Starting phenix.real_space_refine on Mon Aug 25 08:55:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eyh_28688/08_2025/8eyh_28688.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eyh_28688/08_2025/8eyh_28688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8eyh_28688/08_2025/8eyh_28688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eyh_28688/08_2025/8eyh_28688.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eyh_28688/08_2025/8eyh_28688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eyh_28688/08_2025/8eyh_28688.map" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.755 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 120 5.16 5 C 16917 2.51 5 N 4394 2.21 5 O 5144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26575 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 868 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "B" Number of atoms: 8515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8515 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 Chain: "C" Number of atoms: 8350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8350 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 56, 'TRANS': 1010} Chain breaks: 5 Chain: "A" Number of atoms: 8366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8366 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 56, 'TRANS': 1012} Chain breaks: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 4.98, per 1000 atoms: 0.19 Number of scatterers: 26575 At special positions: 0 Unit cell: (167.849, 155.02, 228.787, 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 120 16.00 O 5144 8.00 N 4394 7.00 C 16917 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " 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=2.02 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 A 391 " - pdb=" SG CYS A 525 " 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 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1201 " - " ASN A 282 " " NAG A1202 " - " ASN A 331 " " NAG A1203 " - " ASN A 603 " " NAG A1204 " - " ASN A 616 " " NAG A1205 " - " ASN A 709 " " NAG A1206 " - " ASN A 717 " " NAG A1207 " - " ASN A1098 " " NAG A1208 " - " ASN A1134 " " NAG A1209 " - " ASN A 343 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 331 " " NAG C1201 " - " ASN C 331 " " NAG C1202 " - " ASN C 603 " " NAG C1203 " - " ASN C 616 " " NAG C1204 " - " ASN C 657 " " NAG C1205 " - " ASN C 709 " " NAG C1206 " - " ASN C 717 " " NAG C1207 " - " ASN C1134 " " NAG E 1 " - " ASN B1134 " " NAG F 1 " - " ASN B1098 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B 343 " Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6240 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 53 sheets defined 20.4% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'D' and resid 26 through 30 removed outlier: 3.776A pdb=" N SER D 30 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.738A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.674A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 371' Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 631 through 639 removed outlier: 3.755A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 639 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.042A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.677A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.699A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 4.224A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 4.262A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.796A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.831A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.513A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.667A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1034 removed outlier: 4.572A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1149 removed outlier: 3.603A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 336 through 343 removed outlier: 4.285A pdb=" N GLU C 340 " --> pdb=" O CYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 748 through 753 Processing helix chain 'C' and resid 754 through 756 No H-bonds generated for 'chain 'C' and resid 754 through 756' Processing helix chain 'C' and resid 760 through 783 removed outlier: 5.496A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.684A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 855 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.815A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.792A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.868A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.567A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.594A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.778A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C1014 " --> pdb=" O GLN C1010 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C1028 " --> pdb=" O LEU C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.668A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1141 through 1146' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 336 through 340 removed outlier: 4.415A pdb=" N GLY A 339 " --> pdb=" O CYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 4.099A pdb=" N TYR A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 502 through 506' Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 756 Processing helix chain 'A' and resid 762 through 783 removed outlier: 3.928A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 883 removed outlier: 3.681A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.874A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.583A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.826A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 933 removed outlier: 3.627A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.670A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 981 removed outlier: 4.000A pdb=" N LEU A 981 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.443A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.695A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.595A pdb=" N VAL D 113 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.743A pdb=" N ARG B 78 " --> pdb=" O HIS B 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.543A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 49 removed outlier: 4.380A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.543A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.682A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR B 144 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER B 155 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AB1, first strand: chain 'B' and resid 401 through 402 Processing sheet with id=AB2, first strand: chain 'B' and resid 541 through 543 removed outlier: 3.807A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 551 through 553 Processing sheet with id=AB4, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.854A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.625A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AB7, first strand: chain 'B' and resid 720 through 727 removed outlier: 3.638A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.210A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AC1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.751A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.791A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 224 through 229 removed outlier: 3.559A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 101 through 105 removed outlier: 7.585A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.521A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 311 through 313 Processing sheet with id=AC8, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.631A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AD1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AD2, first strand: chain 'C' and resid 551 through 553 removed outlier: 3.576A pdb=" N ASP C 586 " --> pdb=" O THR C 553 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 653 through 655 removed outlier: 3.657A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AD5, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.553A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C1062 " --> pdb=" O GLU C 725 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.553A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C1062 " --> pdb=" O GLU C 725 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AD8, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 3.702A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.804A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.917A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AE3, first strand: chain 'A' and resid 115 through 121 removed outlier: 3.751A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.905A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 144 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 190 through 195 removed outlier: 3.691A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 311 through 316 removed outlier: 5.516A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 401 through 402 removed outlier: 3.741A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AE9, first strand: chain 'A' and resid 539 through 543 Processing sheet with id=AF1, first strand: chain 'A' and resid 642 through 644 Processing sheet with id=AF2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.097A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'A' and resid 664 through 667 removed outlier: 3.687A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.589A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.589A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AF7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AF8, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 3.530A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) 722 hydrogen bonds defined for protein. 1956 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: 5.70 Time building geometry restraints manager: 3.52 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: 6692 1.33 - 1.45: 5458 1.45 - 1.57: 14885 1.57 - 1.69: 2 1.69 - 1.81: 152 Bond restraints: 27189 Sorted by residual: bond pdb=" C5 NAG A1202 " pdb=" O5 NAG A1202 " ideal model delta sigma weight residual 1.413 1.516 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" N ASN B 164 " pdb=" CA ASN B 164 " ideal model delta sigma weight residual 1.457 1.489 -0.032 6.40e-03 2.44e+04 2.51e+01 bond pdb=" C4 NAG A1202 " pdb=" O4 NAG A1202 " ideal model delta sigma weight residual 1.409 1.507 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C2 NAG A1202 " pdb=" C3 NAG A1202 " ideal model delta sigma weight residual 1.526 1.610 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C7 NAG A1202 " pdb=" C8 NAG A1202 " ideal model delta sigma weight residual 1.509 1.429 0.080 2.00e-02 2.50e+03 1.61e+01 ... (remaining 27184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 36404 2.41 - 4.81: 584 4.81 - 7.22: 13 7.22 - 9.62: 2 9.62 - 12.03: 1 Bond angle restraints: 37004 Sorted by residual: angle pdb=" N PRO A 337 " pdb=" CA PRO A 337 " pdb=" C PRO A 337 " ideal model delta sigma weight residual 114.92 107.65 7.27 1.19e+00 7.06e-01 3.74e+01 angle pdb=" O ASN B 164 " pdb=" C ASN B 164 " pdb=" N ASN B 165 " ideal model delta sigma weight residual 121.47 124.91 -3.44 7.50e-01 1.78e+00 2.10e+01 angle pdb=" CA VAL C 382 " pdb=" C VAL C 382 " pdb=" O VAL C 382 " ideal model delta sigma weight residual 121.63 117.11 4.52 9.90e-01 1.02e+00 2.09e+01 angle pdb=" CA ASN A 334 " pdb=" CB ASN A 334 " pdb=" CG ASN A 334 " ideal model delta sigma weight residual 112.60 116.92 -4.32 1.00e+00 1.00e+00 1.87e+01 angle pdb=" C SER A 373 " pdb=" CA SER A 373 " pdb=" CB SER A 373 " ideal model delta sigma weight residual 116.34 110.42 5.92 1.40e+00 5.10e-01 1.79e+01 ... (remaining 36999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.59: 15685 25.59 - 51.17: 703 51.17 - 76.76: 116 76.76 - 102.34: 52 102.34 - 127.93: 26 Dihedral angle restraints: 16582 sinusoidal: 6872 harmonic: 9710 Sorted by residual: dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -161.31 75.31 1 1.00e+01 1.00e-02 7.17e+01 dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -157.78 71.78 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -23.73 -62.27 1 1.00e+01 1.00e-02 5.13e+01 ... (remaining 16579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.273: 4265 0.273 - 0.546: 1 0.546 - 0.820: 1 0.820 - 1.093: 1 1.093 - 1.366: 2 Chirality restraints: 4270 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.77 1.37 2.00e-01 2.50e+01 4.67e+01 chirality pdb=" C1 NAG C1201 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1201 " pdb=" O5 NAG C1201 " both_signs ideal model delta sigma weight residual False -2.40 -3.53 1.13 2.00e-01 2.50e+01 3.21e+01 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -3.32 0.92 2.00e-01 2.50e+01 2.10e+01 ... (remaining 4267 not shown) Planarity restraints: 4790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.015 2.00e-02 2.50e+03 3.31e-02 1.37e+01 pdb=" CG ASN A 331 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.061 2.00e-02 2.50e+03 pdb=" C1 NAG A1202 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " -0.012 2.00e-02 2.50e+03 2.91e-02 1.06e+01 pdb=" CG ASN B1074 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " 0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " -0.046 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 334 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" CG ASN A 334 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 334 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 334 " -0.014 2.00e-02 2.50e+03 ... (remaining 4787 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 527 2.62 - 3.19: 27093 3.19 - 3.76: 39745 3.76 - 4.33: 55116 4.33 - 4.90: 87624 Nonbonded interactions: 210105 Sorted by model distance: nonbonded pdb=" O4 NAG C1201 " pdb=" O7 NAG C1201 " model vdw 2.055 3.040 nonbonded pdb=" OD1 ASN C 717 " pdb=" N PHE C 718 " model vdw 2.106 3.120 nonbonded pdb=" ND1 HIS C1083 " pdb=" OD1 ASP C1084 " model vdw 2.108 3.120 nonbonded pdb=" N GLU B 309 " pdb=" OE1 GLU B 309 " model vdw 2.130 3.120 nonbonded pdb=" O3 NAG B1304 " pdb=" O7 NAG B1304 " model vdw 2.134 3.040 ... (remaining 210100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 675 or resid 690 through 827 or resid 852 throu \ gh 1146 or resid 1203 through 1208)) selection = (chain 'B' and (resid 14 through 617 or resid 641 through 827 or resid 852 throu \ gh 940 or resid 944 through 1146 or resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 675 or resid 690 through 827 or resid 852 throu \ gh 1146 or resid 1203 through 1208)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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=0.00 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: 5.820 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.410 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.487 27241 Z= 0.349 Angle : 0.752 53.106 37141 Z= 0.406 Chirality : 0.057 1.366 4270 Planarity : 0.003 0.038 4762 Dihedral : 15.751 127.929 10285 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 50.91 Ramachandran Plot: Outliers : 0.91 % Allowed : 9.47 % Favored : 89.62 % Rotamer: Outliers : 2.85 % Allowed : 16.33 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.15), residues: 3306 helix: 0.62 (0.24), residues: 540 sheet: -1.38 (0.24), residues: 538 loop : -2.52 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 328 TYR 0.012 0.001 TYR C 695 PHE 0.021 0.001 PHE B1075 TRP 0.009 0.001 TRP C 886 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00449 (27189) covalent geometry : angle 0.61657 (37004) SS BOND : bond 0.00303 ( 19) SS BOND : angle 1.08659 ( 38) hydrogen bonds : bond 0.28060 ( 694) hydrogen bonds : angle 10.76030 ( 1956) link_BETA1-4 : bond 0.00435 ( 5) link_BETA1-4 : angle 1.19773 ( 15) link_NAG-ASN : bond 0.12105 ( 28) link_NAG-ASN : angle 9.04729 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 302 time to evaluate : 0.958 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: B 602 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8323 (m) REVERT: B 740 MET cc_start: 0.7910 (ppp) cc_final: 0.7555 (ppp) REVERT: B 935 GLN cc_start: 0.8268 (tt0) cc_final: 0.8039 (tt0) REVERT: C 341 VAL cc_start: 0.3773 (OUTLIER) cc_final: 0.3487 (t) REVERT: C 343 ASN cc_start: 0.3967 (OUTLIER) cc_final: 0.1845 (t0) REVERT: C 386 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.6014 (pttt) REVERT: C 882 ILE cc_start: 0.9384 (mt) cc_final: 0.9183 (mp) REVERT: C 974 SER cc_start: 0.3556 (OUTLIER) cc_final: 0.3255 (m) REVERT: A 265 TYR cc_start: 0.3066 (p90) cc_final: 0.2853 (p90) outliers start: 83 outliers final: 34 residues processed: 369 average time/residue: 0.1502 time to fit residues: 92.2503 Evaluate side-chains 327 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 288 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 734 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.0370 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.0970 overall best weight: 0.1414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 501 ASN B 544 ASN B 563 GLN B 907 ASN B 954 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN C 804 GLN C1036 GLN A 334 ASN A 450 ASN A 487 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 658 ASN A 764 ASN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.286612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.230052 restraints weight = 37519.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.226738 restraints weight = 39774.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.223898 restraints weight = 38791.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.221128 restraints weight = 32941.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.222425 restraints weight = 30457.595| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 27241 Z= 0.159 Angle : 0.764 17.992 37141 Z= 0.367 Chirality : 0.050 0.399 4270 Planarity : 0.005 0.108 4762 Dihedral : 13.585 115.183 4372 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.17 % Favored : 90.47 % Rotamer: Outliers : 3.81 % Allowed : 15.51 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.14), residues: 3306 helix: 0.26 (0.22), residues: 589 sheet: -1.26 (0.22), residues: 575 loop : -2.56 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1000 TYR 0.023 0.002 TYR A1067 PHE 0.028 0.002 PHE C 888 TRP 0.019 0.001 TRP D 36 HIS 0.014 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00341 (27189) covalent geometry : angle 0.72671 (37004) SS BOND : bond 0.00294 ( 19) SS BOND : angle 1.38396 ( 38) hydrogen bonds : bond 0.05817 ( 694) hydrogen bonds : angle 7.15599 ( 1956) link_BETA1-4 : bond 0.00907 ( 5) link_BETA1-4 : angle 2.30573 ( 15) link_NAG-ASN : bond 0.00882 ( 28) link_NAG-ASN : angle 4.86207 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 298 time to evaluate : 0.700 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: B 205 SER cc_start: 0.8398 (p) cc_final: 0.8131 (p) REVERT: B 340 GLU cc_start: 0.5686 (OUTLIER) cc_final: 0.3753 (tp30) REVERT: B 602 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8495 (m) REVERT: B 663 ASP cc_start: 0.8168 (t0) cc_final: 0.7774 (t0) REVERT: B 894 LEU cc_start: 0.7862 (mt) cc_final: 0.7494 (mt) REVERT: B 912 THR cc_start: 0.7107 (OUTLIER) cc_final: 0.5645 (m) REVERT: B 914 ASN cc_start: 0.7568 (p0) cc_final: 0.7166 (p0) REVERT: B 915 VAL cc_start: 0.7562 (OUTLIER) cc_final: 0.7096 (m) REVERT: B 935 GLN cc_start: 0.8313 (tt0) cc_final: 0.8013 (tt0) REVERT: B 1083 HIS cc_start: 0.6865 (OUTLIER) cc_final: 0.5884 (m-70) REVERT: B 1092 GLU cc_start: 0.8053 (pt0) cc_final: 0.7781 (pt0) REVERT: B 1137 VAL cc_start: 0.1953 (OUTLIER) cc_final: 0.1697 (p) REVERT: C 343 ASN cc_start: 0.3559 (OUTLIER) cc_final: 0.2002 (t0) REVERT: C 386 LYS cc_start: 0.6675 (OUTLIER) cc_final: 0.6268 (pptt) REVERT: C 661 GLU cc_start: 0.7234 (tm-30) cc_final: 0.7033 (tm-30) REVERT: C 737 ASP cc_start: 0.4972 (OUTLIER) cc_final: 0.4041 (m-30) REVERT: C 974 SER cc_start: 0.2958 (OUTLIER) cc_final: 0.2642 (m) REVERT: C 978 ASN cc_start: 0.4232 (OUTLIER) cc_final: 0.3806 (m-40) REVERT: C 1055 SER cc_start: 0.9164 (p) cc_final: 0.8832 (p) REVERT: C 1113 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8865 (mm-40) REVERT: A 220 PHE cc_start: 0.1444 (OUTLIER) cc_final: -0.0331 (t80) REVERT: A 425 LEU cc_start: 0.5996 (OUTLIER) cc_final: 0.5298 (pp) REVERT: A 535 LYS cc_start: 0.6602 (tmmm) cc_final: 0.6348 (ttmt) REVERT: A 1038 LYS cc_start: 0.8405 (mmmt) cc_final: 0.7766 (mptt) REVERT: A 1091 ARG cc_start: 0.7087 (tpp-160) cc_final: 0.6879 (tpp80) REVERT: A 1092 GLU cc_start: 0.7203 (pp20) cc_final: 0.6746 (pp20) REVERT: A 1113 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8045 (mm-40) outliers start: 111 outliers final: 57 residues processed: 377 average time/residue: 0.1332 time to fit residues: 83.5055 Evaluate side-chains 345 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 275 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1126 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 283 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 247 optimal weight: 10.0000 chunk 318 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 330 optimal weight: 0.9990 chunk 259 optimal weight: 10.0000 chunk 276 optimal weight: 2.9990 chunk 305 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN B 125 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 949 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C 919 ASN A 122 ASN A 165 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 804 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.278982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.216349 restraints weight = 36995.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.204946 restraints weight = 41029.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.207458 restraints weight = 33993.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.207508 restraints weight = 24764.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.207805 restraints weight = 22284.398| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 27241 Z= 0.240 Angle : 0.767 12.910 37141 Z= 0.373 Chirality : 0.051 0.483 4270 Planarity : 0.005 0.087 4762 Dihedral : 12.148 115.781 4346 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.71 % Favored : 89.02 % Rotamer: Outliers : 5.87 % Allowed : 15.16 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.72 (0.14), residues: 3306 helix: 0.16 (0.22), residues: 584 sheet: -1.41 (0.21), residues: 582 loop : -2.67 (0.12), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 509 TYR 0.029 0.002 TYR C 904 PHE 0.031 0.002 PHE C 888 TRP 0.023 0.002 TRP B 64 HIS 0.012 0.002 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00568 (27189) covalent geometry : angle 0.73462 (37004) SS BOND : bond 0.00540 ( 19) SS BOND : angle 1.69899 ( 38) hydrogen bonds : bond 0.05377 ( 694) hydrogen bonds : angle 6.72266 ( 1956) link_BETA1-4 : bond 0.00829 ( 5) link_BETA1-4 : angle 2.61117 ( 15) link_NAG-ASN : bond 0.00668 ( 28) link_NAG-ASN : angle 4.41933 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 293 time to evaluate : 1.028 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: B 340 GLU cc_start: 0.5908 (OUTLIER) cc_final: 0.4040 (tp30) REVERT: B 568 ASP cc_start: -0.1213 (OUTLIER) cc_final: -0.3091 (p0) REVERT: B 872 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7989 (tp-100) REVERT: B 894 LEU cc_start: 0.8136 (mt) cc_final: 0.7739 (mt) REVERT: B 895 GLN cc_start: 0.5820 (OUTLIER) cc_final: 0.5519 (mt0) REVERT: B 912 THR cc_start: 0.7201 (OUTLIER) cc_final: 0.6414 (m) REVERT: B 935 GLN cc_start: 0.8411 (tt0) cc_final: 0.8042 (tt0) REVERT: B 1083 HIS cc_start: 0.7043 (OUTLIER) cc_final: 0.5394 (m-70) REVERT: B 1137 VAL cc_start: 0.2923 (OUTLIER) cc_final: 0.2602 (p) REVERT: C 58 PHE cc_start: 0.6280 (OUTLIER) cc_final: 0.4390 (m-80) REVERT: C 343 ASN cc_start: 0.3843 (OUTLIER) cc_final: 0.2433 (t0) REVERT: C 642 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8910 (p) REVERT: C 737 ASP cc_start: 0.5425 (OUTLIER) cc_final: 0.4198 (m-30) REVERT: C 919 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.7061 (p0) REVERT: C 935 GLN cc_start: 0.8409 (tt0) cc_final: 0.8133 (tt0) REVERT: C 978 ASN cc_start: 0.4547 (OUTLIER) cc_final: 0.4098 (m-40) REVERT: C 1055 SER cc_start: 0.9077 (OUTLIER) cc_final: 0.8761 (p) REVERT: A 175 PHE cc_start: 0.2372 (OUTLIER) cc_final: 0.1179 (p90) REVERT: A 220 PHE cc_start: 0.1520 (OUTLIER) cc_final: -0.0286 (t80) REVERT: A 265 TYR cc_start: 0.3655 (p90) cc_final: 0.3451 (p90) REVERT: A 294 ASP cc_start: 0.7919 (p0) cc_final: 0.7532 (p0) REVERT: A 425 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.5995 (pp) REVERT: A 528 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7072 (ttmt) REVERT: A 535 LYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6479 (ttmt) REVERT: A 811 LYS cc_start: 0.7104 (tptp) cc_final: 0.6546 (mmtp) REVERT: A 1089 PHE cc_start: 0.7573 (m-80) cc_final: 0.7078 (m-80) outliers start: 171 outliers final: 91 residues processed: 427 average time/residue: 0.1581 time to fit residues: 113.7992 Evaluate side-chains 394 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 284 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 200 optimal weight: 0.9990 chunk 93 optimal weight: 0.0070 chunk 175 optimal weight: 0.0270 chunk 123 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 271 optimal weight: 9.9990 chunk 193 optimal weight: 0.7980 chunk 278 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN A 165 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN A 926 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.282416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.221719 restraints weight = 36878.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.215579 restraints weight = 40520.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.217501 restraints weight = 34197.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.217944 restraints weight = 23484.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.218101 restraints weight = 21601.945| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27241 Z= 0.135 Angle : 0.688 13.946 37141 Z= 0.330 Chirality : 0.048 0.448 4270 Planarity : 0.004 0.082 4762 Dihedral : 11.142 114.057 4330 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.04 % Favored : 90.68 % Rotamer: Outliers : 4.43 % Allowed : 16.78 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.14), residues: 3306 helix: 0.44 (0.22), residues: 587 sheet: -1.21 (0.22), residues: 554 loop : -2.60 (0.12), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1014 TYR 0.023 0.001 TYR A1067 PHE 0.027 0.001 PHE C 888 TRP 0.018 0.001 TRP B 64 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00297 (27189) covalent geometry : angle 0.65664 (37004) SS BOND : bond 0.00320 ( 19) SS BOND : angle 1.31330 ( 38) hydrogen bonds : bond 0.04324 ( 694) hydrogen bonds : angle 6.28079 ( 1956) link_BETA1-4 : bond 0.00570 ( 5) link_BETA1-4 : angle 2.68531 ( 15) link_NAG-ASN : bond 0.00646 ( 28) link_NAG-ASN : angle 4.18662 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 302 time to evaluate : 0.991 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: B 340 GLU cc_start: 0.5799 (OUTLIER) cc_final: 0.3917 (tp30) REVERT: B 663 ASP cc_start: 0.8126 (t0) cc_final: 0.7837 (t0) REVERT: B 912 THR cc_start: 0.6997 (OUTLIER) cc_final: 0.6084 (m) REVERT: B 935 GLN cc_start: 0.8339 (tt0) cc_final: 0.7954 (tt0) REVERT: B 1066 THR cc_start: 0.8852 (m) cc_final: 0.8575 (p) REVERT: B 1076 THR cc_start: 0.8855 (m) cc_final: 0.8626 (p) REVERT: B 1083 HIS cc_start: 0.6768 (OUTLIER) cc_final: 0.6057 (m-70) REVERT: B 1137 VAL cc_start: 0.3050 (OUTLIER) cc_final: 0.2795 (p) REVERT: C 58 PHE cc_start: 0.6075 (OUTLIER) cc_final: 0.4363 (m-80) REVERT: C 275 PHE cc_start: 0.6963 (m-80) cc_final: 0.6714 (m-80) REVERT: C 343 ASN cc_start: 0.3764 (OUTLIER) cc_final: 0.2722 (t0) REVERT: C 737 ASP cc_start: 0.5117 (OUTLIER) cc_final: 0.4191 (m-30) REVERT: C 978 ASN cc_start: 0.4431 (OUTLIER) cc_final: 0.3949 (m-40) REVERT: C 1045 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8325 (mmtm) REVERT: C 1111 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8238 (tt0) REVERT: A 175 PHE cc_start: 0.1947 (OUTLIER) cc_final: 0.1162 (p90) REVERT: A 220 PHE cc_start: 0.1286 (OUTLIER) cc_final: -0.0764 (t80) REVERT: A 294 ASP cc_start: 0.7788 (p0) cc_final: 0.7427 (p0) REVERT: A 298 GLU cc_start: 0.8287 (tt0) cc_final: 0.8012 (tt0) REVERT: A 425 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5564 (pp) REVERT: A 528 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6900 (ttmt) REVERT: A 1038 LYS cc_start: 0.8331 (mmmt) cc_final: 0.7956 (mptt) REVERT: A 1113 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8049 (mm-40) outliers start: 129 outliers final: 78 residues processed: 395 average time/residue: 0.1600 time to fit residues: 106.0220 Evaluate side-chains 372 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 282 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 30 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 200 optimal weight: 0.9990 chunk 264 optimal weight: 0.0870 chunk 268 optimal weight: 7.9990 chunk 229 optimal weight: 5.9990 chunk 181 optimal weight: 0.0020 chunk 197 optimal weight: 1.9990 chunk 245 optimal weight: 0.4980 chunk 240 optimal weight: 4.9990 overall best weight: 0.5170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 954 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 926 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.283766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.222985 restraints weight = 36928.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.215480 restraints weight = 38110.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.217823 restraints weight = 32674.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.218440 restraints weight = 22404.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.218476 restraints weight = 20314.564| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27241 Z= 0.144 Angle : 0.680 13.140 37141 Z= 0.327 Chirality : 0.048 0.434 4270 Planarity : 0.005 0.075 4762 Dihedral : 10.473 113.310 4326 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.68 % Favored : 90.08 % Rotamer: Outliers : 4.77 % Allowed : 17.22 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.14), residues: 3306 helix: 0.63 (0.22), residues: 574 sheet: -1.17 (0.21), residues: 588 loop : -2.59 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 577 TYR 0.022 0.001 TYR A1067 PHE 0.036 0.001 PHE A 55 TRP 0.020 0.001 TRP B 64 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00324 (27189) covalent geometry : angle 0.64857 (37004) SS BOND : bond 0.00349 ( 19) SS BOND : angle 1.16223 ( 38) hydrogen bonds : bond 0.04106 ( 694) hydrogen bonds : angle 6.03872 ( 1956) link_BETA1-4 : bond 0.00348 ( 5) link_BETA1-4 : angle 2.92082 ( 15) link_NAG-ASN : bond 0.00629 ( 28) link_NAG-ASN : angle 4.09154 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 300 time to evaluate : 0.595 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: B 340 GLU cc_start: 0.5954 (OUTLIER) cc_final: 0.4382 (tp30) REVERT: B 568 ASP cc_start: -0.1047 (OUTLIER) cc_final: -0.2080 (t70) REVERT: B 663 ASP cc_start: 0.8153 (t0) cc_final: 0.7834 (t0) REVERT: B 872 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8156 (tp-100) REVERT: B 895 GLN cc_start: 0.5790 (OUTLIER) cc_final: 0.5420 (mt0) REVERT: B 912 THR cc_start: 0.6796 (OUTLIER) cc_final: 0.6078 (m) REVERT: B 935 GLN cc_start: 0.8415 (tt0) cc_final: 0.8026 (tt0) REVERT: B 1066 THR cc_start: 0.8894 (m) cc_final: 0.8526 (p) REVERT: B 1076 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8571 (p) REVERT: B 1083 HIS cc_start: 0.6901 (OUTLIER) cc_final: 0.5945 (m-70) REVERT: C 58 PHE cc_start: 0.6060 (OUTLIER) cc_final: 0.4318 (m-80) REVERT: C 343 ASN cc_start: 0.4019 (OUTLIER) cc_final: 0.2998 (t0) REVERT: C 737 ASP cc_start: 0.5300 (OUTLIER) cc_final: 0.4517 (m-30) REVERT: C 919 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.6308 (p0) REVERT: C 935 GLN cc_start: 0.8336 (tt0) cc_final: 0.8086 (tt0) REVERT: C 978 ASN cc_start: 0.4535 (OUTLIER) cc_final: 0.4092 (m-40) REVERT: C 1045 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8312 (mmtm) REVERT: C 1111 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8300 (tt0) REVERT: A 52 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6637 (tm-30) REVERT: A 175 PHE cc_start: 0.2055 (OUTLIER) cc_final: 0.1251 (p90) REVERT: A 220 PHE cc_start: 0.1341 (OUTLIER) cc_final: -0.0647 (t80) REVERT: A 298 GLU cc_start: 0.8357 (tt0) cc_final: 0.8147 (tt0) REVERT: A 425 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5321 (pp) REVERT: A 528 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.7030 (ttmt) REVERT: A 960 ASN cc_start: 0.8567 (t0) cc_final: 0.8141 (t0) REVERT: A 1089 PHE cc_start: 0.7476 (m-80) cc_final: 0.6998 (m-80) REVERT: A 1092 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6686 (pp20) REVERT: A 1113 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8088 (mm-40) outliers start: 139 outliers final: 91 residues processed: 402 average time/residue: 0.1467 time to fit residues: 98.5626 Evaluate side-chains 393 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 284 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 211 optimal weight: 1.9990 chunk 302 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 263 optimal weight: 20.0000 chunk 177 optimal weight: 2.9990 chunk 238 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 171 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 437 ASN B 777 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 GLN A 165 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 675 GLN A 787 GLN A 953 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.271782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.209481 restraints weight = 36379.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.205721 restraints weight = 44189.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.202264 restraints weight = 39384.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.197514 restraints weight = 37838.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.200047 restraints weight = 29919.799| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 27241 Z= 0.335 Angle : 0.867 13.441 37141 Z= 0.430 Chirality : 0.054 0.502 4270 Planarity : 0.006 0.087 4762 Dihedral : 10.581 116.335 4325 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.19 % Favored : 87.51 % Rotamer: Outliers : 6.21 % Allowed : 17.26 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.00 (0.13), residues: 3306 helix: -0.23 (0.21), residues: 585 sheet: -1.57 (0.20), residues: 594 loop : -2.81 (0.12), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1039 TYR 0.033 0.002 TYR C 904 PHE 0.034 0.003 PHE C 888 TRP 0.020 0.002 TRP B 64 HIS 0.020 0.002 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00798 (27189) covalent geometry : angle 0.83286 (37004) SS BOND : bond 0.00579 ( 19) SS BOND : angle 2.01150 ( 38) hydrogen bonds : bond 0.05404 ( 694) hydrogen bonds : angle 6.60629 ( 1956) link_BETA1-4 : bond 0.00583 ( 5) link_BETA1-4 : angle 3.55810 ( 15) link_NAG-ASN : bond 0.00764 ( 28) link_NAG-ASN : angle 4.75333 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 298 time to evaluate : 1.029 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: D 83 MET cc_start: 0.4950 (pmm) cc_final: 0.4467 (pmm) REVERT: B 269 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7712 (t80) REVERT: B 271 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7762 (mm-40) REVERT: B 326 ILE cc_start: -0.1831 (OUTLIER) cc_final: -0.2259 (mt) REVERT: B 340 GLU cc_start: 0.6104 (OUTLIER) cc_final: 0.5717 (tm-30) REVERT: B 568 ASP cc_start: -0.1267 (OUTLIER) cc_final: -0.2939 (p0) REVERT: B 663 ASP cc_start: 0.8291 (t0) cc_final: 0.8003 (t0) REVERT: B 664 ILE cc_start: 0.9090 (mt) cc_final: 0.8837 (mt) REVERT: B 912 THR cc_start: 0.6931 (OUTLIER) cc_final: 0.6401 (m) REVERT: B 935 GLN cc_start: 0.8489 (tt0) cc_final: 0.8105 (tt0) REVERT: B 1024 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8686 (tt) REVERT: B 1083 HIS cc_start: 0.6963 (OUTLIER) cc_final: 0.6691 (m-70) REVERT: C 58 PHE cc_start: 0.6495 (OUTLIER) cc_final: 0.4511 (m-80) REVERT: C 78 ARG cc_start: 0.4941 (OUTLIER) cc_final: 0.3773 (ptt-90) REVERT: C 343 ASN cc_start: 0.3919 (OUTLIER) cc_final: 0.3172 (t0) REVERT: C 605 SER cc_start: 0.9291 (OUTLIER) cc_final: 0.8845 (m) REVERT: C 703 ASN cc_start: 0.8281 (p0) cc_final: 0.7981 (p0) REVERT: C 737 ASP cc_start: 0.5518 (OUTLIER) cc_final: 0.4439 (m-30) REVERT: C 856 ASN cc_start: 0.7653 (p0) cc_final: 0.7263 (p0) REVERT: C 873 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.7385 (m-10) REVERT: C 919 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.7804 (m110) REVERT: C 935 GLN cc_start: 0.8384 (tt0) cc_final: 0.8144 (tt0) REVERT: C 978 ASN cc_start: 0.5035 (OUTLIER) cc_final: 0.4450 (m-40) REVERT: A 52 GLN cc_start: 0.7515 (pm20) cc_final: 0.7048 (tm-30) REVERT: A 175 PHE cc_start: 0.2385 (OUTLIER) cc_final: 0.1662 (p90) REVERT: A 220 PHE cc_start: 0.1731 (OUTLIER) cc_final: -0.0359 (t80) REVERT: A 425 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5863 (pp) REVERT: A 528 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7172 (ttmt) REVERT: A 670 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6505 (mm) REVERT: A 674 TYR cc_start: 0.7674 (t80) cc_final: 0.7270 (t80) REVERT: A 811 LYS cc_start: 0.7649 (tptp) cc_final: 0.6947 (mmtp) REVERT: A 960 ASN cc_start: 0.8502 (t0) cc_final: 0.8082 (t0) REVERT: A 1038 LYS cc_start: 0.8221 (mmmm) cc_final: 0.7909 (mptt) outliers start: 181 outliers final: 114 residues processed: 432 average time/residue: 0.1400 time to fit residues: 101.5930 Evaluate side-chains 413 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 279 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 262 optimal weight: 10.0000 chunk 305 optimal weight: 0.5980 chunk 58 optimal weight: 8.9990 chunk 307 optimal weight: 0.7980 chunk 199 optimal weight: 0.5980 chunk 182 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 198 optimal weight: 0.4980 chunk 167 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** 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 = 0.4774 r_free = 0.4774 target = 0.277442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.215389 restraints weight = 36634.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.208856 restraints weight = 39117.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.210952 restraints weight = 34051.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.209919 restraints weight = 23071.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.210150 restraints weight = 21514.040| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27241 Z= 0.163 Angle : 0.712 12.506 37141 Z= 0.345 Chirality : 0.049 0.469 4270 Planarity : 0.005 0.071 4762 Dihedral : 9.966 114.331 4321 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.50 % Favored : 90.20 % Rotamer: Outliers : 4.70 % Allowed : 19.04 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.14), residues: 3306 helix: 0.22 (0.22), residues: 589 sheet: -1.38 (0.21), residues: 574 loop : -2.73 (0.12), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 646 TYR 0.025 0.001 TYR A1067 PHE 0.027 0.001 PHE C 888 TRP 0.019 0.001 TRP B 64 HIS 0.007 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00371 (27189) covalent geometry : angle 0.67682 (37004) SS BOND : bond 0.00331 ( 19) SS BOND : angle 1.41850 ( 38) hydrogen bonds : bond 0.04259 ( 694) hydrogen bonds : angle 6.11485 ( 1956) link_BETA1-4 : bond 0.00357 ( 5) link_BETA1-4 : angle 3.32941 ( 15) link_NAG-ASN : bond 0.00636 ( 28) link_NAG-ASN : angle 4.38054 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 308 time to evaluate : 0.644 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: D 83 MET cc_start: 0.4663 (pmm) cc_final: 0.4206 (pmm) REVERT: B 271 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7682 (mm-40) REVERT: B 340 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.4358 (tp30) REVERT: B 568 ASP cc_start: -0.1127 (OUTLIER) cc_final: -0.3108 (p0) REVERT: B 663 ASP cc_start: 0.8173 (t0) cc_final: 0.7916 (t0) REVERT: B 872 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8100 (tp-100) REVERT: B 895 GLN cc_start: 0.5656 (OUTLIER) cc_final: 0.5404 (mt0) REVERT: B 912 THR cc_start: 0.7126 (OUTLIER) cc_final: 0.6489 (m) REVERT: B 916 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.6998 (tp) REVERT: B 935 GLN cc_start: 0.8400 (tt0) cc_final: 0.7987 (tt0) REVERT: B 1024 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8588 (tt) REVERT: B 1066 THR cc_start: 0.8918 (m) cc_final: 0.8687 (p) REVERT: B 1083 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6496 (m-70) REVERT: C 58 PHE cc_start: 0.6153 (OUTLIER) cc_final: 0.4291 (m-80) REVERT: C 343 ASN cc_start: 0.3896 (OUTLIER) cc_final: 0.3334 (t0) REVERT: C 565 PHE cc_start: 0.6313 (m-80) cc_final: 0.6041 (m-80) REVERT: C 703 ASN cc_start: 0.8331 (p0) cc_final: 0.8041 (p0) REVERT: C 737 ASP cc_start: 0.5580 (OUTLIER) cc_final: 0.4784 (m-30) REVERT: C 856 ASN cc_start: 0.7484 (p0) cc_final: 0.7051 (p0) REVERT: C 935 GLN cc_start: 0.8352 (tt0) cc_final: 0.8094 (tt0) REVERT: C 978 ASN cc_start: 0.5042 (OUTLIER) cc_final: 0.4509 (m-40) REVERT: A 52 GLN cc_start: 0.7491 (pm20) cc_final: 0.7022 (tm-30) REVERT: A 175 PHE cc_start: 0.2456 (OUTLIER) cc_final: 0.1686 (p90) REVERT: A 216 LEU cc_start: 0.6151 (mt) cc_final: 0.5916 (mt) REVERT: A 220 PHE cc_start: 0.1553 (OUTLIER) cc_final: -0.0525 (t80) REVERT: A 528 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7159 (ttmt) REVERT: A 577 ARG cc_start: 0.6401 (tpp-160) cc_final: 0.4526 (tpp-160) REVERT: A 811 LYS cc_start: 0.7503 (tptp) cc_final: 0.6886 (mmtp) REVERT: A 960 ASN cc_start: 0.8428 (t0) cc_final: 0.8020 (t0) REVERT: A 1038 LYS cc_start: 0.8220 (mmmm) cc_final: 0.7857 (mptt) REVERT: A 1113 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8139 (mm-40) outliers start: 137 outliers final: 96 residues processed: 405 average time/residue: 0.1311 time to fit residues: 89.3081 Evaluate side-chains 400 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 289 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 224 optimal weight: 0.9980 chunk 216 optimal weight: 0.5980 chunk 308 optimal weight: 0.5980 chunk 279 optimal weight: 2.9990 chunk 306 optimal weight: 0.6980 chunk 290 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 312 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 901 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 784 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.277485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.223402 restraints weight = 36647.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.210427 restraints weight = 51782.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.205650 restraints weight = 37815.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.205164 restraints weight = 30942.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.206333 restraints weight = 22833.686| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27241 Z= 0.162 Angle : 0.699 12.629 37141 Z= 0.339 Chirality : 0.049 0.463 4270 Planarity : 0.005 0.070 4762 Dihedral : 9.577 113.543 4321 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.53 % Favored : 89.17 % Rotamer: Outliers : 4.53 % Allowed : 19.59 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.14), residues: 3306 helix: 0.34 (0.22), residues: 589 sheet: -1.26 (0.21), residues: 563 loop : -2.68 (0.12), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 646 TYR 0.024 0.001 TYR A1067 PHE 0.027 0.001 PHE C 888 TRP 0.018 0.001 TRP B 64 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00374 (27189) covalent geometry : angle 0.66493 (37004) SS BOND : bond 0.00306 ( 19) SS BOND : angle 1.25681 ( 38) hydrogen bonds : bond 0.04090 ( 694) hydrogen bonds : angle 5.95486 ( 1956) link_BETA1-4 : bond 0.00378 ( 5) link_BETA1-4 : angle 3.36217 ( 15) link_NAG-ASN : bond 0.00625 ( 28) link_NAG-ASN : angle 4.29572 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 301 time to evaluate : 0.715 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: D 83 MET cc_start: 0.5026 (pmm) cc_final: 0.4479 (pmm) REVERT: B 192 PHE cc_start: 0.6283 (m-10) cc_final: 0.6008 (m-10) REVERT: B 271 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7615 (mm-40) REVERT: B 340 GLU cc_start: 0.6112 (OUTLIER) cc_final: 0.4625 (tp30) REVERT: B 568 ASP cc_start: -0.0993 (OUTLIER) cc_final: -0.2619 (p0) REVERT: B 872 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8183 (tp-100) REVERT: B 895 GLN cc_start: 0.5730 (OUTLIER) cc_final: 0.5396 (mt0) REVERT: B 907 ASN cc_start: 0.7906 (t0) cc_final: 0.7649 (t0) REVERT: B 912 THR cc_start: 0.6974 (OUTLIER) cc_final: 0.6450 (m) REVERT: B 916 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7116 (tt) REVERT: B 935 GLN cc_start: 0.8367 (tt0) cc_final: 0.7991 (tt0) REVERT: B 1066 THR cc_start: 0.8988 (m) cc_final: 0.8644 (p) REVERT: B 1083 HIS cc_start: 0.7136 (OUTLIER) cc_final: 0.6630 (m-70) REVERT: C 58 PHE cc_start: 0.6085 (OUTLIER) cc_final: 0.4253 (m-80) REVERT: C 78 ARG cc_start: 0.4769 (OUTLIER) cc_final: 0.4209 (ptt-90) REVERT: C 343 ASN cc_start: 0.4139 (OUTLIER) cc_final: 0.3858 (t0) REVERT: C 565 PHE cc_start: 0.6406 (m-80) cc_final: 0.6136 (m-80) REVERT: C 655 HIS cc_start: 0.6868 (OUTLIER) cc_final: 0.6139 (t-90) REVERT: C 703 ASN cc_start: 0.8322 (p0) cc_final: 0.8047 (p0) REVERT: C 737 ASP cc_start: 0.5610 (OUTLIER) cc_final: 0.4645 (m-30) REVERT: C 856 ASN cc_start: 0.7571 (p0) cc_final: 0.7126 (p0) REVERT: C 935 GLN cc_start: 0.8326 (tt0) cc_final: 0.8086 (tt0) REVERT: C 1111 GLU cc_start: 0.8586 (tt0) cc_final: 0.8283 (tp30) REVERT: A 52 GLN cc_start: 0.7499 (pm20) cc_final: 0.7059 (tm-30) REVERT: A 175 PHE cc_start: 0.2558 (OUTLIER) cc_final: 0.1726 (p90) REVERT: A 220 PHE cc_start: 0.1521 (OUTLIER) cc_final: -0.0601 (t80) REVERT: A 528 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.7048 (ttmt) REVERT: A 577 ARG cc_start: 0.6328 (tpp-160) cc_final: 0.4498 (tpp-160) REVERT: A 811 LYS cc_start: 0.7493 (tptp) cc_final: 0.6894 (mmtp) REVERT: A 918 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7878 (mp0) REVERT: A 960 ASN cc_start: 0.8421 (t0) cc_final: 0.8024 (t0) REVERT: A 1113 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8130 (mm-40) outliers start: 132 outliers final: 99 residues processed: 396 average time/residue: 0.1333 time to fit residues: 89.1331 Evaluate side-chains 404 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 290 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 267 optimal weight: 0.0070 chunk 74 optimal weight: 3.9990 chunk 269 optimal weight: 0.0970 chunk 167 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 316 optimal weight: 0.7980 chunk 108 optimal weight: 0.0980 chunk 212 optimal weight: 0.9990 chunk 242 optimal weight: 0.7980 chunk 241 optimal weight: 3.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 992 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 784 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A 957 GLN ** 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 = 0.4804 r_free = 0.4804 target = 0.280957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.218630 restraints weight = 36758.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.208391 restraints weight = 38880.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.211287 restraints weight = 37813.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.211930 restraints weight = 23606.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.212667 restraints weight = 19936.546| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27241 Z= 0.131 Angle : 0.678 12.584 37141 Z= 0.327 Chirality : 0.048 0.456 4270 Planarity : 0.005 0.070 4762 Dihedral : 9.246 112.483 4321 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.07 % Favored : 90.59 % Rotamer: Outliers : 4.19 % Allowed : 19.73 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.14), residues: 3306 helix: 0.59 (0.22), residues: 580 sheet: -1.13 (0.21), residues: 561 loop : -2.59 (0.12), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1014 TYR 0.041 0.001 TYR B 91 PHE 0.024 0.001 PHE C 888 TRP 0.027 0.001 TRP B 436 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00292 (27189) covalent geometry : angle 0.64424 (37004) SS BOND : bond 0.00255 ( 19) SS BOND : angle 1.12943 ( 38) hydrogen bonds : bond 0.03833 ( 694) hydrogen bonds : angle 5.77868 ( 1956) link_BETA1-4 : bond 0.00364 ( 5) link_BETA1-4 : angle 3.31929 ( 15) link_NAG-ASN : bond 0.00632 ( 28) link_NAG-ASN : angle 4.19605 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 300 time to evaluate : 0.945 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: D 83 MET cc_start: 0.4771 (pmm) cc_final: 0.4396 (pmm) REVERT: B 271 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7525 (mm-40) REVERT: B 568 ASP cc_start: -0.1399 (OUTLIER) cc_final: -0.3097 (p0) REVERT: B 740 MET cc_start: 0.7879 (ptm) cc_final: 0.7669 (ptm) REVERT: B 872 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8130 (tp-100) REVERT: B 907 ASN cc_start: 0.7923 (t0) cc_final: 0.7628 (t0) REVERT: B 912 THR cc_start: 0.7000 (OUTLIER) cc_final: 0.6443 (m) REVERT: B 916 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.6788 (tp) REVERT: B 935 GLN cc_start: 0.8296 (tt0) cc_final: 0.7894 (tt0) REVERT: B 1076 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8659 (p) REVERT: B 1083 HIS cc_start: 0.7036 (OUTLIER) cc_final: 0.6604 (m-70) REVERT: C 58 PHE cc_start: 0.6162 (OUTLIER) cc_final: 0.4391 (m-80) REVERT: C 78 ARG cc_start: 0.4919 (OUTLIER) cc_final: 0.4488 (ptt-90) REVERT: C 565 PHE cc_start: 0.6229 (m-80) cc_final: 0.5957 (m-80) REVERT: C 655 HIS cc_start: 0.6708 (OUTLIER) cc_final: 0.6001 (t-90) REVERT: C 737 ASP cc_start: 0.5524 (OUTLIER) cc_final: 0.4623 (m-30) REVERT: C 1111 GLU cc_start: 0.8529 (tt0) cc_final: 0.8272 (tp30) REVERT: A 52 GLN cc_start: 0.7495 (pm20) cc_final: 0.7049 (tm-30) REVERT: A 175 PHE cc_start: 0.2461 (OUTLIER) cc_final: 0.1641 (p90) REVERT: A 220 PHE cc_start: 0.1704 (OUTLIER) cc_final: -0.0598 (t80) REVERT: A 528 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.7187 (ttmt) REVERT: A 577 ARG cc_start: 0.6235 (tpp-160) cc_final: 0.4385 (tpp-160) REVERT: A 811 LYS cc_start: 0.7385 (tptp) cc_final: 0.6816 (mmtp) REVERT: A 918 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7851 (mp0) REVERT: A 960 ASN cc_start: 0.8343 (t0) cc_final: 0.7956 (t0) REVERT: A 1113 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8064 (mm-40) outliers start: 122 outliers final: 94 residues processed: 387 average time/residue: 0.1476 time to fit residues: 96.0848 Evaluate side-chains 396 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 289 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 134 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 206 optimal weight: 0.6980 chunk 325 optimal weight: 0.8980 chunk 194 optimal weight: 0.0170 chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 0.0570 chunk 263 optimal weight: 0.0040 chunk 1 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.3148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.282253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.221754 restraints weight = 36752.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.214712 restraints weight = 38271.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.217664 restraints weight = 33678.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.216444 restraints weight = 23035.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.216554 restraints weight = 20695.980| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27241 Z= 0.126 Angle : 0.671 12.532 37141 Z= 0.322 Chirality : 0.047 0.451 4270 Planarity : 0.005 0.070 4762 Dihedral : 8.798 111.318 4315 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.04 % Favored : 90.62 % Rotamer: Outliers : 3.67 % Allowed : 20.38 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.37 (0.14), residues: 3306 helix: 0.72 (0.22), residues: 576 sheet: -1.09 (0.21), residues: 570 loop : -2.53 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 34 TYR 0.042 0.001 TYR B 91 PHE 0.022 0.001 PHE A 55 TRP 0.025 0.001 TRP A 64 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00280 (27189) covalent geometry : angle 0.63822 (37004) SS BOND : bond 0.00310 ( 19) SS BOND : angle 1.10988 ( 38) hydrogen bonds : bond 0.03665 ( 694) hydrogen bonds : angle 5.60552 ( 1956) link_BETA1-4 : bond 0.00398 ( 5) link_BETA1-4 : angle 3.32979 ( 15) link_NAG-ASN : bond 0.00635 ( 28) link_NAG-ASN : angle 4.12743 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 305 time to evaluate : 0.942 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: D 83 MET cc_start: 0.4792 (pmm) cc_final: 0.4500 (pmm) REVERT: B 271 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7515 (mm-40) REVERT: B 289 VAL cc_start: 0.9223 (p) cc_final: 0.9019 (m) REVERT: B 568 ASP cc_start: -0.1487 (OUTLIER) cc_final: -0.2762 (t0) REVERT: B 740 MET cc_start: 0.7715 (ptm) cc_final: 0.7509 (ptm) REVERT: B 872 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8147 (tp-100) REVERT: B 907 ASN cc_start: 0.7792 (t0) cc_final: 0.7435 (t0) REVERT: B 912 THR cc_start: 0.6818 (OUTLIER) cc_final: 0.6390 (m) REVERT: B 916 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6759 (tp) REVERT: B 935 GLN cc_start: 0.8297 (tt0) cc_final: 0.7934 (tt0) REVERT: B 1076 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8555 (p) REVERT: B 1083 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.6664 (m-70) REVERT: C 58 PHE cc_start: 0.6072 (OUTLIER) cc_final: 0.4361 (m-80) REVERT: C 565 PHE cc_start: 0.6132 (m-80) cc_final: 0.5884 (m-80) REVERT: C 655 HIS cc_start: 0.6692 (OUTLIER) cc_final: 0.6003 (t-90) REVERT: C 737 ASP cc_start: 0.5204 (OUTLIER) cc_final: 0.4470 (m-30) REVERT: C 1111 GLU cc_start: 0.8545 (tt0) cc_final: 0.8276 (tp30) REVERT: A 52 GLN cc_start: 0.7622 (pm20) cc_final: 0.7143 (tm-30) REVERT: A 175 PHE cc_start: 0.2396 (OUTLIER) cc_final: 0.1599 (p90) REVERT: A 215 ASP cc_start: 0.4381 (OUTLIER) cc_final: 0.3618 (p0) REVERT: A 220 PHE cc_start: 0.1402 (OUTLIER) cc_final: -0.0723 (t80) REVERT: A 528 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7263 (ttmt) REVERT: A 577 ARG cc_start: 0.6184 (tpp-160) cc_final: 0.4381 (tpp-160) REVERT: A 811 LYS cc_start: 0.7480 (tptp) cc_final: 0.6811 (mmtp) REVERT: A 918 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7825 (mp0) REVERT: A 960 ASN cc_start: 0.8359 (t0) cc_final: 0.7972 (t0) REVERT: A 1038 LYS cc_start: 0.8333 (mmmm) cc_final: 0.7938 (mptt) REVERT: A 1092 GLU cc_start: 0.7075 (pp20) cc_final: 0.6509 (pp20) REVERT: A 1113 GLN cc_start: 0.8711 (mm-40) cc_final: 0.7952 (mm-40) outliers start: 107 outliers final: 83 residues processed: 386 average time/residue: 0.1492 time to fit residues: 96.6514 Evaluate side-chains 385 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 289 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 205 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 186 optimal weight: 0.2980 chunk 80 optimal weight: 0.0670 chunk 22 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 197 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 279 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 784 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** 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 = 0.4796 r_free = 0.4796 target = 0.280107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.216155 restraints weight = 36692.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.205097 restraints weight = 35133.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.207516 restraints weight = 35937.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.208235 restraints weight = 23269.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.208845 restraints weight = 19328.992| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27241 Z= 0.135 Angle : 0.674 12.489 37141 Z= 0.323 Chirality : 0.048 0.444 4270 Planarity : 0.005 0.097 4762 Dihedral : 8.613 111.279 4315 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.17 % Favored : 90.53 % Rotamer: Outliers : 3.46 % Allowed : 20.86 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.14), residues: 3306 helix: 0.79 (0.22), residues: 570 sheet: -1.03 (0.21), residues: 571 loop : -2.53 (0.12), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 34 TYR 0.041 0.001 TYR B 91 PHE 0.023 0.001 PHE C 888 TRP 0.018 0.001 TRP B 64 HIS 0.007 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00310 (27189) covalent geometry : angle 0.64103 (37004) SS BOND : bond 0.00281 ( 19) SS BOND : angle 1.19407 ( 38) hydrogen bonds : bond 0.03667 ( 694) hydrogen bonds : angle 5.52418 ( 1956) link_BETA1-4 : bond 0.00368 ( 5) link_BETA1-4 : angle 3.33666 ( 15) link_NAG-ASN : bond 0.00616 ( 28) link_NAG-ASN : angle 4.13886 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5000.87 seconds wall clock time: 87 minutes 22.37 seconds (5242.37 seconds total)