Starting phenix.real_space_refine on Sun Jul 5 08:35:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eyh_28688/07_2026/8eyh_28688.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eyh_28688/07_2026/8eyh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8eyh_28688/07_2026/8eyh_28688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eyh_28688/07_2026/8eyh_28688.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8eyh_28688/07_2026/8eyh_28688.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eyh_28688/07_2026/8eyh_28688.cif" model { file = "/net/cci-nas-00/data/ceres_data/8eyh_28688/07_2026/8eyh_28688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eyh_28688/07_2026/8eyh_28688.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 chiralities: 9 Time building chain proxies: 6.42, per 1000 atoms: 0.24 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: 2.51 Conformation dependent library (CDL) restraints added in 995.7 milliseconds 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: 0.93 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: 5.89 Time building geometry restraints manager: 3.34 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 - 17.35: 14526 17.35 - 34.69: 1056 34.69 - 52.04: 224 52.04 - 69.39: 39 69.39 - 86.73: 23 Dihedral angle restraints: 15868 sinusoidal: 6158 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 15865 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: 7.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.820 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 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 : 12.687 86.735 9571 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 are 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/Z covalent geometry : bond 0.00449 / 0.29 (27189) covalent geometry : angle 0.61657 / 0.38 (37004) SS BOND : bond 0.00303 / 0.18 ( 19) SS BOND : angle 1.08659 / 0.68 ( 38) hydrogen bonds : bond 0.28060 / 18.75 ( 694) hydrogen bonds : angle 10.76030 / 7.58 ( 1956) link_BETA1-4 : bond 0.00435 / 0.23 ( 5) link_BETA1-4 : angle 1.19773 / 0.68 ( 15) link_NAG-ASN : bond 0.12105 / 7.89 ( 28) link_NAG-ASN : angle 9.04729 / 7.83 ( 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 : 0.984 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: 0.1614 time to fit residues: 99.1879 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 : 0.959 ------------------------------------------------------------------------------- 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... ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN 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 C 856 ASN 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 853 GLN A 992 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.285675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.223785 restraints weight = 37222.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.219025 restraints weight = 44163.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.220646 restraints weight = 36688.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.218064 restraints weight = 27734.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.219042 restraints weight = 23874.390| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27241 Z= 0.156 Angle : 0.753 15.239 37141 Z= 0.366 Chirality : 0.052 0.487 4270 Planarity : 0.005 0.102 4762 Dihedral : 6.365 91.440 3658 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.20 % Favored : 90.47 % Rotamer: Outliers : 3.98 % Allowed : 15.51 % Favored : 80.51 % 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 are not related in a simple way. whole: -2.56 (0.14), residues: 3306 helix: 0.21 (0.22), residues: 589 sheet: -1.25 (0.22), residues: 580 loop : -2.56 (0.12), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 44 TYR 0.025 0.002 TYR A1067 PHE 0.029 0.002 PHE C 888 TRP 0.021 0.002 TRP D 36 HIS 0.017 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (27189) covalent geometry : angle 0.73029 / 0.36 (37004) SS BOND : bond 0.00271 / 0.18 ( 19) SS BOND : angle 1.36025 / 0.81 ( 38) hydrogen bonds : bond 0.05334 / 3.63 ( 694) hydrogen bonds : angle 7.00763 / 5.02 ( 1956) link_BETA1-4 : bond 0.00609 / 0.30 ( 5) link_BETA1-4 : angle 1.99252 / 1.16 ( 15) link_NAG-ASN : bond 0.00775 / 0.52 ( 28) link_NAG-ASN : angle 3.81330 / 2.72 ( 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 419 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 303 time to evaluate : 0.940 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: B 340 GLU cc_start: 0.5689 (OUTLIER) cc_final: 0.3726 (tp30) REVERT: B 602 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8493 (m) REVERT: B 673 SER cc_start: 0.8521 (t) cc_final: 0.8317 (m) REVERT: B 894 LEU cc_start: 0.7743 (mt) cc_final: 0.7344 (mt) REVERT: B 912 THR cc_start: 0.6934 (OUTLIER) cc_final: 0.5534 (m) REVERT: B 914 ASN cc_start: 0.7607 (p0) cc_final: 0.7216 (p0) REVERT: B 915 VAL cc_start: 0.7516 (OUTLIER) cc_final: 0.7108 (m) REVERT: B 935 GLN cc_start: 0.8251 (tt0) cc_final: 0.7933 (tt0) REVERT: B 1066 THR cc_start: 0.9048 (m) cc_final: 0.8751 (p) REVERT: B 1083 HIS cc_start: 0.6828 (OUTLIER) cc_final: 0.6003 (m-70) REVERT: B 1092 GLU cc_start: 0.8061 (pt0) cc_final: 0.7746 (pt0) REVERT: C 343 ASN cc_start: 0.3551 (OUTLIER) cc_final: 0.2020 (t0) REVERT: C 386 LYS cc_start: 0.6666 (OUTLIER) cc_final: 0.6275 (pptt) REVERT: C 737 ASP cc_start: 0.4933 (OUTLIER) cc_final: 0.4026 (m-30) REVERT: C 974 SER cc_start: 0.2872 (OUTLIER) cc_final: 0.2555 (m) REVERT: C 978 ASN cc_start: 0.4192 (OUTLIER) cc_final: 0.3756 (m-40) REVERT: C 1055 SER cc_start: 0.9159 (p) cc_final: 0.8955 (p) REVERT: C 1113 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8886 (mm-40) REVERT: A 220 PHE cc_start: 0.1434 (OUTLIER) cc_final: -0.0354 (t80) REVERT: A 425 LEU cc_start: 0.5924 (OUTLIER) cc_final: 0.5536 (pp) REVERT: A 535 LYS cc_start: 0.6599 (tmmm) cc_final: 0.6345 (ttmt) REVERT: A 1038 LYS cc_start: 0.8382 (mmmt) cc_final: 0.7768 (mptt) REVERT: A 1091 ARG cc_start: 0.7174 (tpp-160) cc_final: 0.6929 (tpp80) REVERT: A 1092 GLU cc_start: 0.7169 (pp20) cc_final: 0.6732 (pp20) REVERT: A 1113 GLN cc_start: 0.8786 (mm-40) cc_final: 0.7981 (mm-40) outliers start: 116 outliers final: 58 residues processed: 388 average time/residue: 0.1586 time to fit residues: 103.4767 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 : 0.928 ------------------------------------------------------------------------------- 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 524 VAL 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 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: 0.8980 chunk 81 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 318 optimal weight: 0.7980 chunk 201 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 330 optimal weight: 0.0980 chunk 259 optimal weight: 9.9990 chunk 276 optimal weight: 4.9990 chunk 305 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 74 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 907 ASN B 949 GLN B 992 GLN B1101 HIS ** C 49 HIS ** 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 914 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 764 ASN A 926 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.282819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.222645 restraints weight = 37048.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.219191 restraints weight = 40908.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.218112 restraints weight = 36263.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.214783 restraints weight = 30699.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.216171 restraints weight = 27785.413| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 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 : 0.004 0.048 27241 Z= 0.163 Angle : 0.666 12.719 37141 Z= 0.327 Chirality : 0.049 0.461 4270 Planarity : 0.005 0.087 4762 Dihedral : 5.742 59.594 3632 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.47 % Favored : 90.26 % Rotamer: Outliers : 5.08 % Allowed : 14.82 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.14), residues: 3306 helix: 0.44 (0.22), residues: 581 sheet: -1.29 (0.22), residues: 550 loop : -2.56 (0.12), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1091 TYR 0.023 0.001 TYR C 279 PHE 0.027 0.001 PHE C 888 TRP 0.023 0.001 TRP B 64 HIS 0.011 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (27189) covalent geometry : angle 0.64357 / 0.32 (37004) SS BOND : bond 0.00424 / 0.20 ( 19) SS BOND : angle 1.26096 / 0.81 ( 38) hydrogen bonds : bond 0.04937 / 3.35 ( 694) hydrogen bonds : angle 6.48395 / 4.67 ( 1956) link_BETA1-4 : bond 0.00597 / 0.30 ( 5) link_BETA1-4 : angle 1.81724 / 1.07 ( 15) link_NAG-ASN : bond 0.00689 / 0.47 ( 28) link_NAG-ASN : angle 3.48061 / 2.29 ( 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 437 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 289 time to evaluate : 0.962 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: B 340 GLU cc_start: 0.5741 (OUTLIER) cc_final: 0.3828 (tp30) REVERT: B 568 ASP cc_start: -0.1164 (OUTLIER) cc_final: -0.2341 (t70) REVERT: B 663 ASP cc_start: 0.8260 (t0) cc_final: 0.7608 (t0) REVERT: B 872 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7931 (tp-100) REVERT: B 894 LEU cc_start: 0.7929 (mt) cc_final: 0.7343 (mt) REVERT: B 912 THR cc_start: 0.7094 (OUTLIER) cc_final: 0.6149 (m) REVERT: B 916 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.6700 (tp) REVERT: B 935 GLN cc_start: 0.8404 (tt0) cc_final: 0.8014 (tt0) REVERT: B 1076 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8555 (p) REVERT: B 1083 HIS cc_start: 0.7006 (OUTLIER) cc_final: 0.5472 (m-70) REVERT: B 1115 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7367 (tp) REVERT: B 1137 VAL cc_start: 0.2311 (OUTLIER) cc_final: 0.1882 (p) REVERT: C 58 PHE cc_start: 0.6159 (OUTLIER) cc_final: 0.4300 (m-80) REVERT: C 343 ASN cc_start: 0.3728 (OUTLIER) cc_final: 0.2614 (t0) REVERT: C 737 ASP cc_start: 0.5400 (OUTLIER) cc_final: 0.4375 (m-30) REVERT: C 978 ASN cc_start: 0.4313 (OUTLIER) cc_final: 0.3887 (m-40) REVERT: C 1055 SER cc_start: 0.9112 (OUTLIER) cc_final: 0.8764 (p) REVERT: C 1113 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8900 (mm110) REVERT: A 175 PHE cc_start: 0.2295 (OUTLIER) cc_final: 0.1256 (p90) REVERT: A 220 PHE cc_start: 0.1264 (OUTLIER) cc_final: -0.0591 (t80) REVERT: A 425 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5715 (pp) REVERT: A 535 LYS cc_start: 0.6574 (OUTLIER) cc_final: 0.6358 (ttmt) REVERT: A 1092 GLU cc_start: 0.7223 (pp20) cc_final: 0.6692 (pp20) REVERT: A 1113 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8061 (mm-40) outliers start: 148 outliers final: 71 residues processed: 397 average time/residue: 0.1547 time to fit residues: 104.4254 Evaluate side-chains 364 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 275 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 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 349 SER 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 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 734 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 872 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 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 1115 ILE 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 193 VAL Chi-restraints excluded: chain C residue 285 ILE 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 577 ARG Chi-restraints excluded: chain C residue 611 LEU 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 737 ASP Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 759 PHE 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 978 ASN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1055 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 298 GLU Chi-restraints excluded: chain A residue 308 VAL 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 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 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 916 LEU 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 1033 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 200 optimal weight: 1.9990 chunk 93 optimal weight: 0.1980 chunk 175 optimal weight: 0.2980 chunk 123 optimal weight: 5.9990 chunk 49 optimal weight: 0.0060 chunk 271 optimal weight: 0.8980 chunk 193 optimal weight: 0.0770 chunk 278 optimal weight: 0.9990 chunk 163 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.287795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.235084 restraints weight = 37437.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.232178 restraints weight = 62111.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.234373 restraints weight = 45673.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.234681 restraints weight = 24694.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.235573 restraints weight = 21626.654| |-----------------------------------------------------------------------------| r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27241 Z= 0.123 Angle : 0.638 14.788 37141 Z= 0.310 Chirality : 0.048 0.448 4270 Planarity : 0.004 0.082 4762 Dihedral : 5.468 58.093 3623 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.62 % Favored : 91.05 % Rotamer: Outliers : 3.98 % Allowed : 16.19 % Favored : 79.83 % 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 are not related in a simple way. whole: -2.33 (0.14), residues: 3306 helix: 0.68 (0.22), residues: 581 sheet: -1.11 (0.22), residues: 552 loop : -2.47 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1091 TYR 0.021 0.001 TYR C 279 PHE 0.021 0.001 PHE C 888 TRP 0.020 0.001 TRP B 64 HIS 0.007 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (27189) covalent geometry : angle 0.61593 / 0.31 (37004) SS BOND : bond 0.00249 / 0.15 ( 19) SS BOND : angle 1.16056 / 0.74 ( 38) hydrogen bonds : bond 0.04020 / 2.73 ( 694) hydrogen bonds : angle 6.01572 / 4.34 ( 1956) link_BETA1-4 : bond 0.00436 / 0.22 ( 5) link_BETA1-4 : angle 1.79548 / 1.05 ( 15) link_NAG-ASN : bond 0.00667 / 0.44 ( 28) link_NAG-ASN : angle 3.39419 / 2.22 ( 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 412 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 296 time to evaluate : 0.931 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 298 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7247 (tt0) REVERT: B 340 GLU cc_start: 0.5664 (OUTLIER) cc_final: 0.3916 (tp30) REVERT: B 663 ASP cc_start: 0.7935 (t0) cc_final: 0.7700 (t0) REVERT: B 872 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7950 (tp-100) REVERT: B 895 GLN cc_start: 0.5785 (OUTLIER) cc_final: 0.5356 (mt0) REVERT: B 912 THR cc_start: 0.6959 (OUTLIER) cc_final: 0.6158 (m) REVERT: B 916 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6447 (tp) REVERT: B 935 GLN cc_start: 0.8297 (tt0) cc_final: 0.7915 (tt0) REVERT: B 1066 THR cc_start: 0.8903 (m) cc_final: 0.8577 (p) REVERT: B 1076 THR cc_start: 0.8884 (m) cc_final: 0.8607 (p) REVERT: B 1083 HIS cc_start: 0.6784 (OUTLIER) cc_final: 0.6061 (m-70) REVERT: C 58 PHE cc_start: 0.5849 (OUTLIER) cc_final: 0.4055 (m-80) REVERT: C 153 MET cc_start: 0.5505 (mtm) cc_final: 0.4784 (mpp) REVERT: C 343 ASN cc_start: 0.3701 (OUTLIER) cc_final: 0.2970 (t0) REVERT: C 737 ASP cc_start: 0.5426 (OUTLIER) cc_final: 0.4276 (m-30) REVERT: C 978 ASN cc_start: 0.4061 (OUTLIER) cc_final: 0.3641 (m-40) REVERT: C 1045 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8288 (mmtm) REVERT: C 1111 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8173 (tt0) REVERT: A 175 PHE cc_start: 0.2008 (OUTLIER) cc_final: 0.1115 (p90) REVERT: A 220 PHE cc_start: 0.1162 (OUTLIER) cc_final: -0.0707 (t80) REVERT: A 425 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5292 (pp) REVERT: A 821 LEU cc_start: 0.9261 (tp) cc_final: 0.8951 (mm) REVERT: A 1038 LYS cc_start: 0.8540 (mmmt) cc_final: 0.7820 (mptt) REVERT: A 1089 PHE cc_start: 0.7238 (m-80) cc_final: 0.6891 (m-80) REVERT: A 1092 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6628 (pp20) REVERT: A 1113 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8054 (mm-40) outliers start: 116 outliers final: 73 residues processed: 378 average time/residue: 0.1557 time to fit residues: 99.5654 Evaluate side-chains 357 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 269 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 298 GLU 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 587 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 767 LEU 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 973 ILE 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 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 58 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 525 CYS 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 655 HIS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 699 LEU 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 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR 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 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 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 551 VAL 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 752 LEU 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 916 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 1033 VAL Chi-restraints excluded: chain A residue 1092 GLU 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: 2.9990 chunk 130 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 264 optimal weight: 0.9990 chunk 268 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 437 ASN B1064 HIS B1101 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN A 122 ASN 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 787 GLN A 804 GLN A 953 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.274903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.221996 restraints weight = 36643.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.207023 restraints weight = 56932.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.202137 restraints weight = 45729.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.201053 restraints weight = 36551.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.201464 restraints weight = 26925.589| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 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 : 0.007 0.084 27241 Z= 0.314 Angle : 0.802 13.014 37141 Z= 0.400 Chirality : 0.054 0.543 4270 Planarity : 0.006 0.080 4762 Dihedral : 5.839 59.988 3619 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.77 % Favored : 88.93 % Rotamer: Outliers : 5.32 % Allowed : 16.33 % Favored : 78.35 % 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 are not related in a simple way. whole: -2.79 (0.14), residues: 3306 helix: 0.01 (0.21), residues: 588 sheet: -1.38 (0.21), residues: 589 loop : -2.72 (0.12), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1014 TYR 0.036 0.002 TYR C 904 PHE 0.029 0.002 PHE C 888 TRP 0.022 0.002 TRP C 886 HIS 0.038 0.003 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.31 (27189) covalent geometry : angle 0.77606 / 0.39 (37004) SS BOND : bond 0.00499 / 0.27 ( 19) SS BOND : angle 1.82684 / 1.28 ( 38) hydrogen bonds : bond 0.05143 / 3.46 ( 694) hydrogen bonds : angle 6.45736 / 4.64 ( 1956) link_BETA1-4 : bond 0.00770 / 0.38 ( 5) link_BETA1-4 : angle 2.06249 / 1.20 ( 15) link_NAG-ASN : bond 0.00752 / 0.52 ( 28) link_NAG-ASN : angle 4.09739 / 2.62 ( 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 449 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 294 time to evaluate : 0.957 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: 0.6052 (OUTLIER) cc_final: 0.4161 (tp30) REVERT: B 568 ASP cc_start: -0.0914 (OUTLIER) cc_final: -0.2879 (p0) REVERT: B 664 ILE cc_start: 0.8956 (mt) cc_final: 0.8754 (mt) REVERT: B 872 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8182 (tp-100) REVERT: B 912 THR cc_start: 0.7121 (OUTLIER) cc_final: 0.6606 (m) REVERT: B 935 GLN cc_start: 0.8448 (tt0) cc_final: 0.8078 (tt0) REVERT: B 1083 HIS cc_start: 0.7097 (OUTLIER) cc_final: 0.5423 (m-70) REVERT: C 58 PHE cc_start: 0.6519 (OUTLIER) cc_final: 0.4603 (m-80) REVERT: C 276 LEU cc_start: 0.7484 (tp) cc_final: 0.7274 (tt) REVERT: C 309 GLU cc_start: 0.7613 (mp0) cc_final: 0.7380 (mt-10) REVERT: C 343 ASN cc_start: 0.4254 (OUTLIER) cc_final: 0.3507 (t0) REVERT: C 703 ASN cc_start: 0.8261 (p0) cc_final: 0.7959 (p0) REVERT: C 737 ASP cc_start: 0.5278 (OUTLIER) cc_final: 0.4069 (m-30) REVERT: C 873 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.7470 (m-10) REVERT: C 919 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.7372 (p0) REVERT: C 978 ASN cc_start: 0.4627 (OUTLIER) cc_final: 0.4158 (m-40) REVERT: A 175 PHE cc_start: 0.2460 (OUTLIER) cc_final: 0.1652 (p90) REVERT: A 425 LEU cc_start: 0.6213 (OUTLIER) cc_final: 0.5803 (pp) REVERT: A 660 TYR cc_start: 0.6974 (m-80) cc_final: 0.6659 (m-80) REVERT: A 960 ASN cc_start: 0.8581 (t0) cc_final: 0.8143 (t0) REVERT: A 1089 PHE cc_start: 0.7637 (m-80) cc_final: 0.7235 (m-80) outliers start: 155 outliers final: 93 residues processed: 411 average time/residue: 0.1593 time to fit residues: 109.2960 Evaluate side-chains 386 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 280 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 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 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 610 VAL 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 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU 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 1101 HIS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1114 ILE 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 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 277 LEU 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 525 CYS Chi-restraints excluded: chain C residue 577 ARG 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 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 56 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 175 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 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 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 564 GLN 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 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 1006 THR Chi-restraints excluded: chain A residue 1077 THR 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: 0.7980 chunk 302 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 271 optimal weight: 4.9990 chunk 34 optimal weight: 0.0170 chunk 263 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 238 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 171 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 856 ASN B 954 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 784 GLN ** 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 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.282364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.221915 restraints weight = 36915.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.213844 restraints weight = 40001.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.217947 restraints weight = 33410.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.215835 restraints weight = 22072.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.216928 restraints weight = 20603.190| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27241 Z= 0.154 Angle : 0.667 13.337 37141 Z= 0.330 Chirality : 0.049 0.503 4270 Planarity : 0.005 0.073 4762 Dihedral : 5.487 58.871 3614 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.32 % Favored : 90.38 % Rotamer: Outliers : 4.32 % Allowed : 17.74 % Favored : 77.94 % 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 are not related in a simple way. whole: -2.60 (0.14), residues: 3306 helix: 0.44 (0.22), residues: 578 sheet: -1.20 (0.22), residues: 552 loop : -2.67 (0.12), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1014 TYR 0.025 0.001 TYR A1067 PHE 0.031 0.001 PHE A 55 TRP 0.020 0.001 TRP B 64 HIS 0.022 0.001 HIS B1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (27189) covalent geometry : angle 0.64167 / 0.32 (37004) SS BOND : bond 0.00397 / 0.23 ( 19) SS BOND : angle 1.25982 / 0.84 ( 38) hydrogen bonds : bond 0.04229 / 2.85 ( 694) hydrogen bonds : angle 6.08797 / 4.37 ( 1956) link_BETA1-4 : bond 0.00579 / 0.30 ( 5) link_BETA1-4 : angle 1.79947 / 1.05 ( 15) link_NAG-ASN : bond 0.00676 / 0.47 ( 28) link_NAG-ASN : angle 3.75599 / 2.43 ( 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 425 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 299 time to evaluate : 0.846 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 271 GLN cc_start: 0.8004 (tp-100) cc_final: 0.7389 (mm-40) REVERT: B 340 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.4285 (tp30) REVERT: B 568 ASP cc_start: -0.0968 (OUTLIER) cc_final: -0.2928 (p0) REVERT: B 872 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7938 (tp-100) REVERT: B 895 GLN cc_start: 0.5665 (OUTLIER) cc_final: 0.5343 (mt0) REVERT: B 912 THR cc_start: 0.6798 (OUTLIER) cc_final: 0.6033 (m) REVERT: B 916 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.6689 (tp) REVERT: B 935 GLN cc_start: 0.8364 (tt0) cc_final: 0.7970 (tt0) REVERT: B 1024 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8565 (tt) REVERT: B 1066 THR cc_start: 0.8955 (m) cc_final: 0.8558 (p) REVERT: B 1083 HIS cc_start: 0.6764 (OUTLIER) cc_final: 0.6028 (m-70) REVERT: C 58 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.4379 (m-80) REVERT: C 78 ARG cc_start: 0.4802 (OUTLIER) cc_final: 0.2507 (ptt-90) REVERT: C 343 ASN cc_start: 0.4294 (OUTLIER) cc_final: 0.3685 (t0) REVERT: C 565 PHE cc_start: 0.6363 (m-80) cc_final: 0.5988 (m-80) REVERT: C 605 SER cc_start: 0.9272 (OUTLIER) cc_final: 0.8955 (p) REVERT: C 737 ASP cc_start: 0.5100 (OUTLIER) cc_final: 0.4070 (m-30) REVERT: C 919 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.6883 (p0) REVERT: C 978 ASN cc_start: 0.4708 (OUTLIER) cc_final: 0.4208 (m-40) REVERT: A 52 GLN cc_start: 0.7658 (mp10) cc_final: 0.7072 (tm-30) REVERT: A 175 PHE cc_start: 0.2253 (OUTLIER) cc_final: 0.1503 (p90) REVERT: A 220 PHE cc_start: 0.1455 (OUTLIER) cc_final: -0.0437 (t80) REVERT: A 436 TRP cc_start: 0.6350 (p-90) cc_final: 0.6036 (p-90) REVERT: A 577 ARG cc_start: 0.6324 (tpp-160) cc_final: 0.4460 (tpp-160) REVERT: A 811 LYS cc_start: 0.7298 (tptp) cc_final: 0.6623 (mmtp) REVERT: A 960 ASN cc_start: 0.8486 (t0) cc_final: 0.8032 (t0) REVERT: A 1038 LYS cc_start: 0.8243 (mmmt) cc_final: 0.7863 (mptt) REVERT: A 1113 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8053 (mm-40) outliers start: 126 outliers final: 86 residues processed: 391 average time/residue: 0.1559 time to fit residues: 102.0458 Evaluate side-chains 390 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 287 time to evaluate : 1.726 ------------------------------------------------------------------------------- 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 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 317 ASN 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 767 LEU 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 973 ILE Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1068 VAL 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 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 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 514 SER 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 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 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR 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 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 362 VAL Chi-restraints excluded: chain A residue 390 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 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 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 866 THR 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 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: 0.9990 chunk 58 optimal weight: 9.9990 chunk 307 optimal weight: 0.9980 chunk 199 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 198 optimal weight: 0.5980 chunk 167 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 82 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** 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 675 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.280100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.228256 restraints weight = 36949.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.212772 restraints weight = 55309.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.208041 restraints weight = 41479.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.207342 restraints weight = 30465.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.208237 restraints weight = 21694.695| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27241 Z= 0.179 Angle : 0.680 12.779 37141 Z= 0.335 Chirality : 0.049 0.513 4270 Planarity : 0.005 0.128 4762 Dihedral : 5.437 58.919 3610 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.19 % Favored : 89.50 % Rotamer: Outliers : 4.77 % Allowed : 17.74 % Favored : 77.50 % 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 are not related in a simple way. whole: -2.59 (0.14), residues: 3306 helix: 0.44 (0.22), residues: 583 sheet: -1.18 (0.22), residues: 563 loop : -2.68 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1014 TYR 0.024 0.001 TYR A1067 PHE 0.028 0.002 PHE A 55 TRP 0.019 0.001 TRP B 64 HIS 0.008 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (27189) covalent geometry : angle 0.65430 / 0.33 (37004) SS BOND : bond 0.00425 / 0.19 ( 19) SS BOND : angle 1.42541 / 0.96 ( 38) hydrogen bonds : bond 0.04197 / 2.83 ( 694) hydrogen bonds : angle 6.01879 / 4.32 ( 1956) link_BETA1-4 : bond 0.00600 / 0.32 ( 5) link_BETA1-4 : angle 1.82909 / 1.07 ( 15) link_NAG-ASN : bond 0.00644 / 0.44 ( 28) link_NAG-ASN : angle 3.77601 / 2.44 ( 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 425 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 286 time to evaluate : 0.850 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 56 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8452 (pt) REVERT: B 340 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.4574 (tp30) REVERT: B 568 ASP cc_start: -0.1208 (OUTLIER) cc_final: -0.2563 (t0) REVERT: B 872 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8141 (tp-100) REVERT: B 895 GLN cc_start: 0.5543 (OUTLIER) cc_final: 0.5242 (mt0) REVERT: B 912 THR cc_start: 0.7004 (OUTLIER) cc_final: 0.6463 (m) REVERT: B 935 GLN cc_start: 0.8390 (tt0) cc_final: 0.8031 (tt0) REVERT: B 1024 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8521 (tt) REVERT: B 1066 THR cc_start: 0.8968 (m) cc_final: 0.8517 (p) REVERT: B 1083 HIS cc_start: 0.6923 (OUTLIER) cc_final: 0.6069 (m-70) REVERT: C 58 PHE cc_start: 0.6201 (OUTLIER) cc_final: 0.4408 (m-80) REVERT: C 78 ARG cc_start: 0.4964 (OUTLIER) cc_final: 0.3868 (ptt-90) REVERT: C 343 ASN cc_start: 0.4334 (OUTLIER) cc_final: 0.3931 (t0) REVERT: C 565 PHE cc_start: 0.6426 (m-80) cc_final: 0.6044 (m-80) REVERT: C 605 SER cc_start: 0.9285 (OUTLIER) cc_final: 0.8978 (p) REVERT: C 737 ASP cc_start: 0.5211 (OUTLIER) cc_final: 0.4293 (m-30) REVERT: C 873 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.7491 (m-10) REVERT: C 935 GLN cc_start: 0.8374 (tt0) cc_final: 0.8102 (tt0) REVERT: C 978 ASN cc_start: 0.4663 (OUTLIER) cc_final: 0.4123 (m-40) REVERT: A 52 GLN cc_start: 0.7687 (mp10) cc_final: 0.7081 (tm-30) REVERT: A 175 PHE cc_start: 0.2446 (OUTLIER) cc_final: 0.1616 (p90) REVERT: A 220 PHE cc_start: 0.1364 (OUTLIER) cc_final: -0.0436 (t80) REVERT: A 436 TRP cc_start: 0.6663 (p-90) cc_final: 0.6236 (p-90) REVERT: A 577 ARG cc_start: 0.6395 (tpp-160) cc_final: 0.4454 (tpp-160) REVERT: A 811 LYS cc_start: 0.7352 (tptp) cc_final: 0.6673 (mmtp) REVERT: A 960 ASN cc_start: 0.8531 (t0) cc_final: 0.8113 (t0) REVERT: A 1038 LYS cc_start: 0.8423 (mmmt) cc_final: 0.7918 (mptt) REVERT: A 1113 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8066 (mm-40) outliers start: 139 outliers final: 96 residues processed: 388 average time/residue: 0.1505 time to fit residues: 97.6974 Evaluate side-chains 393 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 280 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 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 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 538 CYS 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 785 VAL 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 973 ILE Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1024 LEU 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 1101 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 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 285 ILE 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 514 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS 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 724 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET 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 873 TYR Chi-restraints excluded: chain C residue 900 MET 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 C residue 1114 ILE 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 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 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 596 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 658 ASN 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 866 THR 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 1077 THR Chi-restraints excluded: chain A residue 1082 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: 0.8980 chunk 216 optimal weight: 0.5980 chunk 308 optimal weight: 0.2980 chunk 279 optimal weight: 0.9980 chunk 306 optimal weight: 0.6980 chunk 290 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 312 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN C 710 ASN ** 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 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.281199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.222501 restraints weight = 37049.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.217755 restraints weight = 41705.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.213031 restraints weight = 37228.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.205350 restraints weight = 23795.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.205944 restraints weight = 23607.122| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27241 Z= 0.150 Angle : 0.658 12.651 37141 Z= 0.324 Chirality : 0.049 0.499 4270 Planarity : 0.005 0.093 4762 Dihedral : 5.213 58.634 3607 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.53 % Favored : 90.20 % Rotamer: Outliers : 4.46 % Allowed : 18.11 % Favored : 77.43 % 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 are not related in a simple way. whole: -2.48 (0.14), residues: 3306 helix: 0.60 (0.22), residues: 574 sheet: -1.12 (0.22), residues: 561 loop : -2.61 (0.12), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 34 TYR 0.024 0.001 TYR A1067 PHE 0.026 0.001 PHE A 55 TRP 0.018 0.001 TRP B 64 HIS 0.013 0.001 HIS B1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (27189) covalent geometry : angle 0.63260 / 0.32 (37004) SS BOND : bond 0.00281 / 0.16 ( 19) SS BOND : angle 1.23923 / 0.82 ( 38) hydrogen bonds : bond 0.03987 / 2.69 ( 694) hydrogen bonds : angle 5.87836 / 4.23 ( 1956) link_BETA1-4 : bond 0.00486 / 0.28 ( 5) link_BETA1-4 : angle 1.84054 / 1.08 ( 15) link_NAG-ASN : bond 0.00663 / 0.45 ( 28) link_NAG-ASN : angle 3.69575 / 2.38 ( 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 421 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 291 time to evaluate : 0.955 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: D 83 MET cc_start: 0.5643 (pmm) cc_final: 0.4958 (pmm) REVERT: B 56 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8424 (pt) REVERT: B 340 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5124 (tp30) REVERT: B 568 ASP cc_start: -0.1747 (OUTLIER) cc_final: -0.3022 (t0) REVERT: B 740 MET cc_start: 0.7949 (ptm) cc_final: 0.7621 (ptm) REVERT: B 872 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8167 (tp-100) REVERT: B 895 GLN cc_start: 0.5445 (OUTLIER) cc_final: 0.5125 (mt0) REVERT: B 912 THR cc_start: 0.6991 (OUTLIER) cc_final: 0.6338 (m) REVERT: B 935 GLN cc_start: 0.8369 (tt0) cc_final: 0.7968 (tt0) REVERT: B 1024 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8459 (tt) REVERT: B 1066 THR cc_start: 0.8945 (m) cc_final: 0.8576 (p) REVERT: B 1083 HIS cc_start: 0.6982 (OUTLIER) cc_final: 0.6305 (m-70) REVERT: C 58 PHE cc_start: 0.6333 (OUTLIER) cc_final: 0.4470 (m-80) REVERT: C 78 ARG cc_start: 0.5010 (OUTLIER) cc_final: 0.4340 (ptt-90) REVERT: C 343 ASN cc_start: 0.4682 (OUTLIER) cc_final: 0.4136 (t0) REVERT: C 565 PHE cc_start: 0.6475 (m-80) cc_final: 0.6036 (m-80) REVERT: C 605 SER cc_start: 0.9303 (OUTLIER) cc_final: 0.9001 (p) REVERT: C 737 ASP cc_start: 0.5298 (OUTLIER) cc_final: 0.4345 (m-30) REVERT: C 873 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.7593 (m-10) REVERT: C 935 GLN cc_start: 0.8359 (tt0) cc_final: 0.8074 (tt0) REVERT: C 978 ASN cc_start: 0.5099 (OUTLIER) cc_final: 0.4653 (m-40) REVERT: A 52 GLN cc_start: 0.7876 (mp10) cc_final: 0.7139 (tm-30) REVERT: A 175 PHE cc_start: 0.2667 (OUTLIER) cc_final: 0.1727 (p90) REVERT: A 215 ASP cc_start: 0.3834 (OUTLIER) cc_final: 0.3534 (p0) REVERT: A 220 PHE cc_start: 0.1310 (OUTLIER) cc_final: -0.0659 (t80) REVERT: A 436 TRP cc_start: 0.6952 (p-90) cc_final: 0.6438 (p-90) REVERT: A 577 ARG cc_start: 0.6438 (tpp-160) cc_final: 0.4352 (tpp-160) REVERT: A 670 ILE cc_start: 0.6375 (OUTLIER) cc_final: 0.5953 (mm) REVERT: A 811 LYS cc_start: 0.7435 (tptp) cc_final: 0.6711 (mmtp) REVERT: A 918 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7842 (mp0) REVERT: A 960 ASN cc_start: 0.8408 (t0) cc_final: 0.8005 (t0) REVERT: A 1038 LYS cc_start: 0.8476 (mmmt) cc_final: 0.7927 (mptt) REVERT: A 1089 PHE cc_start: 0.7437 (m-80) cc_final: 0.6951 (m-80) REVERT: A 1113 GLN cc_start: 0.8748 (mm-40) cc_final: 0.7995 (mm-40) outliers start: 130 outliers final: 93 residues processed: 387 average time/residue: 0.1555 time to fit residues: 100.5872 Evaluate side-chains 393 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 281 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 269 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 ASN 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 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 767 LEU Chi-restraints excluded: chain B residue 785 VAL 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 973 ILE Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1068 VAL 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 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 285 ILE 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 514 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS 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 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 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR 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 215 ASP 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 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 564 GLN 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 670 ILE 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 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: 0.9980 chunk 74 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 316 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 710 ASN ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 926 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 = 0.4759 r_free = 0.4759 target = 0.275558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.212956 restraints weight = 36585.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.204226 restraints weight = 41179.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.206645 restraints weight = 35137.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.206657 restraints weight = 24314.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.206712 restraints weight = 23075.231| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 27241 Z= 0.251 Angle : 0.744 12.621 37141 Z= 0.371 Chirality : 0.052 0.533 4270 Planarity : 0.005 0.070 4762 Dihedral : 5.568 58.276 3607 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.68 % Favored : 88.02 % Rotamer: Outliers : 4.49 % Allowed : 18.49 % Favored : 77.02 % 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 are not related in a simple way. whole: -2.73 (0.14), residues: 3306 helix: 0.13 (0.21), residues: 589 sheet: -1.27 (0.21), residues: 574 loop : -2.72 (0.12), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 34 TYR 0.025 0.002 TYR A1067 PHE 0.026 0.002 PHE C 400 TRP 0.014 0.002 TRP B 64 HIS 0.009 0.002 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.25 (27189) covalent geometry : angle 0.71601 / 0.36 (37004) SS BOND : bond 0.00420 / 0.26 ( 19) SS BOND : angle 1.81535 / 1.25 ( 38) hydrogen bonds : bond 0.04643 / 3.13 ( 694) hydrogen bonds : angle 6.13050 / 4.41 ( 1956) link_BETA1-4 : bond 0.00609 / 0.33 ( 5) link_BETA1-4 : angle 1.93495 / 1.13 ( 15) link_NAG-ASN : bond 0.00676 / 0.47 ( 28) link_NAG-ASN : angle 4.07370 / 2.62 ( 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 433 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 302 time to evaluate : 0.931 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: 0.4772 (pmm) cc_final: 0.4264 (pmm) REVERT: B 309 GLU cc_start: 0.7706 (mp0) cc_final: 0.7407 (mm-30) REVERT: B 568 ASP cc_start: -0.0795 (OUTLIER) cc_final: -0.2512 (p0) REVERT: B 740 MET cc_start: 0.8306 (ptm) cc_final: 0.8000 (ptm) REVERT: B 872 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8170 (tp-100) REVERT: B 912 THR cc_start: 0.6834 (OUTLIER) cc_final: 0.6437 (m) REVERT: B 935 GLN cc_start: 0.8423 (tt0) cc_final: 0.8050 (tt0) REVERT: B 1024 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8669 (tt) REVERT: B 1066 THR cc_start: 0.8951 (m) cc_final: 0.8409 (p) REVERT: B 1083 HIS cc_start: 0.7132 (OUTLIER) cc_final: 0.5877 (m-70) REVERT: C 58 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.4274 (m-80) REVERT: C 78 ARG cc_start: 0.4829 (OUTLIER) cc_final: 0.4169 (ptt-90) REVERT: C 605 SER cc_start: 0.9292 (OUTLIER) cc_final: 0.8853 (m) REVERT: C 703 ASN cc_start: 0.8330 (p0) cc_final: 0.8035 (p0) REVERT: C 737 ASP cc_start: 0.5319 (OUTLIER) cc_final: 0.4320 (m-30) REVERT: C 873 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.7515 (m-10) REVERT: A 52 GLN cc_start: 0.7797 (mp10) cc_final: 0.7248 (tm-30) REVERT: A 175 PHE cc_start: 0.2482 (OUTLIER) cc_final: 0.1786 (p90) REVERT: A 215 ASP cc_start: 0.4157 (OUTLIER) cc_final: 0.3807 (p0) REVERT: A 220 PHE cc_start: 0.1537 (OUTLIER) cc_final: -0.0529 (t80) REVERT: A 436 TRP cc_start: 0.6545 (p-90) cc_final: 0.6198 (p-90) REVERT: A 670 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.6396 (mm) REVERT: A 674 TYR cc_start: 0.7604 (t80) cc_final: 0.7330 (t80) REVERT: A 811 LYS cc_start: 0.7552 (tptp) cc_final: 0.6910 (mmtp) REVERT: A 918 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7859 (mp0) REVERT: A 960 ASN cc_start: 0.8438 (t0) cc_final: 0.8058 (t0) REVERT: A 1089 PHE cc_start: 0.7505 (m-80) cc_final: 0.7141 (m-80) outliers start: 131 outliers final: 103 residues processed: 398 average time/residue: 0.1502 time to fit residues: 100.3293 Evaluate side-chains 412 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 295 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 315 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 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 709 ASN 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 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 973 ILE Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1068 VAL 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 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 192 PHE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 310 LYS 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 525 CYS Chi-restraints excluded: chain C residue 529 LYS 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 724 THR Chi-restraints excluded: chain C residue 732 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 865 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 886 TRP 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 215 ASP 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 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 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 596 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 658 ASN 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 742 ILE 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 883 THR 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 1077 THR Chi-restraints excluded: chain A residue 1082 CYS 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: 3.9990 chunk 87 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 325 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 263 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 954 GLN ** 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 519 HIS A 824 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.276266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.213273 restraints weight = 36386.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.207165 restraints weight = 40411.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.210388 restraints weight = 35371.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.208379 restraints weight = 24111.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.208851 restraints weight = 24999.235| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27241 Z= 0.183 Angle : 0.691 12.148 37141 Z= 0.343 Chirality : 0.050 0.531 4270 Planarity : 0.005 0.068 4762 Dihedral : 5.337 58.405 3602 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.89 % Favored : 89.78 % Rotamer: Outliers : 3.88 % Allowed : 19.18 % Favored : 76.95 % 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 are not related in a simple way. whole: -2.66 (0.14), residues: 3306 helix: 0.30 (0.22), residues: 586 sheet: -1.29 (0.21), residues: 565 loop : -2.69 (0.12), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 646 TYR 0.025 0.001 TYR A1067 PHE 0.027 0.002 PHE C 888 TRP 0.018 0.001 TRP B 64 HIS 0.007 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (27189) covalent geometry : angle 0.66394 / 0.34 (37004) SS BOND : bond 0.00291 / 0.17 ( 19) SS BOND : angle 1.44370 / 0.97 ( 38) hydrogen bonds : bond 0.04153 / 2.81 ( 694) hydrogen bonds : angle 5.92276 / 4.27 ( 1956) link_BETA1-4 : bond 0.00631 / 0.34 ( 5) link_BETA1-4 : angle 1.88419 / 1.11 ( 15) link_NAG-ASN : bond 0.00613 / 0.42 ( 28) link_NAG-ASN : angle 3.92120 / 2.52 ( 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 407 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 294 time to evaluate : 0.924 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: 0.4993 (pmm) cc_final: 0.4543 (pmm) REVERT: B 271 GLN cc_start: 0.8079 (tp-100) cc_final: 0.7702 (mm-40) REVERT: B 568 ASP cc_start: -0.1324 (OUTLIER) cc_final: -0.2952 (p0) REVERT: B 740 MET cc_start: 0.8294 (ptm) cc_final: 0.8003 (ptm) REVERT: B 872 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8114 (tp-100) REVERT: B 895 GLN cc_start: 0.5657 (OUTLIER) cc_final: 0.5322 (mt0) REVERT: B 935 GLN cc_start: 0.8448 (tt0) cc_final: 0.8043 (tt0) REVERT: B 1024 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8540 (tt) REVERT: B 1066 THR cc_start: 0.8865 (m) cc_final: 0.8552 (p) REVERT: B 1083 HIS cc_start: 0.6853 (OUTLIER) cc_final: 0.6156 (m-70) REVERT: C 58 PHE cc_start: 0.6122 (OUTLIER) cc_final: 0.4260 (m-80) REVERT: C 565 PHE cc_start: 0.6272 (m-80) cc_final: 0.6067 (m-80) REVERT: C 605 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.8961 (p) REVERT: C 703 ASN cc_start: 0.8321 (p0) cc_final: 0.8025 (p0) REVERT: C 737 ASP cc_start: 0.5196 (OUTLIER) cc_final: 0.4316 (m-30) REVERT: C 869 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8292 (mtm) REVERT: C 873 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.7549 (m-10) REVERT: C 935 GLN cc_start: 0.8326 (tt0) cc_final: 0.8088 (tt0) REVERT: A 52 GLN cc_start: 0.7985 (mp10) cc_final: 0.7433 (tm-30) REVERT: A 175 PHE cc_start: 0.2485 (OUTLIER) cc_final: 0.1781 (p90) REVERT: A 215 ASP cc_start: 0.4035 (OUTLIER) cc_final: 0.3687 (p0) REVERT: A 220 PHE cc_start: 0.1739 (OUTLIER) cc_final: -0.0500 (t80) REVERT: A 436 TRP cc_start: 0.6539 (p-90) cc_final: 0.6201 (p-90) REVERT: A 577 ARG cc_start: 0.6281 (tpp-160) cc_final: 0.4379 (tpp-160) REVERT: A 670 ILE cc_start: 0.6477 (OUTLIER) cc_final: 0.5953 (mm) REVERT: A 674 TYR cc_start: 0.7591 (t80) cc_final: 0.7276 (t80) REVERT: A 811 LYS cc_start: 0.7595 (tptp) cc_final: 0.6942 (mmtp) REVERT: A 918 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7942 (mp0) REVERT: A 960 ASN cc_start: 0.8425 (t0) cc_final: 0.8024 (t0) REVERT: A 1089 PHE cc_start: 0.7385 (m-80) cc_final: 0.7078 (m-80) REVERT: A 1113 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8159 (mm-40) outliers start: 113 outliers final: 92 residues processed: 378 average time/residue: 0.1519 time to fit residues: 95.6780 Evaluate side-chains 387 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 281 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 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 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 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 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 973 ILE Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1068 VAL 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 83 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 310 LYS 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 529 LYS 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 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 865 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR 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 215 ASP 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 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 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 596 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 742 ILE 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 1006 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1082 CYS 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: 0.5980 chunk 223 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 80 optimal weight: 0.0770 chunk 22 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 279 optimal weight: 0.0870 chunk 92 optimal weight: 0.9980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 901 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 784 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 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 = 0.4805 r_free = 0.4805 target = 0.281003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.219215 restraints weight = 36836.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.209509 restraints weight = 38413.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.213357 restraints weight = 33138.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.213182 restraints weight = 21600.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.213328 restraints weight = 19202.092| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.3754 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= 0.136 Angle : 0.655 12.129 37141 Z= 0.324 Chirality : 0.048 0.498 4270 Planarity : 0.005 0.068 4762 Dihedral : 5.122 56.706 3601 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.56 % Favored : 90.11 % Rotamer: Outliers : 3.46 % Allowed : 19.55 % Favored : 76.98 % 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 are not related in a simple way. whole: -2.50 (0.14), residues: 3306 helix: 0.60 (0.22), residues: 574 sheet: -1.14 (0.21), residues: 565 loop : -2.63 (0.12), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 646 TYR 0.025 0.001 TYR B 91 PHE 0.024 0.001 PHE C 888 TRP 0.021 0.001 TRP B 64 HIS 0.010 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (27189) covalent geometry : angle 0.62969 / 0.32 (37004) SS BOND : bond 0.00253 / 0.15 ( 19) SS BOND : angle 1.27460 / 0.84 ( 38) hydrogen bonds : bond 0.03775 / 2.55 ( 694) hydrogen bonds : angle 5.67765 / 4.09 ( 1956) link_BETA1-4 : bond 0.00621 / 0.35 ( 5) link_BETA1-4 : angle 1.68306 / 0.98 ( 15) link_NAG-ASN : bond 0.00655 / 0.45 ( 28) link_NAG-ASN : angle 3.71990 / 2.38 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5191.03 seconds wall clock time: 106 minutes 10.93 seconds (6370.93 seconds total)