01 3.65e+01 angle pdb=" C ASN B 122 " pdb=" N ALA B 123 " pdb=" CA ALA B 123 " ideal model delta sigma weight residual 121.54 132.68 -11.14 1.91e+00 2.74e-01 3.40e+01 angle pdb=" C GLY B 639 " pdb=" N SER B 640 " pdb=" CA SER B 640 " ideal model delta sigma weight residual 121.54 131.99 -10.45 1.91e+00 2.74e-01 3.00e+01 angle pdb=" N SER B 161 " pdb=" CA SER B 161 " pdb=" C SER B 161 " ideal model delta sigma weight residual 111.04 102.66 8.38 1.55e+00 4.16e-01 2.92e+01 angle pdb=" C GLY C 639 " pdb=" N SER C 640 " pdb=" CA SER C 640 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 ... (remaining 43691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.49: 18535 14.49 - 28.98: 489 28.98 - 43.47: 119 43.47 - 57.97: 18 57.97 - 72.46: 15 Dihedral angle restraints: 19176 sinusoidal: 7466 harmonic: 11710 Sorted by residual: dihedral pdb=" CA LYS C 795 " pdb=" C LYS C 795 " pdb=" N TYR C 796 " pdb=" CA TYR C 796 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA CYS C 525 " pdb=" C CYS C 525 " pdb=" N GLY C 526 " pdb=" CA GLY C 526 " ideal model delta harmonic sigma weight residual 180.00 156.20 23.80 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ARG C 634 " pdb=" C ARG C 634 " pdb=" N VAL C 635 " pdb=" CA VAL C 635 " ideal model delta harmonic sigma weight residual 180.00 -157.38 -22.62 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 19173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 4292 0.082 - 0.163: 593 0.163 - 0.245: 44 0.245 - 0.327: 5 0.327 - 0.408: 1 Chirality restraints: 4935 Sorted by residual: chirality pdb=" CA VAL B 159 " pdb=" N VAL B 159 " pdb=" C VAL B 159 " pdb=" CB VAL B 159 " both_signs ideal model delta sigma weight residual False 2.44 2.85 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CB ILE A 312 " pdb=" CA ILE A 312 " pdb=" CG1 ILE A 312 " pdb=" CG2 ILE A 312 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE C 312 " pdb=" CA ILE C 312 " pdb=" CG1 ILE C 312 " pdb=" CG2 ILE C 312 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 4932 not shown) Planarity restraints: 5629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 266 " -0.017 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C TYR A 266 " 0.061 2.00e-02 2.50e+03 pdb=" O TYR A 266 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL A 267 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 22 " -0.016 2.00e-02 2.50e+03 3.11e-02 9.68e+00 pdb=" C THR B 22 " 0.054 2.00e-02 2.50e+03 pdb=" O THR B 22 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN B 23 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 23 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C GLN C 23 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN C 23 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU C 24 " 0.017 2.00e-02 2.50e+03 ... (remaining 5626 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 9878 2.86 - 3.37: 23783 3.37 - 3.88: 50617 3.88 - 4.39: 52037 4.39 - 4.90: 94601 Nonbonded interactions: 230916 Sorted by model distance: nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.353 3.040 nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.354 3.040 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.356 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.356 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.360 3.040 ... (remaining 230911 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'a' selection = chain 'c' } ncs_group { reference = chain 'b' selection = chain 'd' } 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 group one per residue 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: 2.760 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: 1.230 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 73.390 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 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 : 0.005 0.102 32154 Z= 0.252 Angle : 0.794 11.544 43788 Z= 0.464 Chirality : 0.054 0.408 4935 Planarity : 0.006 0.072 5629 Dihedral : 8.145 66.816 11498 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.74 % Favored : 96.14 % Rotamer: Outliers : 0.23 % Allowed : 0.71 % Favored : 99.06 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.05 % 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: -2.58 (0.11), residues: 3961 helix: -4.92 (0.06), residues: 522 sheet: -0.32 (0.14), residues: 963 loop : -1.59 (0.10), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP a 33 HIS 0.015 0.002 HIS B 954 PHE 0.027 0.003 PHE B 490 TYR 0.019 0.002 TYR a 103 ARG 0.007 0.001 ARG B1039 Details of bonding type rmsd hydrogen bonds : bond 0.32888 ( 901) hydrogen bonds : angle 11.26990 ( 2469) SS BOND : bond 0.00196 ( 46) SS BOND : angle 0.81570 ( 92) covalent geometry : bond 0.00466 (32108) covalent geometry : angle 0.79397 (43696) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 950 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.8321 (t80) cc_final: 0.8094 (t80) REVERT: A 206 LYS cc_start: 0.7858 (tptt) cc_final: 0.7628 (tppt) REVERT: A 275 PHE cc_start: 0.8231 (m-10) cc_final: 0.7888 (m-80) REVERT: A 277 LEU cc_start: 0.8671 (mt) cc_final: 0.8411 (mp) REVERT: A 339 ASP cc_start: 0.8599 (m-30) cc_final: 0.8115 (t70) REVERT: A 385 THR cc_start: 0.8976 (p) cc_final: 0.8740 (p) REVERT: A 386 LYS cc_start: 0.7920 (mttt) cc_final: 0.7635 (mttt) REVERT: A 546 LEU cc_start: 0.8168 (tt) cc_final: 0.7887 (tt) REVERT: A 654 GLU cc_start: 0.7923 (tt0) cc_final: 0.7555 (tt0) REVERT: A 663 ASP cc_start: 0.7020 (m-30) cc_final: 0.6811 (m-30) REVERT: A 743 CYS cc_start: 0.6662 (m) cc_final: 0.6108 (m) REVERT: A 814 LYS cc_start: 0.8694 (mttt) cc_final: 0.8425 (mmmt) REVERT: A 964 LYS cc_start: 0.8639 (mttt) cc_final: 0.8372 (tppt) REVERT: A 1033 VAL cc_start: 0.7823 (t) cc_final: 0.7600 (t) REVERT: A 1109 PHE cc_start: 0.5439 (p90) cc_final: 0.5152 (p90) REVERT: C 49 HIS cc_start: 0.7202 (t70) cc_final: 0.6792 (t70) REVERT: C 106 PHE cc_start: 0.7284 (m-10) cc_final: 0.6744 (m-10) REVERT: C 115 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7081 (mt0) REVERT: C 206 LYS cc_start: 0.7726 (tptt) cc_final: 0.7255 (tppt) REVERT: C 226 LEU cc_start: 0.7433 (tp) cc_final: 0.7214 (mt) REVERT: C 270 LEU cc_start: 0.8053 (mt) cc_final: 0.7733 (mt) REVERT: C 305 SER cc_start: 0.8796 (p) cc_final: 0.8462 (t) REVERT: C 338 PHE cc_start: 0.6882 (m-10) cc_final: 0.6099 (m-10) REVERT: C 339 ASP cc_start: 0.7535 (m-30) cc_final: 0.7298 (m-30) REVERT: C 540 ASN cc_start: 0.6191 (m-40) cc_final: 0.5989 (t0) REVERT: C 552 LEU cc_start: 0.7639 (mt) cc_final: 0.7258 (mt) REVERT: C 585 LEU cc_start: 0.6596 (mt) cc_final: 0.6392 (mt) REVERT: C 654 GLU cc_start: 0.7724 (tt0) cc_final: 0.7454 (tt0) REVERT: C 719 THR cc_start: 0.8078 (t) cc_final: 0.7767 (p) REVERT: C 725 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6290 (mt-10) REVERT: C 747 THR cc_start: 0.8021 (p) cc_final: 0.7717 (p) REVERT: C 751 ASN cc_start: 0.8597 (m-40) cc_final: 0.8343 (m-40) REVERT: C 775 ASP cc_start: 0.8080 (m-30) cc_final: 0.7801 (m-30) REVERT: C 780 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7280 (mt-10) REVERT: C 867 ASP cc_start: 0.8135 (m-30) cc_final: 0.7890 (m-30) REVERT: C 884 SER cc_start: 0.8491 (m) cc_final: 0.8228 (p) REVERT: C 894 LEU cc_start: 0.7091 (mp) cc_final: 0.6638 (mp) REVERT: C 953 ASN cc_start: 0.8447 (m-40) cc_final: 0.8036 (m-40) REVERT: C 969 LYS cc_start: 0.8471 (mttt) cc_final: 0.8153 (mmtm) REVERT: C 990 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7369 (mt-10) REVERT: C 1051 SER cc_start: 0.8598 (m) cc_final: 0.8218 (p) REVERT: C 1061 VAL cc_start: 0.8763 (t) cc_final: 0.8508 (p) REVERT: C 1073 LYS cc_start: 0.8215 (tttt) cc_final: 0.8006 (tttp) REVERT: C 1084 ASP cc_start: 0.7502 (p0) cc_final: 0.6936 (p0) REVERT: C 1125 ASN cc_start: 0.8152 (p0) cc_final: 0.7944 (p0) REVERT: c 102 ASP cc_start: 0.3369 (OUTLIER) cc_final: 0.3061 (t0) REVERT: B 33 THR cc_start: 0.8330 (p) cc_final: 0.8076 (t) REVERT: B 36 VAL cc_start: 0.8765 (t) cc_final: 0.8454 (p) REVERT: B 55 PHE cc_start: 0.7334 (m-10) cc_final: 0.6592 (m-10) REVERT: B 106 PHE cc_start: 0.6238 (m-10) cc_final: 0.5979 (m-80) REVERT: B 119 ILE cc_start: 0.8889 (mt) cc_final: 0.8329 (mm) REVERT: B 127 VAL cc_start: 0.8617 (t) cc_final: 0.8310 (m) REVERT: B 189 LEU cc_start: 0.8591 (tp) cc_final: 0.8290 (tp) REVERT: B 204 TYR cc_start: 0.5870 (m-80) cc_final: 0.5617 (m-80) REVERT: B 221 SER cc_start: 0.8752 (t) cc_final: 0.8368 (m) REVERT: B 296 LEU cc_start: 0.8734 (tp) cc_final: 0.8482 (tp) REVERT: B 309 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7259 (mt-10) REVERT: B 492 LEU cc_start: 0.8337 (tp) cc_final: 0.8038 (pt) REVERT: B 534 VAL cc_start: 0.7721 (t) cc_final: 0.7293 (m) REVERT: B 535 LYS cc_start: 0.7992 (mtpt) cc_final: 0.7637 (tmtt) REVERT: B 654 GLU cc_start: 0.7420 (tt0) cc_final: 0.7167 (tt0) REVERT: B 658 ASN cc_start: 0.8919 (m-40) cc_final: 0.8023 (m-40) REVERT: B 721 SER cc_start: 0.7856 (t) cc_final: 0.7322 (p) REVERT: B 740 MET cc_start: 0.7478 (mtp) cc_final: 0.7257 (mtt) REVERT: B 969 LYS cc_start: 0.8549 (mttt) cc_final: 0.8073 (mttm) REVERT: B 979 ASP cc_start: 0.8231 (m-30) cc_final: 0.7372 (m-30) REVERT: B 990 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7924 (mt-10) REVERT: B 1000 ARG cc_start: 0.8143 (mtt180) cc_final: 0.7344 (mtm-85) REVERT: B 1073 LYS cc_start: 0.8083 (tttt) cc_final: 0.7819 (mtpp) REVERT: B 1106 GLN cc_start: 0.6251 (mm-40) cc_final: 0.6043 (mm-40) REVERT: B 1116 THR cc_start: 0.7278 (p) cc_final: 0.7015 (p) REVERT: B 1119 ASN cc_start: 0.7925 (m-40) cc_final: 0.7545 (m110) REVERT: a 33 TRP cc_start: 0.4327 (m-10) cc_final: 0.3414 (m-10) REVERT: a 61 ASN cc_start: 0.8206 (t0) cc_final: 0.7436 (t0) REVERT: a 69 THR cc_start: 0.7032 (m) cc_final: 0.6609 (p) REVERT: a 81 MET cc_start: 0.4890 (ttp) cc_final: 0.3028 (ttp) REVERT: b 43 LYS cc_start: 0.8017 (mttt) cc_final: 0.7816 (mmtt) REVERT: b 53 TYR cc_start: 0.6516 (p90) cc_final: 0.6289 (p90) REVERT: b 140 LEU cc_start: 0.5156 (mp) cc_final: 0.4613 (mp) outliers start: 8 outliers final: 4 residues processed: 958 average time/residue: 0.4777 time to fit residues: 711.6915 Evaluate side-chains 682 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 677 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain d residue 34 TYR Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain B residue 161 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 0.9990 chunk 302 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 161 optimal weight: 0.0000 chunk 312 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 232 optimal weight: 20.0000 chunk 362 optimal weight: 0.0970 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 188 ASN A 505 HIS ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 755 GLN A 895 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS A1054 GLN A1083 HIS A1088 HIS C 317 ASN C 343 ASN C 394 ASN C 519 HIS C 717 ASN C1054 GLN C1088 HIS C1106 GLN c 52 HIS d 6 GLN ** d 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 170 GLN B 239 GLN B 505 HIS B 544 ASN B 717 ASN B 895 GLN B 901 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1054 GLN B1113 GLN a 171 HIS b 93 HIS ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.189088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.149582 restraints weight = 77628.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.153812 restraints weight = 38408.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.156460 restraints weight = 23067.633| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 32154 Z= 0.142 Angle : 0.621 10.152 43788 Z= 0.329 Chirality : 0.045 0.281 4935 Planarity : 0.006 0.231 5629 Dihedral : 4.782 48.013 4319 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.94 % Favored : 97.96 % Rotamer: Outliers : 1.94 % Allowed : 8.32 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % 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: -1.71 (0.11), residues: 3961 helix: -2.69 (0.15), residues: 596 sheet: 0.23 (0.15), residues: 985 loop : -1.34 (0.11), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP a 36 HIS 0.005 0.001 HIS A1083 PHE 0.033 0.002 PHE C 400 TYR 0.021 0.001 TYR B1110 ARG 0.021 0.001 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.05619 ( 901) hydrogen bonds : angle 7.13900 ( 2469) SS BOND : bond 0.00387 ( 46) SS BOND : angle 0.92831 ( 92) covalent geometry : bond 0.00311 (32108) covalent geometry : angle 0.62057 (43696) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 712 time to evaluate : 4.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6695 (t80) cc_final: 0.6274 (t80) REVERT: A 226 LEU cc_start: 0.8052 (tp) cc_final: 0.7646 (mm) REVERT: A 290 ASP cc_start: 0.7925 (t0) cc_final: 0.7715 (t0) REVERT: A 339 ASP cc_start: 0.8527 (m-30) cc_final: 0.8144 (t0) REVERT: A 386 LYS cc_start: 0.8062 (mttt) cc_final: 0.7734 (ptpt) REVERT: A 546 LEU cc_start: 0.8251 (tt) cc_final: 0.7961 (tt) REVERT: A 654 GLU cc_start: 0.7578 (tt0) cc_final: 0.7296 (tt0) REVERT: A 721 SER cc_start: 0.8085 (t) cc_final: 0.7680 (p) REVERT: A 764 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8278 (ttmt) REVERT: A 823 PHE cc_start: 0.7976 (t80) cc_final: 0.7674 (t80) REVERT: A 883 THR cc_start: 0.8269 (m) cc_final: 0.7326 (p) REVERT: A 935 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7853 (mm-40) REVERT: A 964 LYS cc_start: 0.8375 (mttt) cc_final: 0.8113 (tppt) REVERT: A 969 LYS cc_start: 0.8462 (mttt) cc_final: 0.8050 (mmtm) REVERT: A 1010 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7966 (mp10) REVERT: A 1031 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7104 (mm-30) REVERT: A 1072 GLU cc_start: 0.8900 (pm20) cc_final: 0.8336 (pm20) REVERT: A 1073 LYS cc_start: 0.8706 (mtmm) cc_final: 0.8489 (mtmt) REVERT: A 1075 PHE cc_start: 0.8518 (m-10) cc_final: 0.7994 (m-80) REVERT: A 1119 ASN cc_start: 0.8217 (m-40) cc_final: 0.7835 (m-40) REVERT: A 1122 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8125 (p) REVERT: C 98 SER cc_start: 0.8426 (p) cc_final: 0.8008 (m) REVERT: C 195 LYS cc_start: 0.5660 (mmmt) cc_final: 0.5349 (mmmt) REVERT: C 201 PHE cc_start: 0.7219 (t80) cc_final: 0.6979 (t80) REVERT: C 224 GLU cc_start: 0.8340 (mp0) cc_final: 0.8135 (mp0) REVERT: C 226 LEU cc_start: 0.7668 (tp) cc_final: 0.7377 (mm) REVERT: C 269 TYR cc_start: 0.5240 (m-80) cc_final: 0.4993 (m-80) REVERT: C 271 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7664 (mm-40) REVERT: C 298 GLU cc_start: 0.8717 (tp30) cc_final: 0.8110 (tm-30) REVERT: C 305 SER cc_start: 0.8823 (p) cc_final: 0.8572 (t) REVERT: C 328 ARG cc_start: 0.4818 (mmt180) cc_final: 0.4243 (mmp-170) REVERT: C 396 TYR cc_start: 0.7999 (m-80) cc_final: 0.7677 (m-10) REVERT: C 509 ARG cc_start: 0.5017 (tmt170) cc_final: 0.4496 (mmt180) REVERT: C 528 LYS cc_start: 0.8003 (mmtt) cc_final: 0.7768 (mmtm) REVERT: C 533 LEU cc_start: 0.8994 (mt) cc_final: 0.8689 (mp) REVERT: C 654 GLU cc_start: 0.7402 (tt0) cc_final: 0.7140 (tt0) REVERT: C 725 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6434 (mt-10) REVERT: C 747 THR cc_start: 0.8035 (p) cc_final: 0.7754 (p) REVERT: C 773 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7084 (mm-30) REVERT: C 775 ASP cc_start: 0.7989 (m-30) cc_final: 0.7688 (m-30) REVERT: C 776 LYS cc_start: 0.8508 (ttpp) cc_final: 0.8235 (tmmt) REVERT: C 884 SER cc_start: 0.8601 (m) cc_final: 0.8255 (p) REVERT: C 900 MET cc_start: 0.8417 (tpp) cc_final: 0.8168 (mtp) REVERT: C 990 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7019 (mt-10) REVERT: C 1017 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7069 (mt-10) REVERT: C 1031 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7458 (mm-30) REVERT: C 1051 SER cc_start: 0.8696 (m) cc_final: 0.8457 (p) REVERT: c 106 TRP cc_start: 0.6005 (p90) cc_final: 0.5676 (p90) REVERT: B 36 VAL cc_start: 0.8848 (t) cc_final: 0.8526 (p) REVERT: B 55 PHE cc_start: 0.7336 (m-10) cc_final: 0.6906 (m-10) REVERT: B 106 PHE cc_start: 0.6389 (m-10) cc_final: 0.6016 (m-80) REVERT: B 127 VAL cc_start: 0.8853 (t) cc_final: 0.8490 (p) REVERT: B 133 PHE cc_start: 0.6965 (m-10) cc_final: 0.6568 (m-10) REVERT: B 206 LYS cc_start: 0.7929 (tptp) cc_final: 0.7527 (tptt) REVERT: B 221 SER cc_start: 0.8709 (t) cc_final: 0.8410 (m) REVERT: B 309 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6938 (mt-10) REVERT: B 342 PHE cc_start: 0.6933 (t80) cc_final: 0.6577 (t80) REVERT: B 365 TYR cc_start: 0.7485 (m-80) cc_final: 0.7152 (m-80) REVERT: B 386 LYS cc_start: 0.8260 (mtmt) cc_final: 0.7893 (mtmt) REVERT: B 581 THR cc_start: 0.5781 (p) cc_final: 0.4404 (m) REVERT: B 721 SER cc_start: 0.8613 (t) cc_final: 0.8396 (t) REVERT: B 773 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: B 969 LYS cc_start: 0.8604 (mttt) cc_final: 0.8398 (mttt) REVERT: B 978 ASN cc_start: 0.7808 (p0) cc_final: 0.7317 (p0) REVERT: B 979 ASP cc_start: 0.8162 (m-30) cc_final: 0.7596 (m-30) REVERT: B 980 ILE cc_start: 0.8769 (mt) cc_final: 0.8566 (mm) REVERT: B 1004 LEU cc_start: 0.8813 (tp) cc_final: 0.8570 (tt) REVERT: B 1017 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7607 (tm-30) REVERT: B 1073 LYS cc_start: 0.8381 (tttt) cc_final: 0.8082 (mtpp) REVERT: B 1106 GLN cc_start: 0.6443 (mm-40) cc_final: 0.6189 (mm-40) REVERT: B 1116 THR cc_start: 0.7505 (p) cc_final: 0.7230 (p) REVERT: B 1119 ASN cc_start: 0.8302 (m-40) cc_final: 0.7949 (m110) REVERT: a 34 MET cc_start: 0.7297 (mpp) cc_final: 0.7064 (mmm) REVERT: a 69 THR cc_start: 0.7499 (m) cc_final: 0.7061 (p) REVERT: a 96 CYS cc_start: 0.3085 (p) cc_final: 0.2244 (m) REVERT: a 161 TRP cc_start: 0.5001 (m-90) cc_final: 0.4671 (m-90) REVERT: a 181 LEU cc_start: 0.7792 (tp) cc_final: 0.7533 (tp) REVERT: b 53 TYR cc_start: 0.6607 (p90) cc_final: 0.6333 (p90) outliers start: 68 outliers final: 39 residues processed: 750 average time/residue: 0.5687 time to fit residues: 694.6895 Evaluate side-chains 657 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 616 time to evaluate : 3.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain d residue 34 TYR Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 50 LEU Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 90 optimal weight: 1.9990 chunk 351 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 288 optimal weight: 5.9990 chunk 385 optimal weight: 8.9990 chunk 172 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 276 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 chunk 366 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 787 GLN A 914 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS A1088 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 751 ASN C 926 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS C1113 GLN ** d 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 207 HIS B 334 ASN B 343 ASN ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.179083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.138703 restraints weight = 77164.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.142909 restraints weight = 37496.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.145484 restraints weight = 22274.352| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 32154 Z= 0.203 Angle : 0.649 10.040 43788 Z= 0.340 Chirality : 0.046 0.280 4935 Planarity : 0.005 0.171 5629 Dihedral : 4.735 43.460 4315 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.42 % Favored : 97.48 % Rotamer: Outliers : 2.68 % Allowed : 10.29 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % 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: -1.02 (0.12), residues: 3961 helix: -1.08 (0.19), residues: 617 sheet: 0.44 (0.15), residues: 1016 loop : -1.08 (0.11), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 104 HIS 0.042 0.002 HIS A 66 PHE 0.023 0.002 PHE B 906 TYR 0.024 0.002 TYR A 170 ARG 0.015 0.001 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.04681 ( 901) hydrogen bonds : angle 6.18751 ( 2469) SS BOND : bond 0.00999 ( 46) SS BOND : angle 1.22675 ( 92) covalent geometry : bond 0.00460 (32108) covalent geometry : angle 0.64743 (43696) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 688 time to evaluate : 3.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8369 (m) cc_final: 0.7929 (p) REVERT: A 135 PHE cc_start: 0.7223 (t80) cc_final: 0.6725 (t80) REVERT: A 195 LYS cc_start: 0.4604 (tptp) cc_final: 0.3702 (mmmt) REVERT: A 226 LEU cc_start: 0.8091 (tp) cc_final: 0.7760 (mt) REVERT: A 258 TRP cc_start: 0.5150 (m100) cc_final: 0.3903 (m-10) REVERT: A 313 TYR cc_start: 0.8299 (m-80) cc_final: 0.8083 (m-80) REVERT: A 339 ASP cc_start: 0.8505 (m-30) cc_final: 0.8245 (t70) REVERT: A 342 PHE cc_start: 0.7425 (m-10) cc_final: 0.7124 (m-80) REVERT: A 509 ARG cc_start: 0.1689 (mtt180) cc_final: 0.0929 (ptp-170) REVERT: A 535 LYS cc_start: 0.7513 (ttmt) cc_final: 0.7216 (tmmt) REVERT: A 543 PHE cc_start: 0.8257 (m-80) cc_final: 0.8014 (m-80) REVERT: A 546 LEU cc_start: 0.8353 (tt) cc_final: 0.8030 (tt) REVERT: A 654 GLU cc_start: 0.7687 (tt0) cc_final: 0.7482 (tt0) REVERT: A 696 THR cc_start: 0.8963 (m) cc_final: 0.8613 (p) REVERT: A 743 CYS cc_start: 0.5868 (m) cc_final: 0.5651 (m) REVERT: A 764 LYS cc_start: 0.8743 (ttpp) cc_final: 0.8328 (ttpp) REVERT: A 780 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7286 (mt-10) REVERT: A 814 LYS cc_start: 0.8740 (mmmt) cc_final: 0.8448 (mmmt) REVERT: A 823 PHE cc_start: 0.8175 (t80) cc_final: 0.7903 (t80) REVERT: A 868 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7777 (mm-30) REVERT: A 884 SER cc_start: 0.8559 (m) cc_final: 0.8256 (t) REVERT: A 914 ASN cc_start: 0.8365 (m110) cc_final: 0.6175 (m-40) REVERT: A 935 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8020 (mm-40) REVERT: A 969 LYS cc_start: 0.8757 (mttt) cc_final: 0.8374 (mmtm) REVERT: A 1031 GLU cc_start: 0.7750 (mm-30) cc_final: 0.6756 (mp0) REVERT: A 1045 LYS cc_start: 0.8724 (mmmm) cc_final: 0.8442 (mmmm) REVERT: A 1092 GLU cc_start: 0.7752 (tp30) cc_final: 0.7465 (tp30) REVERT: A 1111 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8119 (pt0) REVERT: A 1119 ASN cc_start: 0.8222 (m-40) cc_final: 0.7895 (m110) REVERT: C 56 LEU cc_start: 0.8418 (tp) cc_final: 0.8176 (tp) REVERT: C 190 ARG cc_start: 0.2024 (mmt90) cc_final: 0.1802 (mmm-85) REVERT: C 194 PHE cc_start: 0.8056 (m-80) cc_final: 0.7639 (m-80) REVERT: C 271 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7805 (mm-40) REVERT: C 528 LYS cc_start: 0.8283 (mmtt) cc_final: 0.8062 (mmtm) REVERT: C 613 GLN cc_start: 0.7514 (pt0) cc_final: 0.7147 (pt0) REVERT: C 654 GLU cc_start: 0.7437 (tt0) cc_final: 0.7195 (tt0) REVERT: C 663 ASP cc_start: 0.7088 (m-30) cc_final: 0.6872 (m-30) REVERT: C 725 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6660 (mt-10) REVERT: C 762 GLN cc_start: 0.7751 (tp40) cc_final: 0.7394 (tp40) REVERT: C 816 SER cc_start: 0.8048 (p) cc_final: 0.6777 (m) REVERT: C 821 LEU cc_start: 0.8596 (mt) cc_final: 0.8365 (mt) REVERT: C 884 SER cc_start: 0.8594 (m) cc_final: 0.8130 (t) REVERT: C 933 LYS cc_start: 0.8416 (mttt) cc_final: 0.8182 (mmmm) REVERT: C 935 GLN cc_start: 0.8178 (tp40) cc_final: 0.7514 (tm-30) REVERT: C 983 ARG cc_start: 0.5916 (mmm160) cc_final: 0.5682 (tmt170) REVERT: C 990 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6986 (mt-10) REVERT: C 1031 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7622 (mm-30) REVERT: C 1051 SER cc_start: 0.8856 (m) cc_final: 0.8556 (p) REVERT: C 1073 LYS cc_start: 0.8516 (tttt) cc_final: 0.8308 (mtpp) REVERT: c 106 TRP cc_start: 0.6215 (p90) cc_final: 0.5998 (p90) REVERT: B 36 VAL cc_start: 0.8898 (t) cc_final: 0.8550 (m) REVERT: B 55 PHE cc_start: 0.7272 (m-10) cc_final: 0.6987 (m-10) REVERT: B 119 ILE cc_start: 0.8890 (mm) cc_final: 0.8667 (mm) REVERT: B 129 LYS cc_start: 0.8487 (mttt) cc_final: 0.8217 (mmmm) REVERT: B 133 PHE cc_start: 0.7589 (m-80) cc_final: 0.6836 (m-10) REVERT: B 221 SER cc_start: 0.8841 (t) cc_final: 0.8516 (m) REVERT: B 315 THR cc_start: 0.8133 (m) cc_final: 0.7883 (m) REVERT: B 386 LYS cc_start: 0.8406 (mtmt) cc_final: 0.8087 (mtmt) REVERT: B 515 PHE cc_start: 0.7000 (m-10) cc_final: 0.6755 (m-10) REVERT: B 537 LYS cc_start: 0.9232 (tptt) cc_final: 0.8851 (tptp) REVERT: B 654 GLU cc_start: 0.6882 (mp0) cc_final: 0.6655 (mp0) REVERT: B 978 ASN cc_start: 0.8076 (p0) cc_final: 0.7610 (p0) REVERT: B 979 ASP cc_start: 0.8185 (m-30) cc_final: 0.7653 (m-30) REVERT: B 1017 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7713 (tm-30) REVERT: B 1019 ARG cc_start: 0.7707 (ttp80) cc_final: 0.7372 (ttp-110) REVERT: B 1073 LYS cc_start: 0.8471 (tttt) cc_final: 0.8225 (mtpp) REVERT: B 1106 GLN cc_start: 0.6798 (mm-40) cc_final: 0.6572 (mm-40) REVERT: B 1119 ASN cc_start: 0.8735 (m-40) cc_final: 0.8260 (m110) REVERT: a 4 LEU cc_start: 0.6623 (mp) cc_final: 0.6222 (mm) REVERT: a 161 TRP cc_start: 0.5246 (m-90) cc_final: 0.4986 (m-90) REVERT: b 41 GLN cc_start: 0.7434 (pm20) cc_final: 0.7225 (pm20) REVERT: b 49 LYS cc_start: 0.7509 (mttt) cc_final: 0.7273 (mttt) outliers start: 94 outliers final: 50 residues processed: 740 average time/residue: 0.4359 time to fit residues: 506.7714 Evaluate side-chains 673 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 622 time to evaluate : 3.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 156 optimal weight: 3.9990 chunk 245 optimal weight: 20.0000 chunk 148 optimal weight: 0.0040 chunk 340 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 265 optimal weight: 7.9990 chunk 342 optimal weight: 0.9980 chunk 133 optimal weight: 0.0970 chunk 177 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 142 optimal weight: 0.0570 overall best weight: 0.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 690 GLN A 914 ASN A 935 GLN A1010 GLN A1113 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** d 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN ** a 52 HIS ** 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 = 0.4536 r_free = 0.4536 target = 0.182385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.140227 restraints weight = 76384.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.144513 restraints weight = 37599.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.147179 restraints weight = 22659.612| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.129 32154 Z= 0.105 Angle : 0.566 11.358 43788 Z= 0.288 Chirality : 0.044 0.250 4935 Planarity : 0.004 0.133 5629 Dihedral : 4.308 27.925 4311 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.02 % Favored : 97.88 % Rotamer: Outliers : 1.82 % Allowed : 13.23 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.12), residues: 3961 helix: -0.13 (0.21), residues: 611 sheet: 0.63 (0.16), residues: 979 loop : -1.01 (0.11), residues: 2371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 104 HIS 0.008 0.001 HIS C1083 PHE 0.025 0.001 PHE C 306 TYR 0.015 0.001 TYR a 182 ARG 0.013 0.001 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 901) hydrogen bonds : angle 5.74303 ( 2469) SS BOND : bond 0.00264 ( 46) SS BOND : angle 0.85811 ( 92) covalent geometry : bond 0.00243 (32108) covalent geometry : angle 0.56477 (43696) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 636 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8326 (m) cc_final: 0.7911 (p) REVERT: A 104 TRP cc_start: 0.6582 (m-10) cc_final: 0.6355 (m-10) REVERT: A 135 PHE cc_start: 0.6988 (t80) cc_final: 0.6563 (t80) REVERT: A 226 LEU cc_start: 0.7941 (tp) cc_final: 0.7734 (mm) REVERT: A 258 TRP cc_start: 0.5185 (m100) cc_final: 0.4009 (m-10) REVERT: A 339 ASP cc_start: 0.8460 (m-30) cc_final: 0.8050 (t70) REVERT: A 356 LYS cc_start: 0.6878 (mptt) cc_final: 0.6609 (mmtm) REVERT: A 386 LYS cc_start: 0.7958 (mttt) cc_final: 0.7583 (mttt) REVERT: A 535 LYS cc_start: 0.7489 (ttmt) cc_final: 0.7234 (tmmt) REVERT: A 543 PHE cc_start: 0.8174 (m-80) cc_final: 0.7965 (m-80) REVERT: A 546 LEU cc_start: 0.8327 (tt) cc_final: 0.8013 (tt) REVERT: A 654 GLU cc_start: 0.7477 (tt0) cc_final: 0.7224 (tt0) REVERT: A 696 THR cc_start: 0.8894 (m) cc_final: 0.8657 (p) REVERT: A 764 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8226 (ttpp) REVERT: A 775 ASP cc_start: 0.8023 (m-30) cc_final: 0.7808 (t0) REVERT: A 814 LYS cc_start: 0.8767 (mmmt) cc_final: 0.8529 (mmmt) REVERT: A 823 PHE cc_start: 0.8191 (t80) cc_final: 0.7871 (t80) REVERT: A 868 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7438 (tp30) REVERT: A 884 SER cc_start: 0.8433 (m) cc_final: 0.8220 (t) REVERT: A 935 GLN cc_start: 0.8280 (mm110) cc_final: 0.8037 (mm-40) REVERT: A 964 LYS cc_start: 0.8684 (tppt) cc_final: 0.8450 (tppt) REVERT: A 965 GLN cc_start: 0.8307 (tp40) cc_final: 0.8058 (tp40) REVERT: A 1031 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7113 (mm-30) REVERT: A 1045 LYS cc_start: 0.8695 (mmmm) cc_final: 0.8318 (mmmm) REVERT: A 1097 SER cc_start: 0.8920 (t) cc_final: 0.8650 (p) REVERT: A 1111 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: A 1119 ASN cc_start: 0.8118 (m-40) cc_final: 0.7819 (m110) REVERT: C 276 LEU cc_start: 0.8505 (tp) cc_final: 0.8265 (tt) REVERT: C 277 LEU cc_start: 0.8823 (mm) cc_final: 0.8532 (mp) REVERT: C 298 GLU cc_start: 0.8798 (tp30) cc_final: 0.8143 (tm-30) REVERT: C 313 TYR cc_start: 0.8066 (m-80) cc_final: 0.7642 (m-80) REVERT: C 357 ARG cc_start: 0.8664 (tmm-80) cc_final: 0.8073 (ttp80) REVERT: C 396 TYR cc_start: 0.8147 (m-10) cc_final: 0.7537 (m-10) REVERT: C 528 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7968 (mmtm) REVERT: C 613 GLN cc_start: 0.7326 (pt0) cc_final: 0.7090 (pt0) REVERT: C 654 GLU cc_start: 0.7330 (tt0) cc_final: 0.7106 (tt0) REVERT: C 725 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6660 (mt-10) REVERT: C 762 GLN cc_start: 0.7692 (tp40) cc_final: 0.7331 (tp40) REVERT: C 772 VAL cc_start: 0.8879 (t) cc_final: 0.8560 (p) REVERT: C 816 SER cc_start: 0.7947 (p) cc_final: 0.6931 (m) REVERT: C 821 LEU cc_start: 0.8499 (mt) cc_final: 0.8232 (mt) REVERT: C 884 SER cc_start: 0.8477 (m) cc_final: 0.8078 (t) REVERT: C 935 GLN cc_start: 0.8088 (tp40) cc_final: 0.7526 (tm-30) REVERT: C 957 GLN cc_start: 0.7942 (tt0) cc_final: 0.7646 (tt0) REVERT: C 983 ARG cc_start: 0.5858 (mmm160) cc_final: 0.5440 (tmt170) REVERT: C 990 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6945 (mt-10) REVERT: C 1031 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7531 (mm-30) REVERT: C 1135 ASN cc_start: 0.8661 (t0) cc_final: 0.8448 (t0) REVERT: c 81 MET cc_start: 0.5390 (ttp) cc_final: 0.5149 (mtp) REVERT: c 106 TRP cc_start: 0.6006 (p90) cc_final: 0.5725 (p90) REVERT: B 36 VAL cc_start: 0.8818 (t) cc_final: 0.8476 (m) REVERT: B 49 HIS cc_start: 0.7423 (t-90) cc_final: 0.7153 (t-170) REVERT: B 55 PHE cc_start: 0.7128 (m-10) cc_final: 0.6909 (m-10) REVERT: B 67 VAL cc_start: 0.6837 (OUTLIER) cc_final: 0.6510 (p) REVERT: B 119 ILE cc_start: 0.8894 (mm) cc_final: 0.8694 (mm) REVERT: B 129 LYS cc_start: 0.8446 (mttt) cc_final: 0.8192 (mmmm) REVERT: B 133 PHE cc_start: 0.7424 (m-80) cc_final: 0.6642 (m-80) REVERT: B 195 LYS cc_start: 0.3089 (tptt) cc_final: 0.2674 (tptt) REVERT: B 221 SER cc_start: 0.8842 (t) cc_final: 0.8502 (m) REVERT: B 298 GLU cc_start: 0.8158 (tp30) cc_final: 0.7850 (tp30) REVERT: B 386 LYS cc_start: 0.8383 (mtmt) cc_final: 0.8134 (pttt) REVERT: B 515 PHE cc_start: 0.6994 (m-10) cc_final: 0.6763 (m-10) REVERT: B 537 LYS cc_start: 0.9281 (tptt) cc_final: 0.9057 (tmtt) REVERT: B 546 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7261 (pp) REVERT: B 748 GLU cc_start: 0.8349 (pm20) cc_final: 0.8052 (pt0) REVERT: B 765 ARG cc_start: 0.8145 (ttp-170) cc_final: 0.7920 (ttm-80) REVERT: B 776 LYS cc_start: 0.8699 (tttt) cc_final: 0.8354 (tmtt) REVERT: B 784 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8103 (tp40) REVERT: B 787 GLN cc_start: 0.7865 (mp10) cc_final: 0.7640 (mp10) REVERT: B 884 SER cc_start: 0.8707 (m) cc_final: 0.8167 (t) REVERT: B 969 LYS cc_start: 0.8740 (mttt) cc_final: 0.8328 (mtpp) REVERT: B 978 ASN cc_start: 0.8193 (p0) cc_final: 0.7769 (p0) REVERT: B 979 ASP cc_start: 0.8257 (m-30) cc_final: 0.7628 (m-30) REVERT: B 984 LEU cc_start: 0.7600 (mt) cc_final: 0.7318 (tp) REVERT: B 1005 GLN cc_start: 0.8123 (tp40) cc_final: 0.7914 (tp40) REVERT: B 1017 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7647 (tm-30) REVERT: B 1073 LYS cc_start: 0.8433 (tttt) cc_final: 0.8210 (mtpp) REVERT: B 1106 GLN cc_start: 0.6797 (mm-40) cc_final: 0.6516 (mm-40) REVERT: B 1119 ASN cc_start: 0.8683 (m-40) cc_final: 0.8361 (m110) REVERT: a 4 LEU cc_start: 0.6528 (mp) cc_final: 0.6161 (mm) REVERT: a 81 MET cc_start: 0.5473 (ppp) cc_final: 0.2985 (tpt) outliers start: 64 outliers final: 37 residues processed: 670 average time/residue: 0.4536 time to fit residues: 478.1581 Evaluate side-chains 640 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 600 time to evaluate : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 273 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 318 optimal weight: 4.9990 chunk 281 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 228 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 901 GLN A 978 ASN A1113 GLN C 901 GLN C 926 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS C1119 ASN ** d 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B1113 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.171585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.129622 restraints weight = 74767.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.133662 restraints weight = 37032.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.136220 restraints weight = 22368.919| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 32154 Z= 0.251 Angle : 0.699 10.244 43788 Z= 0.368 Chirality : 0.047 0.303 4935 Planarity : 0.005 0.116 5629 Dihedral : 4.803 27.066 4311 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 3.36 % Allowed : 12.46 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.12), residues: 3961 helix: 0.13 (0.21), residues: 619 sheet: 0.56 (0.15), residues: 1019 loop : -1.05 (0.12), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP a 36 HIS 0.048 0.002 HIS A 66 PHE 0.027 0.003 PHE A 515 TYR 0.027 0.002 TYR C 269 ARG 0.010 0.001 ARG B 454 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 901) hydrogen bonds : angle 5.93790 ( 2469) SS BOND : bond 0.00448 ( 46) SS BOND : angle 1.67488 ( 92) covalent geometry : bond 0.00554 (32108) covalent geometry : angle 0.69578 (43696) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 686 time to evaluate : 3.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8421 (m) cc_final: 0.8153 (p) REVERT: A 104 TRP cc_start: 0.7341 (m-90) cc_final: 0.6866 (m-10) REVERT: A 135 PHE cc_start: 0.7250 (t80) cc_final: 0.6801 (t80) REVERT: A 291 CYS cc_start: 0.6747 (t) cc_final: 0.6499 (t) REVERT: A 293 LEU cc_start: 0.8490 (tp) cc_final: 0.8000 (tt) REVERT: A 294 ASP cc_start: 0.7673 (m-30) cc_final: 0.7472 (m-30) REVERT: A 339 ASP cc_start: 0.8485 (m-30) cc_final: 0.8201 (t70) REVERT: A 515 PHE cc_start: 0.8248 (t80) cc_final: 0.8026 (t80) REVERT: A 516 GLU cc_start: 0.6326 (mp0) cc_final: 0.5811 (mp0) REVERT: A 546 LEU cc_start: 0.8480 (tt) cc_final: 0.8123 (tt) REVERT: A 654 GLU cc_start: 0.7705 (tt0) cc_final: 0.7498 (tt0) REVERT: A 675 GLN cc_start: 0.8524 (pp30) cc_final: 0.8181 (pp30) REVERT: A 764 LYS cc_start: 0.8729 (ttpp) cc_final: 0.8403 (ttmm) REVERT: A 775 ASP cc_start: 0.8076 (m-30) cc_final: 0.7859 (t0) REVERT: A 814 LYS cc_start: 0.8754 (mmmt) cc_final: 0.8502 (mmmt) REVERT: A 823 PHE cc_start: 0.8378 (t80) cc_final: 0.7953 (t80) REVERT: A 868 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7842 (tp30) REVERT: A 884 SER cc_start: 0.8519 (m) cc_final: 0.8136 (t) REVERT: A 964 LYS cc_start: 0.8886 (tppt) cc_final: 0.8549 (tppt) REVERT: A 969 LYS cc_start: 0.8976 (mttt) cc_final: 0.8559 (mtpp) REVERT: A 1002 GLN cc_start: 0.8348 (tp40) cc_final: 0.8144 (tp40) REVERT: A 1031 GLU cc_start: 0.7680 (mm-30) cc_final: 0.6789 (mp0) REVERT: A 1073 LYS cc_start: 0.8894 (mtpt) cc_final: 0.8632 (mtpp) REVERT: A 1097 SER cc_start: 0.9005 (t) cc_final: 0.8759 (p) REVERT: C 28 TYR cc_start: 0.5529 (OUTLIER) cc_final: 0.5069 (p90) REVERT: C 56 LEU cc_start: 0.8601 (tp) cc_final: 0.8336 (tp) REVERT: C 276 LEU cc_start: 0.8672 (tp) cc_final: 0.8439 (tt) REVERT: C 277 LEU cc_start: 0.9057 (mm) cc_final: 0.8790 (mp) REVERT: C 298 GLU cc_start: 0.8971 (tp30) cc_final: 0.8353 (tm-30) REVERT: C 357 ARG cc_start: 0.8859 (tmm-80) cc_final: 0.8536 (ttp80) REVERT: C 365 TYR cc_start: 0.7024 (m-10) cc_final: 0.6757 (m-10) REVERT: C 396 TYR cc_start: 0.8365 (m-10) cc_final: 0.7822 (m-10) REVERT: C 613 GLN cc_start: 0.7885 (pt0) cc_final: 0.7563 (pt0) REVERT: C 643 PHE cc_start: 0.8228 (t80) cc_final: 0.7619 (t80) REVERT: C 654 GLU cc_start: 0.7496 (tt0) cc_final: 0.7241 (tt0) REVERT: C 725 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6833 (mt-10) REVERT: C 816 SER cc_start: 0.8220 (p) cc_final: 0.7432 (m) REVERT: C 821 LEU cc_start: 0.8590 (mt) cc_final: 0.8385 (mp) REVERT: C 900 MET cc_start: 0.8826 (mtp) cc_final: 0.8587 (mtp) REVERT: C 933 LYS cc_start: 0.8424 (mttt) cc_final: 0.8202 (mmmm) REVERT: C 935 GLN cc_start: 0.8334 (tp40) cc_final: 0.7870 (tm-30) REVERT: C 969 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8507 (mmmm) REVERT: C 983 ARG cc_start: 0.6326 (mmm160) cc_final: 0.5938 (tmt170) REVERT: C 990 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7016 (mt-10) REVERT: C 1045 LYS cc_start: 0.8264 (mmmm) cc_final: 0.8031 (tppp) REVERT: C 1129 VAL cc_start: 0.9074 (t) cc_final: 0.8799 (m) REVERT: c 81 MET cc_start: 0.5768 (ttp) cc_final: 0.5481 (mtp) REVERT: c 106 TRP cc_start: 0.6157 (p90) cc_final: 0.5837 (p90) REVERT: B 36 VAL cc_start: 0.8918 (t) cc_final: 0.8625 (m) REVERT: B 55 PHE cc_start: 0.7279 (m-10) cc_final: 0.6893 (m-80) REVERT: B 106 PHE cc_start: 0.6692 (m-10) cc_final: 0.6452 (m-10) REVERT: B 119 ILE cc_start: 0.9026 (mm) cc_final: 0.8774 (mm) REVERT: B 129 LYS cc_start: 0.8666 (mttt) cc_final: 0.8294 (mmmm) REVERT: B 195 LYS cc_start: 0.3913 (tptt) cc_final: 0.3388 (tptt) REVERT: B 221 SER cc_start: 0.8951 (t) cc_final: 0.8651 (m) REVERT: B 229 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7988 (mm) REVERT: B 298 GLU cc_start: 0.8267 (tp30) cc_final: 0.7922 (tp30) REVERT: B 364 ASP cc_start: 0.7086 (t0) cc_final: 0.6692 (t0) REVERT: B 386 LYS cc_start: 0.8412 (mtmt) cc_final: 0.8195 (mtmt) REVERT: B 515 PHE cc_start: 0.7429 (m-10) cc_final: 0.7050 (m-10) REVERT: B 533 LEU cc_start: 0.7932 (mm) cc_final: 0.7463 (mp) REVERT: B 537 LYS cc_start: 0.9295 (tptt) cc_final: 0.9059 (tptt) REVERT: B 557 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7604 (pttm) REVERT: B 603 ASN cc_start: 0.8382 (p0) cc_final: 0.7915 (p0) REVERT: B 703 ASN cc_start: 0.8400 (t0) cc_final: 0.8182 (m110) REVERT: B 748 GLU cc_start: 0.8415 (pm20) cc_final: 0.8059 (pt0) REVERT: B 773 GLU cc_start: 0.8408 (tt0) cc_final: 0.7876 (tm-30) REVERT: B 808 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.6947 (p0) REVERT: B 921 LYS cc_start: 0.8670 (mttt) cc_final: 0.8311 (mmmm) REVERT: B 969 LYS cc_start: 0.8819 (mttt) cc_final: 0.8576 (mtpt) REVERT: B 974 SER cc_start: 0.8392 (p) cc_final: 0.8079 (m) REVERT: B 984 LEU cc_start: 0.8029 (mt) cc_final: 0.7653 (tp) REVERT: B 1017 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7769 (tm-30) REVERT: B 1125 ASN cc_start: 0.8212 (p0) cc_final: 0.7900 (p0) REVERT: a 81 MET cc_start: 0.5458 (ppp) cc_final: 0.2598 (tpp) outliers start: 118 outliers final: 82 residues processed: 753 average time/residue: 0.4586 time to fit residues: 542.7676 Evaluate side-chains 724 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 638 time to evaluate : 3.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 384 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 382 optimal weight: 0.7980 chunk 282 optimal weight: 0.8980 chunk 101 optimal weight: 0.4980 chunk 203 optimal weight: 0.9990 chunk 296 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 188 ASN A 506 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN C 49 HIS C 957 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 38 HIS B 394 ASN B 439 ASN B 907 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.173319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.133188 restraints weight = 75979.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.137264 restraints weight = 36766.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.139782 restraints weight = 21800.694| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.6536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 32154 Z= 0.137 Angle : 0.597 11.783 43788 Z= 0.304 Chirality : 0.044 0.269 4935 Planarity : 0.004 0.092 5629 Dihedral : 4.528 26.666 4311 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.47 % Favored : 97.45 % Rotamer: Outliers : 2.31 % Allowed : 15.51 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.13), residues: 3961 helix: 0.52 (0.21), residues: 623 sheet: 0.50 (0.15), residues: 1042 loop : -1.00 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP a 36 HIS 0.017 0.001 HIS C1083 PHE 0.045 0.002 PHE B 855 TYR 0.019 0.001 TYR C1138 ARG 0.011 0.001 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 901) hydrogen bonds : angle 5.64534 ( 2469) SS BOND : bond 0.00334 ( 46) SS BOND : angle 1.17674 ( 92) covalent geometry : bond 0.00314 (32108) covalent geometry : angle 0.59548 (43696) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 650 time to evaluate : 4.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8317 (m) cc_final: 0.8012 (p) REVERT: A 200 TYR cc_start: 0.7150 (t80) cc_final: 0.6856 (t80) REVERT: A 291 CYS cc_start: 0.6589 (t) cc_final: 0.6274 (t) REVERT: A 293 LEU cc_start: 0.8388 (tp) cc_final: 0.7918 (tt) REVERT: A 294 ASP cc_start: 0.7617 (m-30) cc_final: 0.7298 (m-30) REVERT: A 304 LYS cc_start: 0.8185 (mttt) cc_final: 0.7975 (mptt) REVERT: A 338 PHE cc_start: 0.5872 (m-80) cc_final: 0.5607 (m-80) REVERT: A 339 ASP cc_start: 0.8496 (m-30) cc_final: 0.8269 (t70) REVERT: A 515 PHE cc_start: 0.8403 (t80) cc_final: 0.8167 (t80) REVERT: A 516 GLU cc_start: 0.6375 (mp0) cc_final: 0.5757 (mp0) REVERT: A 537 LYS cc_start: 0.8831 (tptp) cc_final: 0.8627 (tmtt) REVERT: A 546 LEU cc_start: 0.8408 (tt) cc_final: 0.8126 (tt) REVERT: A 654 GLU cc_start: 0.7638 (tt0) cc_final: 0.7412 (tt0) REVERT: A 675 GLN cc_start: 0.8468 (pp30) cc_final: 0.8264 (pp30) REVERT: A 751 ASN cc_start: 0.8164 (m-40) cc_final: 0.7920 (m-40) REVERT: A 764 LYS cc_start: 0.8654 (ttpp) cc_final: 0.8382 (ttmm) REVERT: A 775 ASP cc_start: 0.7937 (m-30) cc_final: 0.7722 (t0) REVERT: A 814 LYS cc_start: 0.8788 (mmmt) cc_final: 0.8451 (mmmt) REVERT: A 823 PHE cc_start: 0.8312 (t80) cc_final: 0.7914 (t80) REVERT: A 825 LYS cc_start: 0.8862 (mtpp) cc_final: 0.8536 (mtpt) REVERT: A 856 LYS cc_start: 0.8930 (mppt) cc_final: 0.8662 (mppt) REVERT: A 858 LEU cc_start: 0.9182 (mm) cc_final: 0.8975 (mt) REVERT: A 868 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7586 (mm-30) REVERT: A 884 SER cc_start: 0.8520 (m) cc_final: 0.8207 (t) REVERT: A 900 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8205 (mtt) REVERT: A 950 ASP cc_start: 0.8044 (t0) cc_final: 0.7779 (t0) REVERT: A 964 LYS cc_start: 0.8913 (tppt) cc_final: 0.8618 (tppt) REVERT: A 969 LYS cc_start: 0.8939 (mttt) cc_final: 0.8535 (mtpp) REVERT: A 1031 GLU cc_start: 0.7615 (mm-30) cc_final: 0.6782 (mp0) REVERT: A 1045 LYS cc_start: 0.8724 (mmmm) cc_final: 0.8522 (mmmm) REVERT: A 1073 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8563 (mtpp) REVERT: A 1097 SER cc_start: 0.8992 (t) cc_final: 0.8744 (p) REVERT: C 276 LEU cc_start: 0.8628 (tp) cc_final: 0.8398 (tt) REVERT: C 277 LEU cc_start: 0.8994 (mm) cc_final: 0.8747 (mp) REVERT: C 290 ASP cc_start: 0.7831 (t0) cc_final: 0.7603 (t70) REVERT: C 313 TYR cc_start: 0.8248 (m-80) cc_final: 0.7909 (m-80) REVERT: C 365 TYR cc_start: 0.6892 (m-10) cc_final: 0.6576 (m-10) REVERT: C 396 TYR cc_start: 0.8280 (m-10) cc_final: 0.7826 (m-10) REVERT: C 421 TYR cc_start: 0.6346 (m-10) cc_final: 0.4401 (m-10) REVERT: C 509 ARG cc_start: 0.4218 (tmt170) cc_final: 0.3963 (ptm160) REVERT: C 613 GLN cc_start: 0.7815 (pt0) cc_final: 0.7555 (pt0) REVERT: C 654 GLU cc_start: 0.7336 (tt0) cc_final: 0.7095 (tt0) REVERT: C 725 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6908 (mt-10) REVERT: C 762 GLN cc_start: 0.7825 (tp-100) cc_final: 0.7539 (tp40) REVERT: C 765 ARG cc_start: 0.8077 (ttm170) cc_final: 0.7797 (ttm110) REVERT: C 816 SER cc_start: 0.8462 (p) cc_final: 0.7464 (m) REVERT: C 861 LEU cc_start: 0.8728 (mm) cc_final: 0.8416 (mt) REVERT: C 884 SER cc_start: 0.8556 (m) cc_final: 0.8120 (t) REVERT: C 918 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8182 (mt-10) REVERT: C 935 GLN cc_start: 0.8389 (tp40) cc_final: 0.7736 (tm-30) REVERT: C 969 LYS cc_start: 0.8735 (mmtm) cc_final: 0.8481 (mmmm) REVERT: C 983 ARG cc_start: 0.6145 (mmm160) cc_final: 0.5838 (tmt170) REVERT: C 990 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6947 (mt-10) REVERT: C 1129 VAL cc_start: 0.9005 (t) cc_final: 0.8738 (m) REVERT: C 1139 ASP cc_start: 0.8235 (t0) cc_final: 0.7882 (t0) REVERT: c 50 MET cc_start: 0.6082 (ttp) cc_final: 0.5762 (mmt) REVERT: c 81 MET cc_start: 0.5513 (ttp) cc_final: 0.5208 (mtp) REVERT: c 106 TRP cc_start: 0.6204 (p90) cc_final: 0.5764 (p90) REVERT: B 36 VAL cc_start: 0.8833 (t) cc_final: 0.8538 (m) REVERT: B 55 PHE cc_start: 0.7162 (m-10) cc_final: 0.6780 (m-10) REVERT: B 67 VAL cc_start: 0.6965 (OUTLIER) cc_final: 0.6627 (p) REVERT: B 125 ASN cc_start: 0.5932 (p0) cc_final: 0.4686 (t0) REVERT: B 129 LYS cc_start: 0.8644 (mttt) cc_final: 0.8225 (mmmm) REVERT: B 190 ARG cc_start: 0.5943 (ttm170) cc_final: 0.5539 (ttm170) REVERT: B 221 SER cc_start: 0.8960 (t) cc_final: 0.8642 (m) REVERT: B 229 LEU cc_start: 0.8248 (mm) cc_final: 0.7856 (mm) REVERT: B 239 GLN cc_start: 0.6138 (mt0) cc_final: 0.5912 (mt0) REVERT: B 298 GLU cc_start: 0.8179 (tp30) cc_final: 0.7892 (tp30) REVERT: B 364 ASP cc_start: 0.7096 (t0) cc_final: 0.6744 (t0) REVERT: B 515 PHE cc_start: 0.7418 (m-10) cc_final: 0.7033 (m-10) REVERT: B 533 LEU cc_start: 0.7712 (mm) cc_final: 0.7412 (mp) REVERT: B 537 LYS cc_start: 0.9267 (tptt) cc_final: 0.9007 (tptt) REVERT: B 603 ASN cc_start: 0.8308 (p0) cc_final: 0.7736 (p0) REVERT: B 703 ASN cc_start: 0.8407 (t0) cc_final: 0.8188 (m110) REVERT: B 748 GLU cc_start: 0.8272 (pm20) cc_final: 0.7842 (pt0) REVERT: B 751 ASN cc_start: 0.8318 (m-40) cc_final: 0.8071 (m-40) REVERT: B 755 GLN cc_start: 0.8435 (mp10) cc_final: 0.8196 (mp10) REVERT: B 765 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7802 (ttp-170) REVERT: B 773 GLU cc_start: 0.8234 (tt0) cc_final: 0.7890 (tm-30) REVERT: B 784 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8079 (tp40) REVERT: B 808 ASP cc_start: 0.7520 (t70) cc_final: 0.6917 (p0) REVERT: B 884 SER cc_start: 0.8714 (m) cc_final: 0.8175 (t) REVERT: B 921 LYS cc_start: 0.8604 (mttt) cc_final: 0.8402 (mmmm) REVERT: B 969 LYS cc_start: 0.8733 (mttt) cc_final: 0.8471 (mtpt) REVERT: B 974 SER cc_start: 0.8431 (p) cc_final: 0.7827 (t) REVERT: B 984 LEU cc_start: 0.7976 (mt) cc_final: 0.7631 (tp) REVERT: B 1017 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7725 (tm-30) REVERT: b 89 THR cc_start: 0.6983 (m) cc_final: 0.6756 (p) outliers start: 81 outliers final: 59 residues processed: 694 average time/residue: 0.4561 time to fit residues: 494.8028 Evaluate side-chains 688 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 627 time to evaluate : 3.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 66 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 258 optimal weight: 0.2980 chunk 257 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B1083 HIS B1088 HIS ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.169632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.128102 restraints weight = 75322.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.132017 restraints weight = 36991.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.134513 restraints weight = 22252.039| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.7038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 32154 Z= 0.197 Angle : 0.647 12.563 43788 Z= 0.334 Chirality : 0.046 0.289 4935 Planarity : 0.005 0.087 5629 Dihedral : 4.651 26.229 4311 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.71 % Favored : 96.21 % Rotamer: Outliers : 3.19 % Allowed : 15.31 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 3961 helix: 0.43 (0.21), residues: 655 sheet: 0.45 (0.15), residues: 1052 loop : -1.01 (0.12), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP a 36 HIS 0.008 0.001 HIS A1083 PHE 0.034 0.002 PHE B 855 TYR 0.021 0.002 TYR C 170 ARG 0.009 0.001 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 901) hydrogen bonds : angle 5.68293 ( 2469) SS BOND : bond 0.00438 ( 46) SS BOND : angle 1.39355 ( 92) covalent geometry : bond 0.00446 (32108) covalent geometry : angle 0.64428 (43696) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 660 time to evaluate : 3.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8399 (m) cc_final: 0.8136 (p) REVERT: A 190 ARG cc_start: 0.7451 (mpt180) cc_final: 0.7105 (mmt-90) REVERT: A 200 TYR cc_start: 0.7321 (t80) cc_final: 0.7067 (t80) REVERT: A 291 CYS cc_start: 0.6776 (t) cc_final: 0.6496 (t) REVERT: A 304 LYS cc_start: 0.8292 (mttt) cc_final: 0.8060 (mptt) REVERT: A 338 PHE cc_start: 0.6246 (m-80) cc_final: 0.5705 (m-80) REVERT: A 339 ASP cc_start: 0.8487 (m-30) cc_final: 0.8243 (t70) REVERT: A 516 GLU cc_start: 0.6546 (mp0) cc_final: 0.6280 (mp0) REVERT: A 537 LYS cc_start: 0.8826 (tptp) cc_final: 0.8547 (tmtt) REVERT: A 546 LEU cc_start: 0.8534 (tt) cc_final: 0.8243 (tt) REVERT: A 654 GLU cc_start: 0.7705 (tt0) cc_final: 0.7440 (tt0) REVERT: A 751 ASN cc_start: 0.8459 (m-40) cc_final: 0.8140 (m110) REVERT: A 764 LYS cc_start: 0.8643 (ttpp) cc_final: 0.8395 (ttmm) REVERT: A 814 LYS cc_start: 0.8849 (mmmt) cc_final: 0.8594 (mmmt) REVERT: A 823 PHE cc_start: 0.8371 (t80) cc_final: 0.7932 (t80) REVERT: A 825 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8666 (mtmt) REVERT: A 856 LYS cc_start: 0.9039 (mppt) cc_final: 0.8673 (mppt) REVERT: A 884 SER cc_start: 0.8589 (m) cc_final: 0.8239 (t) REVERT: A 950 ASP cc_start: 0.8019 (t0) cc_final: 0.7762 (t0) REVERT: A 964 LYS cc_start: 0.8959 (tppt) cc_final: 0.8670 (tppt) REVERT: A 969 LYS cc_start: 0.9002 (mttt) cc_final: 0.8593 (mtpp) REVERT: A 1031 GLU cc_start: 0.7635 (mm-30) cc_final: 0.6721 (mp0) REVERT: A 1073 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8570 (mtpp) REVERT: A 1097 SER cc_start: 0.9022 (t) cc_final: 0.8757 (p) REVERT: C 190 ARG cc_start: 0.3766 (tpt-90) cc_final: 0.3450 (tpt170) REVERT: C 276 LEU cc_start: 0.8697 (tp) cc_final: 0.8481 (tt) REVERT: C 277 LEU cc_start: 0.9062 (mm) cc_final: 0.8814 (mp) REVERT: C 365 TYR cc_start: 0.7201 (m-10) cc_final: 0.6798 (m-10) REVERT: C 396 TYR cc_start: 0.8505 (m-10) cc_final: 0.8008 (m-10) REVERT: C 421 TYR cc_start: 0.6421 (m-10) cc_final: 0.6218 (m-10) REVERT: C 613 GLN cc_start: 0.7913 (pt0) cc_final: 0.7635 (pt0) REVERT: C 654 GLU cc_start: 0.7378 (tt0) cc_final: 0.7135 (tt0) REVERT: C 816 SER cc_start: 0.8618 (p) cc_final: 0.8199 (p) REVERT: C 819 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7960 (mt-10) REVERT: C 861 LEU cc_start: 0.8780 (mm) cc_final: 0.8509 (mt) REVERT: C 884 SER cc_start: 0.8582 (m) cc_final: 0.8146 (t) REVERT: C 886 TRP cc_start: 0.8563 (OUTLIER) cc_final: 0.8091 (p90) REVERT: C 935 GLN cc_start: 0.8465 (tp40) cc_final: 0.7856 (tm-30) REVERT: C 969 LYS cc_start: 0.8855 (mmtm) cc_final: 0.8584 (mmmm) REVERT: C 983 ARG cc_start: 0.6557 (mmm160) cc_final: 0.6048 (tmt170) REVERT: C 990 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7061 (mt-10) REVERT: C 1040 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8250 (m) REVERT: C 1051 SER cc_start: 0.8996 (m) cc_final: 0.8696 (p) REVERT: C 1129 VAL cc_start: 0.9141 (t) cc_final: 0.8872 (m) REVERT: C 1139 ASP cc_start: 0.8323 (t0) cc_final: 0.7946 (t0) REVERT: B 36 VAL cc_start: 0.8829 (t) cc_final: 0.8557 (m) REVERT: B 55 PHE cc_start: 0.7308 (m-10) cc_final: 0.6951 (m-10) REVERT: B 106 PHE cc_start: 0.6783 (m-10) cc_final: 0.6496 (m-10) REVERT: B 125 ASN cc_start: 0.6185 (p0) cc_final: 0.4861 (t0) REVERT: B 129 LYS cc_start: 0.8742 (mttt) cc_final: 0.8351 (mmmm) REVERT: B 190 ARG cc_start: 0.5993 (ttm170) cc_final: 0.5556 (ttm170) REVERT: B 194 PHE cc_start: 0.6943 (m-80) cc_final: 0.6602 (m-80) REVERT: B 195 LYS cc_start: 0.3825 (tptt) cc_final: 0.3089 (tppt) REVERT: B 221 SER cc_start: 0.8979 (t) cc_final: 0.8723 (m) REVERT: B 229 LEU cc_start: 0.8196 (mm) cc_final: 0.7845 (mm) REVERT: B 298 GLU cc_start: 0.8291 (tp30) cc_final: 0.7933 (tp30) REVERT: B 386 LYS cc_start: 0.8431 (pttt) cc_final: 0.7971 (pttt) REVERT: B 515 PHE cc_start: 0.7593 (m-10) cc_final: 0.7136 (m-10) REVERT: B 537 LYS cc_start: 0.9267 (tptt) cc_final: 0.9049 (tmtt) REVERT: B 603 ASN cc_start: 0.8395 (p0) cc_final: 0.7896 (p0) REVERT: B 690 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7824 (mm-40) REVERT: B 703 ASN cc_start: 0.8656 (t0) cc_final: 0.8370 (m110) REVERT: B 748 GLU cc_start: 0.8302 (pm20) cc_final: 0.7838 (pt0) REVERT: B 751 ASN cc_start: 0.8431 (m-40) cc_final: 0.8140 (m-40) REVERT: B 773 GLU cc_start: 0.8241 (tt0) cc_final: 0.7938 (tm-30) REVERT: B 784 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8166 (tp40) REVERT: B 808 ASP cc_start: 0.7588 (t70) cc_final: 0.7071 (p0) REVERT: B 884 SER cc_start: 0.8797 (m) cc_final: 0.8233 (t) REVERT: B 969 LYS cc_start: 0.8786 (mttt) cc_final: 0.8429 (mtpp) REVERT: B 974 SER cc_start: 0.8472 (p) cc_final: 0.8094 (t) REVERT: B 979 ASP cc_start: 0.8279 (m-30) cc_final: 0.7686 (m-30) REVERT: B 984 LEU cc_start: 0.7981 (mt) cc_final: 0.7577 (tp) REVERT: B 1017 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7767 (tm-30) REVERT: B 1030 SER cc_start: 0.9118 (m) cc_final: 0.8434 (t) REVERT: B 1038 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8629 (mmmt) REVERT: B 1125 ASN cc_start: 0.8142 (p0) cc_final: 0.7884 (p0) REVERT: b 89 THR cc_start: 0.6996 (m) cc_final: 0.6773 (p) outliers start: 112 outliers final: 84 residues processed: 725 average time/residue: 0.4521 time to fit residues: 515.9978 Evaluate side-chains 722 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 636 time to evaluate : 4.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 139 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 276 optimal weight: 0.9990 chunk 356 optimal weight: 0.4980 chunk 240 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 316 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN C 564 GLN C 957 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 35 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 907 ASN B1083 HIS ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.168783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.127412 restraints weight = 74724.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.131225 restraints weight = 36929.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.133672 restraints weight = 22285.511| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.7433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32154 Z= 0.179 Angle : 0.643 11.971 43788 Z= 0.328 Chirality : 0.046 0.297 4935 Planarity : 0.005 0.089 5629 Dihedral : 4.655 26.045 4311 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.21 % Favored : 96.72 % Rotamer: Outliers : 3.02 % Allowed : 16.45 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.13), residues: 3961 helix: 0.51 (0.21), residues: 655 sheet: 0.41 (0.16), residues: 1059 loop : -1.01 (0.12), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP a 36 HIS 0.007 0.001 HIS C1048 PHE 0.054 0.002 PHE C 192 TYR 0.025 0.002 TYR C 796 ARG 0.013 0.001 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 901) hydrogen bonds : angle 5.59642 ( 2469) SS BOND : bond 0.00452 ( 46) SS BOND : angle 1.26432 ( 92) covalent geometry : bond 0.00406 (32108) covalent geometry : angle 0.64101 (43696) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 656 time to evaluate : 8.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8377 (m) cc_final: 0.8140 (p) REVERT: A 190 ARG cc_start: 0.7513 (mpt180) cc_final: 0.7175 (mmt-90) REVERT: A 237 ARG cc_start: 0.6232 (mmm-85) cc_final: 0.5699 (mmm-85) REVERT: A 304 LYS cc_start: 0.8369 (mttt) cc_final: 0.8152 (mptt) REVERT: A 339 ASP cc_start: 0.8479 (m-30) cc_final: 0.8263 (t70) REVERT: A 516 GLU cc_start: 0.6611 (mp0) cc_final: 0.6382 (mp0) REVERT: A 537 LYS cc_start: 0.8804 (tptp) cc_final: 0.8546 (tmtt) REVERT: A 546 LEU cc_start: 0.8600 (tt) cc_final: 0.8281 (tt) REVERT: A 654 GLU cc_start: 0.7666 (tt0) cc_final: 0.7426 (tt0) REVERT: A 748 GLU cc_start: 0.8302 (pt0) cc_final: 0.8019 (pt0) REVERT: A 750 SER cc_start: 0.9273 (m) cc_final: 0.8939 (p) REVERT: A 751 ASN cc_start: 0.8582 (m-40) cc_final: 0.8243 (m-40) REVERT: A 764 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8429 (ttmm) REVERT: A 814 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8246 (mmmt) REVERT: A 819 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7599 (mt-10) REVERT: A 823 PHE cc_start: 0.8395 (t80) cc_final: 0.7889 (t80) REVERT: A 825 LYS cc_start: 0.9001 (mtpp) cc_final: 0.8663 (mtmt) REVERT: A 856 LYS cc_start: 0.9018 (mppt) cc_final: 0.8616 (mppt) REVERT: A 884 SER cc_start: 0.8592 (m) cc_final: 0.8269 (t) REVERT: A 900 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8198 (mtt) REVERT: A 935 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8103 (mm-40) REVERT: A 950 ASP cc_start: 0.7987 (t0) cc_final: 0.7735 (t0) REVERT: A 964 LYS cc_start: 0.8963 (tppt) cc_final: 0.8632 (tppt) REVERT: A 969 LYS cc_start: 0.9005 (mttt) cc_final: 0.8606 (mtpp) REVERT: A 1031 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6797 (mp0) REVERT: A 1045 LYS cc_start: 0.8778 (mmmm) cc_final: 0.8358 (mmmm) REVERT: A 1073 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8552 (mtpp) REVERT: A 1097 SER cc_start: 0.8942 (t) cc_final: 0.8678 (p) REVERT: C 190 ARG cc_start: 0.4000 (tpt-90) cc_final: 0.3461 (tpt170) REVERT: C 192 PHE cc_start: 0.8037 (m-80) cc_final: 0.7754 (m-10) REVERT: C 277 LEU cc_start: 0.9093 (mm) cc_final: 0.8779 (mp) REVERT: C 298 GLU cc_start: 0.8982 (tp30) cc_final: 0.8305 (tm-30) REVERT: C 365 TYR cc_start: 0.7410 (m-10) cc_final: 0.6941 (m-10) REVERT: C 392 PHE cc_start: 0.8152 (m-80) cc_final: 0.7887 (m-80) REVERT: C 396 TYR cc_start: 0.8426 (m-10) cc_final: 0.7975 (m-10) REVERT: C 613 GLN cc_start: 0.7926 (pt0) cc_final: 0.7640 (pt0) REVERT: C 654 GLU cc_start: 0.7322 (tt0) cc_final: 0.7086 (tt0) REVERT: C 816 SER cc_start: 0.8632 (p) cc_final: 0.8183 (p) REVERT: C 861 LEU cc_start: 0.8772 (mm) cc_final: 0.8500 (mt) REVERT: C 886 TRP cc_start: 0.8578 (OUTLIER) cc_final: 0.8014 (p90) REVERT: C 935 GLN cc_start: 0.8482 (tp40) cc_final: 0.7840 (tm-30) REVERT: C 969 LYS cc_start: 0.8819 (mmtm) cc_final: 0.8456 (mmmm) REVERT: C 990 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7105 (mt-10) REVERT: C 1040 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8304 (m) REVERT: C 1051 SER cc_start: 0.8893 (m) cc_final: 0.8566 (p) REVERT: C 1129 VAL cc_start: 0.9135 (t) cc_final: 0.8926 (m) REVERT: C 1139 ASP cc_start: 0.8379 (t0) cc_final: 0.7974 (t0) REVERT: B 36 VAL cc_start: 0.8808 (t) cc_final: 0.8529 (m) REVERT: B 55 PHE cc_start: 0.7291 (m-10) cc_final: 0.6856 (m-10) REVERT: B 106 PHE cc_start: 0.6719 (m-10) cc_final: 0.6451 (m-10) REVERT: B 119 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8716 (mm) REVERT: B 125 ASN cc_start: 0.6348 (p0) cc_final: 0.4988 (t0) REVERT: B 129 LYS cc_start: 0.8737 (mttt) cc_final: 0.8296 (mmmm) REVERT: B 190 ARG cc_start: 0.6021 (ttm170) cc_final: 0.5561 (ttm170) REVERT: B 194 PHE cc_start: 0.6978 (m-80) cc_final: 0.6585 (m-80) REVERT: B 195 LYS cc_start: 0.3845 (tptt) cc_final: 0.2916 (tppt) REVERT: B 239 GLN cc_start: 0.6703 (mt0) cc_final: 0.6115 (mt0) REVERT: B 298 GLU cc_start: 0.8317 (tp30) cc_final: 0.7912 (tp30) REVERT: B 386 LYS cc_start: 0.8371 (pttt) cc_final: 0.8135 (pttt) REVERT: B 515 PHE cc_start: 0.7665 (m-10) cc_final: 0.7180 (m-10) REVERT: B 537 LYS cc_start: 0.9254 (tptt) cc_final: 0.8989 (tptt) REVERT: B 603 ASN cc_start: 0.8369 (p0) cc_final: 0.7911 (p0) REVERT: B 615 VAL cc_start: 0.9007 (p) cc_final: 0.8756 (m) REVERT: B 690 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7929 (mm-40) REVERT: B 703 ASN cc_start: 0.8781 (t0) cc_final: 0.8151 (t0) REVERT: B 748 GLU cc_start: 0.8243 (pm20) cc_final: 0.7907 (pt0) REVERT: B 751 ASN cc_start: 0.8426 (m-40) cc_final: 0.8189 (m-40) REVERT: B 765 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.7854 (ttp80) REVERT: B 773 GLU cc_start: 0.8224 (tt0) cc_final: 0.7830 (tm-30) REVERT: B 776 LYS cc_start: 0.8817 (tttt) cc_final: 0.8612 (ttpp) REVERT: B 784 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8251 (tp40) REVERT: B 808 ASP cc_start: 0.7536 (t70) cc_final: 0.7051 (p0) REVERT: B 884 SER cc_start: 0.8783 (m) cc_final: 0.8201 (t) REVERT: B 918 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7706 (mt-10) REVERT: B 964 LYS cc_start: 0.8907 (tttp) cc_final: 0.8644 (tmmt) REVERT: B 979 ASP cc_start: 0.8277 (m-30) cc_final: 0.7704 (m-30) REVERT: B 984 LEU cc_start: 0.7987 (mt) cc_final: 0.7591 (tp) REVERT: B 990 GLU cc_start: 0.7562 (pp20) cc_final: 0.7167 (pp20) REVERT: B 1017 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7785 (tm-30) REVERT: B 1030 SER cc_start: 0.9115 (m) cc_final: 0.8493 (t) REVERT: B 1092 GLU cc_start: 0.7836 (tp30) cc_final: 0.7206 (tm-30) REVERT: B 1125 ASN cc_start: 0.8190 (p0) cc_final: 0.7876 (p0) REVERT: a 142 MET cc_start: 0.6433 (mmm) cc_final: 0.5355 (ppp) REVERT: b 59 GLU cc_start: 0.7347 (tp30) cc_final: 0.7057 (tm-30) outliers start: 106 outliers final: 82 residues processed: 718 average time/residue: 0.6311 time to fit residues: 731.2369 Evaluate side-chains 701 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 615 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 45 LEU Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 293 optimal weight: 10.0000 chunk 174 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 232 optimal weight: 0.5980 chunk 73 optimal weight: 0.0270 chunk 149 optimal weight: 6.9990 chunk 238 optimal weight: 30.0000 chunk 323 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN B 61 ASN B 439 ASN B1083 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.169450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.129727 restraints weight = 75210.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.133694 restraints weight = 36444.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.136153 restraints weight = 21669.259| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.7559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32154 Z= 0.142 Angle : 0.635 12.476 43788 Z= 0.323 Chirality : 0.045 0.280 4935 Planarity : 0.004 0.088 5629 Dihedral : 4.615 26.666 4311 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.33 % Favored : 96.59 % Rotamer: Outliers : 2.68 % Allowed : 17.82 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.13), residues: 3961 helix: 0.62 (0.21), residues: 649 sheet: 0.42 (0.16), residues: 1052 loop : -0.97 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP a 36 HIS 0.009 0.001 HIS C1048 PHE 0.031 0.002 PHE C 192 TYR 0.020 0.001 TYR C 796 ARG 0.019 0.001 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 901) hydrogen bonds : angle 5.52226 ( 2469) SS BOND : bond 0.00321 ( 46) SS BOND : angle 1.25170 ( 92) covalent geometry : bond 0.00328 (32108) covalent geometry : angle 0.63335 (43696) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 638 time to evaluate : 3.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8319 (m) cc_final: 0.8064 (p) REVERT: A 190 ARG cc_start: 0.7417 (mpt180) cc_final: 0.7188 (mmt-90) REVERT: A 200 TYR cc_start: 0.7154 (t80) cc_final: 0.6790 (t80) REVERT: A 237 ARG cc_start: 0.5645 (mmm-85) cc_final: 0.5281 (mmm-85) REVERT: A 290 ASP cc_start: 0.8045 (t0) cc_final: 0.7716 (t70) REVERT: A 293 LEU cc_start: 0.8676 (tt) cc_final: 0.8373 (tp) REVERT: A 339 ASP cc_start: 0.8417 (m-30) cc_final: 0.8213 (t70) REVERT: A 516 GLU cc_start: 0.6410 (mp0) cc_final: 0.6203 (mp0) REVERT: A 537 LYS cc_start: 0.8778 (tptp) cc_final: 0.8567 (tmtt) REVERT: A 546 LEU cc_start: 0.8535 (tt) cc_final: 0.8237 (tt) REVERT: A 750 SER cc_start: 0.9255 (m) cc_final: 0.8926 (p) REVERT: A 751 ASN cc_start: 0.8502 (m-40) cc_final: 0.8237 (m110) REVERT: A 764 LYS cc_start: 0.8665 (ttpp) cc_final: 0.8420 (ttmm) REVERT: A 814 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8119 (mmmt) REVERT: A 823 PHE cc_start: 0.8285 (t80) cc_final: 0.7837 (t80) REVERT: A 825 LYS cc_start: 0.8929 (mtpp) cc_final: 0.8617 (mtmt) REVERT: A 868 GLU cc_start: 0.7936 (tp30) cc_final: 0.7689 (tp30) REVERT: A 884 SER cc_start: 0.8596 (m) cc_final: 0.8318 (t) REVERT: A 900 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7991 (mtt) REVERT: A 935 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8056 (mm-40) REVERT: A 950 ASP cc_start: 0.7949 (t0) cc_final: 0.7717 (t0) REVERT: A 964 LYS cc_start: 0.8941 (tppt) cc_final: 0.8626 (tppt) REVERT: A 969 LYS cc_start: 0.8966 (mttt) cc_final: 0.8636 (mtpp) REVERT: A 1031 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6829 (mp0) REVERT: A 1073 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8403 (mtpp) REVERT: A 1097 SER cc_start: 0.8919 (t) cc_final: 0.8636 (p) REVERT: C 138 ASP cc_start: 0.8095 (t0) cc_final: 0.7813 (t0) REVERT: C 170 TYR cc_start: 0.7683 (t80) cc_final: 0.7474 (t80) REVERT: C 192 PHE cc_start: 0.7966 (m-80) cc_final: 0.7761 (m-10) REVERT: C 269 TYR cc_start: 0.7122 (m-80) cc_final: 0.6536 (m-80) REVERT: C 277 LEU cc_start: 0.9054 (mm) cc_final: 0.8779 (mp) REVERT: C 298 GLU cc_start: 0.8942 (tp30) cc_final: 0.8307 (tm-30) REVERT: C 365 TYR cc_start: 0.7277 (m-10) cc_final: 0.6951 (m-10) REVERT: C 396 TYR cc_start: 0.8306 (m-10) cc_final: 0.7883 (m-10) REVERT: C 528 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7711 (mmtm) REVERT: C 562 PHE cc_start: 0.6351 (p90) cc_final: 0.5993 (p90) REVERT: C 613 GLN cc_start: 0.7944 (pt0) cc_final: 0.7672 (pt0) REVERT: C 654 GLU cc_start: 0.7264 (tt0) cc_final: 0.7025 (tt0) REVERT: C 762 GLN cc_start: 0.7944 (tp-100) cc_final: 0.7583 (tp-100) REVERT: C 775 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7648 (t0) REVERT: C 816 SER cc_start: 0.8489 (p) cc_final: 0.7392 (m) REVERT: C 861 LEU cc_start: 0.8789 (mm) cc_final: 0.8519 (mt) REVERT: C 886 TRP cc_start: 0.8520 (OUTLIER) cc_final: 0.7939 (p90) REVERT: C 935 GLN cc_start: 0.8348 (tp40) cc_final: 0.7783 (tm-30) REVERT: C 969 LYS cc_start: 0.8776 (mmtm) cc_final: 0.8397 (mmmm) REVERT: C 990 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7091 (mt-10) REVERT: C 1005 GLN cc_start: 0.8216 (tp40) cc_final: 0.7981 (tp40) REVERT: C 1031 GLU cc_start: 0.6827 (mp0) cc_final: 0.6613 (mp0) REVERT: C 1040 VAL cc_start: 0.9045 (OUTLIER) cc_final: 0.8407 (m) REVERT: C 1051 SER cc_start: 0.8961 (m) cc_final: 0.8711 (p) REVERT: C 1129 VAL cc_start: 0.9085 (t) cc_final: 0.8866 (m) REVERT: C 1139 ASP cc_start: 0.8321 (t0) cc_final: 0.7902 (t0) REVERT: B 36 VAL cc_start: 0.8737 (t) cc_final: 0.8467 (m) REVERT: B 55 PHE cc_start: 0.7134 (m-10) cc_final: 0.6765 (m-10) REVERT: B 106 PHE cc_start: 0.6523 (m-10) cc_final: 0.6267 (m-10) REVERT: B 119 ILE cc_start: 0.9032 (mm) cc_final: 0.8762 (mm) REVERT: B 125 ASN cc_start: 0.6904 (p0) cc_final: 0.5550 (t0) REVERT: B 129 LYS cc_start: 0.8664 (mttt) cc_final: 0.8283 (mmmm) REVERT: B 194 PHE cc_start: 0.6939 (m-80) cc_final: 0.6630 (m-80) REVERT: B 195 LYS cc_start: 0.3814 (tptt) cc_final: 0.2973 (tppt) REVERT: B 239 GLN cc_start: 0.6559 (mt0) cc_final: 0.5972 (mt0) REVERT: B 298 GLU cc_start: 0.8279 (tp30) cc_final: 0.7904 (tp30) REVERT: B 515 PHE cc_start: 0.7590 (m-10) cc_final: 0.7195 (m-10) REVERT: B 537 LYS cc_start: 0.9228 (tptt) cc_final: 0.9011 (tmtt) REVERT: B 603 ASN cc_start: 0.8242 (p0) cc_final: 0.7782 (p0) REVERT: B 615 VAL cc_start: 0.9114 (p) cc_final: 0.8854 (m) REVERT: B 690 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7810 (mm-40) REVERT: B 703 ASN cc_start: 0.8809 (t0) cc_final: 0.8229 (t0) REVERT: B 748 GLU cc_start: 0.8083 (pm20) cc_final: 0.7315 (pt0) REVERT: B 772 VAL cc_start: 0.9164 (p) cc_final: 0.8935 (p) REVERT: B 773 GLU cc_start: 0.8126 (tt0) cc_final: 0.7849 (tm-30) REVERT: B 784 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8322 (tp40) REVERT: B 808 ASP cc_start: 0.7501 (t70) cc_final: 0.7038 (p0) REVERT: B 884 SER cc_start: 0.8757 (m) cc_final: 0.8212 (t) REVERT: B 918 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7715 (mt-10) REVERT: B 964 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8656 (tmmt) REVERT: B 979 ASP cc_start: 0.8250 (m-30) cc_final: 0.7693 (m-30) REVERT: B 981 PHE cc_start: 0.7197 (t80) cc_final: 0.6812 (t80) REVERT: B 984 LEU cc_start: 0.7967 (mt) cc_final: 0.7624 (tp) REVERT: B 990 GLU cc_start: 0.7421 (pp20) cc_final: 0.7007 (pp20) REVERT: B 1017 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7755 (tm-30) REVERT: B 1030 SER cc_start: 0.9154 (m) cc_final: 0.8649 (t) REVERT: B 1092 GLU cc_start: 0.7687 (tp30) cc_final: 0.7113 (tm-30) REVERT: B 1125 ASN cc_start: 0.8074 (p0) cc_final: 0.7785 (p0) REVERT: a 142 MET cc_start: 0.6458 (mmm) cc_final: 0.5455 (ppp) REVERT: b 59 GLU cc_start: 0.7322 (tp30) cc_final: 0.7092 (tm-30) outliers start: 94 outliers final: 76 residues processed: 686 average time/residue: 0.4542 time to fit residues: 489.3805 Evaluate side-chains 711 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 629 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 182 TYR Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 196 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 chunk 383 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 248 optimal weight: 9.9990 chunk 387 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 328 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B1083 HIS ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.168533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.128930 restraints weight = 75178.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.132850 restraints weight = 36489.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.135301 restraints weight = 21708.264| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.7738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 32154 Z= 0.160 Angle : 0.653 11.970 43788 Z= 0.331 Chirality : 0.045 0.283 4935 Planarity : 0.004 0.089 5629 Dihedral : 4.651 26.262 4311 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.58 % Favored : 96.34 % Rotamer: Outliers : 2.68 % Allowed : 17.99 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 3961 helix: 0.64 (0.21), residues: 653 sheet: 0.36 (0.16), residues: 1053 loop : -1.00 (0.13), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP a 36 HIS 0.020 0.001 HIS B1083 PHE 0.051 0.002 PHE A 135 TYR 0.020 0.001 TYR C 796 ARG 0.017 0.001 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 901) hydrogen bonds : angle 5.50822 ( 2469) SS BOND : bond 0.00344 ( 46) SS BOND : angle 1.23391 ( 92) covalent geometry : bond 0.00368 (32108) covalent geometry : angle 0.65112 (43696) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7922 Ramachandran restraints generated. 3961 Oldfield, 0 Emsley, 3961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 628 time to evaluate : 3.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8368 (m) cc_final: 0.8129 (p) REVERT: A 190 ARG cc_start: 0.7486 (mpt180) cc_final: 0.7182 (mmt-90) REVERT: A 200 TYR cc_start: 0.7220 (t80) cc_final: 0.6917 (t80) REVERT: A 237 ARG cc_start: 0.5694 (mmm-85) cc_final: 0.5284 (mmm-85) REVERT: A 290 ASP cc_start: 0.8049 (t0) cc_final: 0.7676 (t70) REVERT: A 293 LEU cc_start: 0.8751 (tt) cc_final: 0.8507 (tp) REVERT: A 537 LYS cc_start: 0.8779 (tptp) cc_final: 0.8563 (tmtt) REVERT: A 546 LEU cc_start: 0.8561 (tt) cc_final: 0.8294 (tt) REVERT: A 711 SER cc_start: 0.8721 (t) cc_final: 0.8145 (p) REVERT: A 750 SER cc_start: 0.9192 (m) cc_final: 0.8846 (p) REVERT: A 751 ASN cc_start: 0.8519 (m-40) cc_final: 0.8228 (m-40) REVERT: A 814 LYS cc_start: 0.8944 (mmmt) cc_final: 0.8233 (mmmt) REVERT: A 819 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7444 (mp0) REVERT: A 823 PHE cc_start: 0.8304 (t80) cc_final: 0.7839 (t80) REVERT: A 825 LYS cc_start: 0.8948 (mtpp) cc_final: 0.8627 (mtmt) REVERT: A 884 SER cc_start: 0.8629 (m) cc_final: 0.8318 (t) REVERT: A 900 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8038 (mtt) REVERT: A 935 GLN cc_start: 0.8376 (mm-40) cc_final: 0.8095 (mm-40) REVERT: A 950 ASP cc_start: 0.7995 (t0) cc_final: 0.7781 (t0) REVERT: A 964 LYS cc_start: 0.8933 (tppt) cc_final: 0.8619 (tppt) REVERT: A 969 LYS cc_start: 0.8972 (mttt) cc_final: 0.8644 (mtpp) REVERT: A 1031 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6782 (mp0) REVERT: A 1045 LYS cc_start: 0.8753 (mmmm) cc_final: 0.8387 (mmmm) REVERT: A 1073 LYS cc_start: 0.8806 (mtpt) cc_final: 0.8408 (mtpp) REVERT: A 1097 SER cc_start: 0.8933 (t) cc_final: 0.8645 (p) REVERT: C 192 PHE cc_start: 0.7990 (m-80) cc_final: 0.7750 (m-10) REVERT: C 201 PHE cc_start: 0.7233 (t80) cc_final: 0.6961 (t80) REVERT: C 269 TYR cc_start: 0.7175 (m-80) cc_final: 0.6569 (m-80) REVERT: C 277 LEU cc_start: 0.9074 (mm) cc_final: 0.8823 (mp) REVERT: C 298 GLU cc_start: 0.8937 (tp30) cc_final: 0.8300 (tm-30) REVERT: C 365 TYR cc_start: 0.7318 (m-10) cc_final: 0.6945 (m-10) REVERT: C 396 TYR cc_start: 0.8237 (m-10) cc_final: 0.7835 (m-10) REVERT: C 528 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7669 (mmtm) REVERT: C 562 PHE cc_start: 0.6487 (p90) cc_final: 0.6238 (p90) REVERT: C 613 GLN cc_start: 0.8033 (pt0) cc_final: 0.7733 (pt0) REVERT: C 654 GLU cc_start: 0.7270 (tt0) cc_final: 0.7024 (tt0) REVERT: C 661 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7834 (tm-30) REVERT: C 762 GLN cc_start: 0.7968 (tp-100) cc_final: 0.7605 (tp-100) REVERT: C 861 LEU cc_start: 0.8780 (mm) cc_final: 0.8523 (mt) REVERT: C 886 TRP cc_start: 0.8547 (OUTLIER) cc_final: 0.7960 (p90) REVERT: C 918 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8051 (mt-10) REVERT: C 935 GLN cc_start: 0.8373 (tp40) cc_final: 0.7799 (tm-30) REVERT: C 969 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8414 (mmmm) REVERT: C 990 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7096 (mt-10) REVERT: C 1005 GLN cc_start: 0.8241 (tp40) cc_final: 0.7975 (tp40) REVERT: C 1040 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8488 (m) REVERT: C 1051 SER cc_start: 0.8969 (m) cc_final: 0.8744 (p) REVERT: C 1107 ARG cc_start: 0.8651 (tpp80) cc_final: 0.8420 (mmm160) REVERT: C 1118 ASP cc_start: 0.8112 (m-30) cc_final: 0.7728 (t0) REVERT: C 1129 VAL cc_start: 0.9099 (t) cc_final: 0.8890 (m) REVERT: C 1139 ASP cc_start: 0.8359 (t0) cc_final: 0.7997 (t0) REVERT: B 36 VAL cc_start: 0.8695 (t) cc_final: 0.8437 (m) REVERT: B 55 PHE cc_start: 0.7122 (m-10) cc_final: 0.6734 (m-10) REVERT: B 106 PHE cc_start: 0.6579 (m-10) cc_final: 0.6327 (m-10) REVERT: B 119 ILE cc_start: 0.9048 (mm) cc_final: 0.8774 (mm) REVERT: B 129 LYS cc_start: 0.8674 (mttt) cc_final: 0.8289 (mmmm) REVERT: B 194 PHE cc_start: 0.7001 (m-80) cc_final: 0.6767 (m-80) REVERT: B 195 LYS cc_start: 0.3975 (tptt) cc_final: 0.2724 (tppt) REVERT: B 298 GLU cc_start: 0.8310 (tp30) cc_final: 0.7912 (tp30) REVERT: B 386 LYS cc_start: 0.8365 (pttt) cc_final: 0.8067 (pttt) REVERT: B 537 LYS cc_start: 0.9237 (tptt) cc_final: 0.9013 (tptt) REVERT: B 603 ASN cc_start: 0.8253 (p0) cc_final: 0.7811 (p0) REVERT: B 615 VAL cc_start: 0.9145 (p) cc_final: 0.8883 (m) REVERT: B 690 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7788 (mm-40) REVERT: B 703 ASN cc_start: 0.8909 (t0) cc_final: 0.8368 (t0) REVERT: B 748 GLU cc_start: 0.8045 (pm20) cc_final: 0.7764 (pt0) REVERT: B 765 ARG cc_start: 0.8140 (ttm-80) cc_final: 0.7772 (ttp80) REVERT: B 773 GLU cc_start: 0.8137 (tt0) cc_final: 0.7836 (tm-30) REVERT: B 784 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8324 (tp40) REVERT: B 808 ASP cc_start: 0.7413 (t70) cc_final: 0.6936 (p0) REVERT: B 884 SER cc_start: 0.8791 (m) cc_final: 0.8244 (t) REVERT: B 918 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7681 (mt-10) REVERT: B 964 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8664 (tmmt) REVERT: B 979 ASP cc_start: 0.8270 (m-30) cc_final: 0.7724 (m-30) REVERT: B 984 LEU cc_start: 0.7896 (mt) cc_final: 0.7516 (tp) REVERT: B 990 GLU cc_start: 0.7414 (pp20) cc_final: 0.7198 (pp20) REVERT: B 1017 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7750 (tm-30) REVERT: B 1030 SER cc_start: 0.9162 (m) cc_final: 0.8658 (t) REVERT: B 1092 GLU cc_start: 0.7654 (tp30) cc_final: 0.7252 (tm-30) REVERT: B 1125 ASN cc_start: 0.8000 (p0) cc_final: 0.7659 (p0) REVERT: a 81 MET cc_start: 0.5528 (ppp) cc_final: 0.2927 (tpp) REVERT: a 142 MET cc_start: 0.6464 (mmm) cc_final: 0.5491 (ppp) REVERT: b 59 GLU cc_start: 0.7342 (tp30) cc_final: 0.7100 (tm-30) outliers start: 94 outliers final: 79 residues processed: 675 average time/residue: 0.4861 time to fit residues: 515.7542 Evaluate side-chains 693 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 609 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 182 TYR Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 34 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 249 optimal weight: 40.0000 chunk 88 optimal weight: 0.9990 chunk 293 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 291 optimal weight: 5.9990 chunk 284 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 342 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 907 ASN B1083 HIS a 35 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.165516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.123501 restraints weight = 73436.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.126876 restraints weight = 36702.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 76)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.129194 restraints weight = 22607.225| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.8134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 32154 Z= 0.222 Angle : 0.709 11.919 43788 Z= 0.363 Chirality : 0.047 0.297 4935 Planarity : 0.005 0.095 5629 Dihedral : 4.915 26.595 4311 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.54 % Favored : 95.38 % Rotamer: Outliers : 2.82 % Allowed : 17.87 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 3961 helix: 0.40 (0.21), residues: 683 sheet: 0.24 (0.16), residues: 1038 loop : -1.13 (0.12), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP a 36 HIS 0.056 0.002 HIS B1083 PHE 0.027 0.002 PHE C 565 TYR 0.025 0.002 TYR C 170 ARG 0.015 0.001 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 901) hydrogen bonds : angle 5.76340 ( 2469) SS BOND : bond 0.00575 ( 46) SS BOND : angle 1.57176 ( 92) covalent geometry : bond 0.00496 (32108) covalent geometry : angle 0.70628 (43696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17075.38 seconds wall clock time: 302 minutes 54.60 seconds (18174.60 seconds total)