Starting phenix.real_space_refine on Mon Jun 23 03:10:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eyh_28688/06_2025/8eyh_28688.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eyh_28688/06_2025/8eyh_28688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eyh_28688/06_2025/8eyh_28688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eyh_28688/06_2025/8eyh_28688.map" model { file = "/net/cci-nas-00/data/ceres_data/8eyh_28688/06_2025/8eyh_28688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eyh_28688/06_2025/8eyh_28688.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.755 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26575 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 868 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "B" Number of atoms: 8515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8515 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 Chain: "C" Number of atoms: 8350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8350 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 56, 'TRANS': 1010} Chain breaks: 5 Chain: "A" Number of atoms: 8366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8366 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 56, 'TRANS': 1012} Chain breaks: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 17.19, per 1000 atoms: 0.65 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: 7.64 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 3.48 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: 10.69 Time building geometry restraints manager: 9.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6692 1.33 - 1.45: 5458 1.45 - 1.57: 14885 1.57 - 1.69: 2 1.69 - 1.81: 152 Bond restraints: 27189 Sorted by residual: bond pdb=" C5 NAG A1202 " pdb=" O5 NAG A1202 " ideal model delta sigma weight residual 1.413 1.516 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" N ASN B 164 " pdb=" CA ASN B 164 " ideal model delta sigma weight residual 1.457 1.489 -0.032 6.40e-03 2.44e+04 2.51e+01 bond pdb=" C4 NAG A1202 " pdb=" O4 NAG A1202 " ideal model delta sigma weight residual 1.409 1.507 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C2 NAG A1202 " pdb=" C3 NAG A1202 " ideal model delta sigma weight residual 1.526 1.610 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C7 NAG A1202 " pdb=" C8 NAG A1202 " ideal model delta sigma weight residual 1.509 1.429 0.080 2.00e-02 2.50e+03 1.61e+01 ... (remaining 27184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 36404 2.41 - 4.81: 584 4.81 - 7.22: 13 7.22 - 9.62: 2 9.62 - 12.03: 1 Bond angle restraints: 37004 Sorted by residual: angle pdb=" N PRO A 337 " pdb=" CA PRO A 337 " pdb=" C PRO A 337 " ideal model delta sigma weight residual 114.92 107.65 7.27 1.19e+00 7.06e-01 3.74e+01 angle pdb=" O ASN B 164 " pdb=" C ASN B 164 " pdb=" N ASN B 165 " ideal model delta sigma weight residual 121.47 124.91 -3.44 7.50e-01 1.78e+00 2.10e+01 angle pdb=" CA VAL C 382 " pdb=" C VAL C 382 " pdb=" O VAL C 382 " ideal model delta sigma weight residual 121.63 117.11 4.52 9.90e-01 1.02e+00 2.09e+01 angle pdb=" CA ASN A 334 " pdb=" CB ASN A 334 " pdb=" CG ASN A 334 " ideal model delta sigma weight residual 112.60 116.92 -4.32 1.00e+00 1.00e+00 1.87e+01 angle pdb=" C SER A 373 " pdb=" CA SER A 373 " pdb=" CB SER A 373 " ideal model delta sigma weight residual 116.34 110.42 5.92 1.40e+00 5.10e-01 1.79e+01 ... (remaining 36999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.59: 15685 25.59 - 51.17: 703 51.17 - 76.76: 116 76.76 - 102.34: 52 102.34 - 127.93: 26 Dihedral angle restraints: 16582 sinusoidal: 6872 harmonic: 9710 Sorted by residual: dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -161.31 75.31 1 1.00e+01 1.00e-02 7.17e+01 dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -157.78 71.78 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -23.73 -62.27 1 1.00e+01 1.00e-02 5.13e+01 ... (remaining 16579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.273: 4265 0.273 - 0.546: 1 0.546 - 0.820: 1 0.820 - 1.093: 1 1.093 - 1.366: 2 Chirality restraints: 4270 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.77 1.37 2.00e-01 2.50e+01 4.67e+01 chirality pdb=" C1 NAG C1201 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1201 " pdb=" O5 NAG C1201 " both_signs ideal model delta sigma weight residual False -2.40 -3.53 1.13 2.00e-01 2.50e+01 3.21e+01 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -3.32 0.92 2.00e-01 2.50e+01 2.10e+01 ... (remaining 4267 not shown) Planarity restraints: 4790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.015 2.00e-02 2.50e+03 3.31e-02 1.37e+01 pdb=" CG ASN A 331 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.061 2.00e-02 2.50e+03 pdb=" C1 NAG A1202 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " -0.012 2.00e-02 2.50e+03 2.91e-02 1.06e+01 pdb=" CG ASN B1074 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " 0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " -0.046 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 334 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" CG ASN A 334 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 334 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 334 " -0.014 2.00e-02 2.50e+03 ... (remaining 4787 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 527 2.62 - 3.19: 27093 3.19 - 3.76: 39745 3.76 - 4.33: 55116 4.33 - 4.90: 87624 Nonbonded interactions: 210105 Sorted by model distance: nonbonded pdb=" O4 NAG C1201 " pdb=" O7 NAG C1201 " model vdw 2.055 3.040 nonbonded pdb=" OD1 ASN C 717 " pdb=" N PHE C 718 " model vdw 2.106 3.120 nonbonded pdb=" ND1 HIS C1083 " pdb=" OD1 ASP C1084 " model vdw 2.108 3.120 nonbonded pdb=" N GLU B 309 " pdb=" OE1 GLU B 309 " model vdw 2.130 3.120 nonbonded pdb=" O3 NAG B1304 " pdb=" O7 NAG B1304 " model vdw 2.134 3.040 ... (remaining 210100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 675 or resid 690 through 827 or resid 852 throu \ gh 1146 or resid 1203 through 1208)) selection = (chain 'B' and (resid 14 through 617 or resid 641 through 827 or resid 852 throu \ gh 940 or resid 944 through 1146 or resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 675 or resid 690 through 827 or resid 852 throu \ gh 1146 or resid 1203 through 1208)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.160 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 64.070 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.487 27241 Z= 0.349 Angle : 0.752 53.106 37141 Z= 0.406 Chirality : 0.057 1.366 4270 Planarity : 0.003 0.038 4762 Dihedral : 15.751 127.929 10285 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 50.94 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (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 TRP 0.009 0.001 TRP C 886 HIS 0.005 0.001 HIS B 519 PHE 0.021 0.001 PHE B1075 TYR 0.012 0.001 TYR C 695 ARG 0.003 0.000 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.12105 ( 28) link_NAG-ASN : angle 9.04729 ( 84) link_BETA1-4 : bond 0.00435 ( 5) link_BETA1-4 : angle 1.19773 ( 15) hydrogen bonds : bond 0.28060 ( 694) hydrogen bonds : angle 10.76030 ( 1956) SS BOND : bond 0.00303 ( 19) SS BOND : angle 1.08659 ( 38) covalent geometry : bond 0.00449 (27189) covalent geometry : angle 0.61657 (37004) *********************** 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 : 2.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.3449 time to fit residues: 210.4741 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 : 2.724 ------------------------------------------------------------------------------- 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 279 optimal weight: 0.0670 chunk 250 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 169 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 259 optimal weight: 0.2980 chunk 100 optimal weight: 0.9980 chunk 157 optimal weight: 0.1980 chunk 193 optimal weight: 0.5980 chunk 300 optimal weight: 2.9990 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 544 ASN B 563 GLN B 954 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN C 804 GLN C1036 GLN A 334 ASN A 450 ASN A 487 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 658 ASN A 764 ASN A 853 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.285419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.226898 restraints weight = 37234.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.218700 restraints weight = 44329.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.220755 restraints weight = 41193.113| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27241 Z= 0.163 Angle : 0.772 18.019 37141 Z= 0.370 Chirality : 0.051 0.428 4270 Planarity : 0.005 0.104 4762 Dihedral : 13.428 114.725 4372 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.56 % Favored : 90.08 % Rotamer: Outliers : 3.84 % Allowed : 15.75 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.14), residues: 3306 helix: 0.21 (0.22), residues: 589 sheet: -1.28 (0.22), residues: 575 loop : -2.58 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 36 HIS 0.016 0.001 HIS C 49 PHE 0.028 0.002 PHE C 888 TYR 0.025 0.002 TYR A1067 ARG 0.006 0.001 ARG C 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00858 ( 28) link_NAG-ASN : angle 4.77198 ( 84) link_BETA1-4 : bond 0.01208 ( 5) link_BETA1-4 : angle 2.43785 ( 15) hydrogen bonds : bond 0.05469 ( 694) hydrogen bonds : angle 7.06762 ( 1956) SS BOND : bond 0.00299 ( 19) SS BOND : angle 1.37192 ( 38) covalent geometry : bond 0.00361 (27189) covalent geometry : angle 0.73610 (37004) *********************** 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 406 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 294 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.5711 (OUTLIER) cc_final: 0.3747 (tp30) REVERT: B 602 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8485 (m) REVERT: B 663 ASP cc_start: 0.8167 (t0) cc_final: 0.7573 (t0) REVERT: B 673 SER cc_start: 0.8612 (t) cc_final: 0.8347 (m) REVERT: B 894 LEU cc_start: 0.7908 (mt) cc_final: 0.7532 (mt) REVERT: B 912 THR cc_start: 0.6842 (OUTLIER) cc_final: 0.5551 (m) REVERT: B 914 ASN cc_start: 0.7589 (p0) cc_final: 0.7170 (p0) REVERT: B 935 GLN cc_start: 0.8277 (tt0) cc_final: 0.7962 (tt0) REVERT: B 1066 THR cc_start: 0.8861 (m) cc_final: 0.8479 (p) REVERT: B 1083 HIS cc_start: 0.6918 (OUTLIER) cc_final: 0.5802 (m-70) REVERT: B 1092 GLU cc_start: 0.8118 (pt0) cc_final: 0.7806 (pt0) REVERT: B 1137 VAL cc_start: 0.2143 (OUTLIER) cc_final: 0.1897 (p) REVERT: C 343 ASN cc_start: 0.3578 (OUTLIER) cc_final: 0.2037 (t0) REVERT: C 386 LYS cc_start: 0.6687 (OUTLIER) cc_final: 0.6264 (pptt) REVERT: C 661 GLU cc_start: 0.7302 (tm-30) cc_final: 0.7081 (tm-30) REVERT: C 737 ASP cc_start: 0.5106 (OUTLIER) cc_final: 0.4180 (m-30) REVERT: C 974 SER cc_start: 0.2982 (OUTLIER) cc_final: 0.2621 (m) REVERT: C 978 ASN cc_start: 0.4253 (OUTLIER) cc_final: 0.3815 (m-40) REVERT: C 1055 SER cc_start: 0.9199 (p) cc_final: 0.8782 (p) REVERT: C 1113 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8914 (mm-40) REVERT: A 220 PHE cc_start: 0.1460 (OUTLIER) cc_final: -0.0331 (t80) REVERT: A 425 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.5594 (pp) REVERT: A 535 LYS cc_start: 0.6611 (tmmm) cc_final: 0.6359 (ttmt) REVERT: A 1038 LYS cc_start: 0.8404 (mmmt) cc_final: 0.7761 (mptt) REVERT: A 1091 ARG cc_start: 0.7127 (tpp-160) cc_final: 0.6869 (tpp80) REVERT: A 1092 GLU cc_start: 0.7262 (pp20) cc_final: 0.6793 (pp20) REVERT: A 1113 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8074 (mm-40) outliers start: 112 outliers final: 57 residues processed: 375 average time/residue: 0.3450 time to fit residues: 216.0353 Evaluate side-chains 342 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 273 time to evaluate : 2.910 ------------------------------------------------------------------------------- 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 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 912 THR 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 281 GLU 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 664 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1126 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 90 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 chunk 235 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 220 optimal weight: 0.7980 chunk 273 optimal weight: 0.0020 chunk 34 optimal weight: 0.4980 chunk 81 optimal weight: 0.0870 overall best weight: 0.3966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 777 ASN B 949 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 914 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 926 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.286483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.228121 restraints weight = 37031.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.226068 restraints weight = 42387.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.223784 restraints weight = 36201.846| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27241 Z= 0.141 Angle : 0.681 13.271 37141 Z= 0.326 Chirality : 0.048 0.406 4270 Planarity : 0.004 0.086 4762 Dihedral : 11.962 114.682 4345 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.80 % Favored : 90.93 % Rotamer: Outliers : 5.01 % Allowed : 15.09 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.14), residues: 3306 helix: 0.44 (0.22), residues: 593 sheet: -1.23 (0.22), residues: 543 loop : -2.54 (0.12), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 64 HIS 0.011 0.001 HIS C 49 PHE 0.025 0.001 PHE C 888 TYR 0.023 0.001 TYR C 279 ARG 0.005 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 28) link_NAG-ASN : angle 4.12708 ( 84) link_BETA1-4 : bond 0.00719 ( 5) link_BETA1-4 : angle 2.47162 ( 15) hydrogen bonds : bond 0.04777 ( 694) hydrogen bonds : angle 6.44482 ( 1956) SS BOND : bond 0.00343 ( 19) SS BOND : angle 1.16353 ( 38) covalent geometry : bond 0.00311 (27189) covalent geometry : angle 0.64994 (37004) *********************** 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 449 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 303 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.5681 (OUTLIER) cc_final: 0.3691 (tp30) REVERT: B 568 ASP cc_start: -0.1258 (OUTLIER) cc_final: -0.2158 (t70) REVERT: B 663 ASP cc_start: 0.8178 (t0) cc_final: 0.7567 (t0) REVERT: B 872 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7936 (tp-100) REVERT: B 894 LEU cc_start: 0.7832 (mt) cc_final: 0.7404 (mt) REVERT: B 912 THR cc_start: 0.7039 (OUTLIER) cc_final: 0.6205 (m) REVERT: B 916 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6523 (tp) REVERT: B 935 GLN cc_start: 0.8372 (tt0) cc_final: 0.7985 (tt0) REVERT: B 1066 THR cc_start: 0.8921 (m) cc_final: 0.8639 (p) REVERT: B 1076 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8547 (p) REVERT: B 1083 HIS cc_start: 0.6935 (OUTLIER) cc_final: 0.5805 (m-70) REVERT: B 1115 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7261 (tp) REVERT: B 1137 VAL cc_start: 0.2353 (OUTLIER) cc_final: 0.1946 (p) REVERT: C 343 ASN cc_start: 0.3749 (OUTLIER) cc_final: 0.2637 (t0) REVERT: C 661 GLU cc_start: 0.7387 (tm-30) cc_final: 0.7127 (tm-30) REVERT: C 737 ASP cc_start: 0.5524 (OUTLIER) cc_final: 0.4435 (m-30) REVERT: C 978 ASN cc_start: 0.4122 (OUTLIER) cc_final: 0.3723 (m-40) REVERT: C 1111 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8102 (tt0) REVERT: C 1113 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8882 (mm110) REVERT: A 175 PHE cc_start: 0.2207 (OUTLIER) cc_final: 0.1199 (p90) REVERT: A 220 PHE cc_start: 0.1311 (OUTLIER) cc_final: -0.0500 (t80) REVERT: A 425 LEU cc_start: 0.5966 (OUTLIER) cc_final: 0.5609 (pp) REVERT: A 535 LYS cc_start: 0.6616 (OUTLIER) cc_final: 0.6397 (ttmt) REVERT: A 1089 PHE cc_start: 0.7326 (m-80) cc_final: 0.6951 (m-80) REVERT: A 1092 GLU cc_start: 0.7247 (pp20) cc_final: 0.6710 (pp20) REVERT: A 1113 GLN cc_start: 0.8755 (mm-40) cc_final: 0.7967 (mm-40) outliers start: 146 outliers final: 72 residues processed: 412 average time/residue: 0.3267 time to fit residues: 227.4478 Evaluate side-chains 368 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 280 time to evaluate : 3.541 ------------------------------------------------------------------------------- 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 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 533 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 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 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 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 693 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 759 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 978 ASN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1081 ILE 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 513 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 664 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 900 MET 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 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 107 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 233 optimal weight: 10.0000 chunk 322 optimal weight: 0.9980 chunk 250 optimal weight: 3.9990 chunk 327 optimal weight: 0.6980 chunk 128 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** 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 804 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.276597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.224181 restraints weight = 36954.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.211402 restraints weight = 56844.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.205809 restraints weight = 45989.458| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 27241 Z= 0.255 Angle : 0.780 13.867 37141 Z= 0.380 Chirality : 0.051 0.515 4270 Planarity : 0.005 0.083 4762 Dihedral : 11.175 115.192 4336 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.01 % Favored : 88.72 % Rotamer: Outliers : 5.52 % Allowed : 16.05 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.14), residues: 3306 helix: 0.17 (0.22), residues: 586 sheet: -1.36 (0.21), residues: 591 loop : -2.69 (0.12), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 64 HIS 0.010 0.002 HIS B1083 PHE 0.028 0.002 PHE C 888 TYR 0.032 0.002 TYR C 904 ARG 0.008 0.001 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00692 ( 28) link_NAG-ASN : angle 4.46339 ( 84) link_BETA1-4 : bond 0.00649 ( 5) link_BETA1-4 : angle 2.81374 ( 15) hydrogen bonds : bond 0.04991 ( 694) hydrogen bonds : angle 6.46277 ( 1956) SS BOND : bond 0.00474 ( 19) SS BOND : angle 1.71746 ( 38) covalent geometry : bond 0.00600 (27189) covalent geometry : angle 0.74728 (37004) *********************** 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 463 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 302 time to evaluate : 2.633 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: 0.5934 (OUTLIER) cc_final: 0.4194 (tp30) REVERT: B 568 ASP cc_start: -0.0988 (OUTLIER) cc_final: -0.2600 (p0) REVERT: B 872 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8008 (tp-100) REVERT: B 907 ASN cc_start: 0.7856 (t0) cc_final: 0.7577 (t0) REVERT: B 912 THR cc_start: 0.6829 (OUTLIER) cc_final: 0.6416 (m) REVERT: B 935 GLN cc_start: 0.8458 (tt0) cc_final: 0.8080 (tt0) REVERT: B 1018 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.9029 (tt) REVERT: B 1066 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8656 (p) REVERT: B 1083 HIS cc_start: 0.6982 (OUTLIER) cc_final: 0.5348 (m-70) REVERT: C 58 PHE cc_start: 0.6315 (OUTLIER) cc_final: 0.4491 (m-80) REVERT: C 343 ASN cc_start: 0.4059 (OUTLIER) cc_final: 0.3193 (t0) REVERT: C 699 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6390 (mt) REVERT: C 737 ASP cc_start: 0.5494 (OUTLIER) cc_final: 0.4196 (m-30) REVERT: C 873 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.7452 (m-10) REVERT: C 919 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.7254 (p0) REVERT: C 978 ASN cc_start: 0.4609 (OUTLIER) cc_final: 0.4075 (m-40) REVERT: C 1045 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8312 (mmtm) REVERT: C 1111 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8282 (tt0) REVERT: C 1113 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8765 (mm110) REVERT: A 175 PHE cc_start: 0.2464 (OUTLIER) cc_final: 0.1521 (p90) REVERT: A 220 PHE cc_start: 0.1572 (OUTLIER) cc_final: -0.0328 (t80) REVERT: A 425 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5871 (pp) REVERT: A 660 TYR cc_start: 0.6927 (m-80) cc_final: 0.6453 (m-80) REVERT: A 960 ASN cc_start: 0.8603 (t0) cc_final: 0.8211 (t0) REVERT: A 1089 PHE cc_start: 0.7604 (m-80) cc_final: 0.7204 (m-80) outliers start: 161 outliers final: 103 residues processed: 428 average time/residue: 0.3387 time to fit residues: 241.3884 Evaluate side-chains 415 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 295 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 673 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 820 ASP Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1066 THR 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 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 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 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 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 723 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 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 C residue 1122 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 305 SER 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 454 ARG 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 564 GLN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 696 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 166 optimal weight: 0.8980 chunk 11 optimal weight: 0.0070 chunk 53 optimal weight: 9.9990 chunk 149 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 208 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 184 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.278234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.214033 restraints weight = 36608.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.205952 restraints weight = 37902.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.210184 restraints weight = 31775.826| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.2597 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= 0.155 Angle : 0.698 13.176 37141 Z= 0.335 Chirality : 0.048 0.456 4270 Planarity : 0.005 0.142 4762 Dihedral : 10.443 102.511 4326 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.68 % Favored : 90.02 % Rotamer: Outliers : 4.53 % Allowed : 17.39 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.14), residues: 3306 helix: 0.43 (0.22), residues: 578 sheet: -1.26 (0.21), residues: 577 loop : -2.65 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 64 HIS 0.008 0.001 HIS B1083 PHE 0.031 0.001 PHE A 55 TYR 0.023 0.001 TYR A1067 ARG 0.007 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 28) link_NAG-ASN : angle 4.23434 ( 84) link_BETA1-4 : bond 0.00424 ( 5) link_BETA1-4 : angle 3.06976 ( 15) hydrogen bonds : bond 0.04300 ( 694) hydrogen bonds : angle 6.16083 ( 1956) SS BOND : bond 0.00393 ( 19) SS BOND : angle 1.18614 ( 38) covalent geometry : bond 0.00351 (27189) covalent geometry : angle 0.66591 (37004) *********************** 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 437 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 305 time to evaluate : 4.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 271 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7486 (mm-40) REVERT: B 340 GLU cc_start: 0.5961 (OUTLIER) cc_final: 0.4198 (tp30) REVERT: B 568 ASP cc_start: -0.0994 (OUTLIER) cc_final: -0.2258 (t0) REVERT: B 663 ASP cc_start: 0.7986 (t0) cc_final: 0.7729 (t0) REVERT: B 872 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7961 (tp-100) REVERT: B 895 GLN cc_start: 0.5697 (OUTLIER) cc_final: 0.5368 (mt0) REVERT: B 907 ASN cc_start: 0.7681 (t0) cc_final: 0.7407 (t0) REVERT: B 912 THR cc_start: 0.7068 (OUTLIER) cc_final: 0.6225 (m) REVERT: B 916 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.6843 (tp) REVERT: B 1076 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8646 (p) REVERT: B 1083 HIS cc_start: 0.6962 (OUTLIER) cc_final: 0.6277 (m-70) REVERT: C 58 PHE cc_start: 0.6209 (OUTLIER) cc_final: 0.4408 (m-80) REVERT: C 343 ASN cc_start: 0.4177 (OUTLIER) cc_final: 0.3463 (t0) REVERT: C 565 PHE cc_start: 0.6310 (m-80) cc_final: 0.5965 (m-80) REVERT: C 655 HIS cc_start: 0.6818 (OUTLIER) cc_final: 0.6451 (t-90) REVERT: C 737 ASP cc_start: 0.5398 (OUTLIER) cc_final: 0.4240 (m-30) REVERT: C 935 GLN cc_start: 0.8249 (tt0) cc_final: 0.8010 (tt0) REVERT: C 978 ASN cc_start: 0.4678 (OUTLIER) cc_final: 0.4184 (m-40) REVERT: C 1045 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8284 (mmtm) REVERT: C 1111 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8147 (tt0) REVERT: C 1113 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8796 (mm110) REVERT: A 52 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: A 175 PHE cc_start: 0.2213 (OUTLIER) cc_final: 0.1458 (p90) REVERT: A 220 PHE cc_start: 0.1469 (OUTLIER) cc_final: -0.0378 (t80) REVERT: A 425 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5670 (pp) REVERT: A 577 ARG cc_start: 0.6305 (tpp-160) cc_final: 0.4464 (tpp-160) REVERT: A 811 LYS cc_start: 0.7264 (tptp) cc_final: 0.6600 (mmtp) REVERT: A 960 ASN cc_start: 0.8517 (t0) cc_final: 0.8071 (t0) REVERT: A 1089 PHE cc_start: 0.7399 (m-80) cc_final: 0.7190 (m-80) REVERT: A 1092 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6718 (pp20) REVERT: A 1113 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8089 (mm-40) outliers start: 132 outliers final: 88 residues processed: 399 average time/residue: 0.4241 time to fit residues: 285.9726 Evaluate side-chains 398 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 292 time to evaluate : 3.758 ------------------------------------------------------------------------------- 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 321 GLN Chi-restraints excluded: chain B residue 326 ILE 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 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 673 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 868 GLU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1114 ILE 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 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 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 611 LEU Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain A residue 52 GLN 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 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 642 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 696 THR 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 1092 GLU Chi-restraints excluded: chain A residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 60 optimal weight: 2.9990 chunk 296 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 269 optimal weight: 0.0370 chunk 287 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 308 optimal weight: 0.5980 chunk 263 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 901 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.281635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.226918 restraints weight = 36738.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.211290 restraints weight = 52306.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.208699 restraints weight = 35137.808| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27241 Z= 0.153 Angle : 0.684 13.560 37141 Z= 0.328 Chirality : 0.048 0.444 4270 Planarity : 0.005 0.074 4762 Dihedral : 9.503 98.543 4326 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.04 % Favored : 89.66 % Rotamer: Outliers : 5.04 % Allowed : 17.60 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.14), residues: 3306 helix: 0.53 (0.22), residues: 580 sheet: -1.16 (0.21), residues: 574 loop : -2.65 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 436 HIS 0.007 0.001 HIS B1083 PHE 0.028 0.001 PHE A 55 TYR 0.022 0.001 TYR A1067 ARG 0.010 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00732 ( 28) link_NAG-ASN : angle 4.48311 ( 84) link_BETA1-4 : bond 0.00348 ( 5) link_BETA1-4 : angle 3.17960 ( 15) hydrogen bonds : bond 0.04087 ( 694) hydrogen bonds : angle 5.96783 ( 1956) SS BOND : bond 0.00514 ( 19) SS BOND : angle 1.25992 ( 38) covalent geometry : bond 0.00348 (27189) covalent geometry : angle 0.64625 (37004) *********************** 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 450 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 303 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 LEU cc_start: 0.8240 (tp) cc_final: 0.7921 (tp) REVERT: B 271 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7431 (mm-40) REVERT: B 340 GLU cc_start: 0.6252 (OUTLIER) cc_final: 0.4717 (tp30) REVERT: B 568 ASP cc_start: -0.1287 (OUTLIER) cc_final: -0.2532 (t0) REVERT: B 872 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8064 (tp-100) REVERT: B 895 GLN cc_start: 0.6133 (OUTLIER) cc_final: 0.5857 (mt0) REVERT: B 907 ASN cc_start: 0.7811 (t0) cc_final: 0.7598 (t0) REVERT: B 912 THR cc_start: 0.6757 (OUTLIER) cc_final: 0.5964 (m) REVERT: B 916 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6719 (tp) REVERT: B 935 GLN cc_start: 0.8332 (tt0) cc_final: 0.7747 (tt0) REVERT: B 1024 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8360 (tt) REVERT: B 1076 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8653 (p) REVERT: B 1083 HIS cc_start: 0.6889 (OUTLIER) cc_final: 0.6095 (m-70) REVERT: C 58 PHE cc_start: 0.6262 (OUTLIER) cc_final: 0.4430 (m-80) REVERT: C 78 ARG cc_start: 0.5018 (OUTLIER) cc_final: 0.3961 (ptt-90) REVERT: C 343 ASN cc_start: 0.4786 (OUTLIER) cc_final: 0.3864 (t0) REVERT: C 565 PHE cc_start: 0.6368 (m-80) cc_final: 0.5919 (m-80) REVERT: C 737 ASP cc_start: 0.5200 (OUTLIER) cc_final: 0.4268 (m-30) REVERT: C 935 GLN cc_start: 0.8368 (tt0) cc_final: 0.8126 (tt0) REVERT: C 978 ASN cc_start: 0.4847 (OUTLIER) cc_final: 0.4404 (m-40) REVERT: A 52 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: A 175 PHE cc_start: 0.2452 (OUTLIER) cc_final: 0.1575 (p90) REVERT: A 220 PHE cc_start: 0.1295 (OUTLIER) cc_final: -0.0500 (t80) REVERT: A 960 ASN cc_start: 0.8721 (t0) cc_final: 0.8324 (t0) REVERT: A 1092 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6748 (pp20) REVERT: A 1113 GLN cc_start: 0.8693 (mm-40) cc_final: 0.7925 (mm-40) outliers start: 147 outliers final: 103 residues processed: 409 average time/residue: 0.3420 time to fit residues: 232.5197 Evaluate side-chains 411 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 290 time to evaluate : 2.763 ------------------------------------------------------------------------------- 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 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 326 ILE 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 493 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 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 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 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 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 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 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 611 LEU Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 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 1097 SER Chi-restraints excluded: chain A residue 52 GLN 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 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 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 696 THR 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 1082 CYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 241 optimal weight: 0.0670 chunk 263 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 270 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 31 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 300 optimal weight: 0.0570 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 784 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** 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 = 0.281523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.220161 restraints weight = 36896.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.208740 restraints weight = 37972.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.211457 restraints weight = 31691.793| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.3034 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= 0.133 Angle : 0.668 13.547 37141 Z= 0.319 Chirality : 0.048 0.440 4270 Planarity : 0.004 0.072 4762 Dihedral : 9.014 95.941 4323 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.23 % Favored : 90.50 % Rotamer: Outliers : 4.70 % Allowed : 18.18 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.14), residues: 3306 helix: 0.66 (0.22), residues: 579 sheet: -1.04 (0.21), residues: 574 loop : -2.61 (0.12), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 64 HIS 0.011 0.001 HIS B1083 PHE 0.027 0.001 PHE A 55 TYR 0.021 0.001 TYR A1067 ARG 0.008 0.000 ARG A1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00724 ( 28) link_NAG-ASN : angle 4.40734 ( 84) link_BETA1-4 : bond 0.00374 ( 5) link_BETA1-4 : angle 3.24000 ( 15) hydrogen bonds : bond 0.03911 ( 694) hydrogen bonds : angle 5.81388 ( 1956) SS BOND : bond 0.00268 ( 19) SS BOND : angle 1.17060 ( 38) covalent geometry : bond 0.00299 (27189) covalent geometry : angle 0.63054 (37004) *********************** 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 430 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 293 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 271 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7484 (mm-40) REVERT: B 340 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.4356 (tp30) REVERT: B 568 ASP cc_start: -0.1180 (OUTLIER) cc_final: -0.2479 (t0) REVERT: B 872 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8118 (tp-100) REVERT: B 895 GLN cc_start: 0.5716 (OUTLIER) cc_final: 0.5399 (mt0) REVERT: B 907 ASN cc_start: 0.7805 (t0) cc_final: 0.7551 (t0) REVERT: B 912 THR cc_start: 0.6947 (OUTLIER) cc_final: 0.6290 (m) REVERT: B 916 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6773 (tp) REVERT: B 935 GLN cc_start: 0.8252 (tt0) cc_final: 0.7670 (tt0) REVERT: B 1076 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8703 (p) REVERT: B 1083 HIS cc_start: 0.6708 (OUTLIER) cc_final: 0.5981 (m-70) REVERT: C 58 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.4400 (m-80) REVERT: C 78 ARG cc_start: 0.4912 (OUTLIER) cc_final: 0.3853 (ptt-90) REVERT: C 343 ASN cc_start: 0.4440 (OUTLIER) cc_final: 0.3834 (t0) REVERT: C 737 ASP cc_start: 0.5217 (OUTLIER) cc_final: 0.4268 (m-30) REVERT: C 873 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.7511 (m-10) REVERT: C 935 GLN cc_start: 0.8294 (tt0) cc_final: 0.8059 (tt0) REVERT: C 978 ASN cc_start: 0.4674 (OUTLIER) cc_final: 0.4252 (m-40) REVERT: C 1045 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8258 (mmtm) REVERT: A 52 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6845 (tm-30) REVERT: A 175 PHE cc_start: 0.2304 (OUTLIER) cc_final: 0.1517 (p90) REVERT: A 220 PHE cc_start: 0.1383 (OUTLIER) cc_final: -0.0712 (t80) REVERT: A 660 TYR cc_start: 0.6606 (OUTLIER) cc_final: 0.6349 (m-80) REVERT: A 811 LYS cc_start: 0.7192 (tptp) cc_final: 0.6392 (mmtp) REVERT: A 918 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7858 (mp0) REVERT: A 960 ASN cc_start: 0.8458 (t0) cc_final: 0.8040 (t0) REVERT: A 1092 GLU cc_start: 0.7070 (pp20) cc_final: 0.6526 (pp20) REVERT: A 1113 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8142 (mm-40) outliers start: 137 outliers final: 95 residues processed: 395 average time/residue: 0.4174 time to fit residues: 282.1238 Evaluate side-chains 397 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 284 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 321 GLN 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 493 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 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 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 611 LEU Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 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 1043 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 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 596 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 696 THR 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 1082 CYS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 93 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 101 optimal weight: 0.0270 chunk 169 optimal weight: 2.9990 chunk 80 optimal weight: 0.0020 chunk 135 optimal weight: 0.0970 chunk 290 optimal weight: 0.9980 chunk 286 optimal weight: 2.9990 overall best weight: 0.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 784 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.283803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.222806 restraints weight = 36894.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.214710 restraints weight = 44782.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.204949 restraints weight = 28112.465| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.3229 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= 0.127 Angle : 0.659 12.906 37141 Z= 0.314 Chirality : 0.047 0.433 4270 Planarity : 0.004 0.072 4762 Dihedral : 8.575 91.873 4323 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.26 % Favored : 90.47 % Rotamer: Outliers : 4.32 % Allowed : 18.80 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.14), residues: 3306 helix: 0.75 (0.22), residues: 579 sheet: -0.98 (0.21), residues: 574 loop : -2.54 (0.12), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 64 HIS 0.006 0.001 HIS B1083 PHE 0.024 0.001 PHE A 55 TYR 0.021 0.001 TYR A1067 ARG 0.004 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00694 ( 28) link_NAG-ASN : angle 4.35606 ( 84) link_BETA1-4 : bond 0.00423 ( 5) link_BETA1-4 : angle 3.30368 ( 15) hydrogen bonds : bond 0.03721 ( 694) hydrogen bonds : angle 5.62273 ( 1956) SS BOND : bond 0.00227 ( 19) SS BOND : angle 1.04429 ( 38) covalent geometry : bond 0.00284 (27189) covalent geometry : angle 0.62236 (37004) *********************** 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 423 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 297 time to evaluate : 3.065 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: 0.5726 (pmm) cc_final: 0.4853 (pmm) REVERT: B 271 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7610 (mm-40) REVERT: B 289 VAL cc_start: 0.9150 (p) cc_final: 0.8906 (m) REVERT: B 568 ASP cc_start: -0.1725 (OUTLIER) cc_final: -0.2888 (t0) REVERT: B 872 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8188 (tp-100) REVERT: B 907 ASN cc_start: 0.7649 (t0) cc_final: 0.7436 (t0) REVERT: B 916 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7041 (tp) REVERT: B 935 GLN cc_start: 0.8135 (tt0) cc_final: 0.7533 (tt0) REVERT: B 1083 HIS cc_start: 0.6941 (OUTLIER) cc_final: 0.6339 (m-70) REVERT: B 1091 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.8226 (ttm-80) REVERT: C 58 PHE cc_start: 0.6254 (OUTLIER) cc_final: 0.4524 (m-80) REVERT: C 78 ARG cc_start: 0.4932 (OUTLIER) cc_final: 0.4280 (ptt-90) REVERT: C 343 ASN cc_start: 0.4853 (OUTLIER) cc_final: 0.4127 (t0) REVERT: C 565 PHE cc_start: 0.6296 (m-80) cc_final: 0.5865 (m-80) REVERT: C 737 ASP cc_start: 0.5194 (OUTLIER) cc_final: 0.4320 (m-30) REVERT: C 873 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.7802 (m-10) REVERT: C 978 ASN cc_start: 0.4880 (OUTLIER) cc_final: 0.4529 (m-40) REVERT: A 52 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: A 175 PHE cc_start: 0.2585 (OUTLIER) cc_final: 0.1652 (p90) REVERT: A 220 PHE cc_start: 0.1213 (OUTLIER) cc_final: -0.0802 (t80) REVERT: A 660 TYR cc_start: 0.6703 (OUTLIER) cc_final: 0.6498 (m-80) REVERT: A 811 LYS cc_start: 0.7316 (tptp) cc_final: 0.6565 (mmtp) REVERT: A 918 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8008 (mp0) REVERT: A 960 ASN cc_start: 0.8446 (t0) cc_final: 0.8035 (t0) REVERT: A 1089 PHE cc_start: 0.7413 (m-80) cc_final: 0.6917 (m-80) REVERT: A 1092 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6604 (pp20) REVERT: A 1113 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8055 (mm-40) outliers start: 126 outliers final: 95 residues processed: 389 average time/residue: 0.3323 time to fit residues: 217.3928 Evaluate side-chains 390 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 280 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 78 ARG 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 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 587 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 785 VAL 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 1043 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain A residue 52 GLN 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 275 PHE 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 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 696 THR 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 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1126 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 262 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 84 optimal weight: 0.3980 chunk 38 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 234 optimal weight: 0.0970 chunk 94 optimal weight: 0.4980 chunk 184 optimal weight: 0.7980 chunk 200 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.281343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.228291 restraints weight = 37018.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.214464 restraints weight = 52366.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.207612 restraints weight = 38283.924| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27241 Z= 0.133 Angle : 0.662 12.751 37141 Z= 0.316 Chirality : 0.047 0.431 4270 Planarity : 0.005 0.074 4762 Dihedral : 8.339 88.894 4320 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.10 % Favored : 90.59 % Rotamer: Outliers : 4.08 % Allowed : 19.18 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.14), residues: 3306 helix: 0.78 (0.22), residues: 576 sheet: -0.96 (0.21), residues: 579 loop : -2.52 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 64 HIS 0.010 0.001 HIS C 49 PHE 0.023 0.001 PHE A 55 TYR 0.021 0.001 TYR A1067 ARG 0.007 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00675 ( 28) link_NAG-ASN : angle 4.37655 ( 84) link_BETA1-4 : bond 0.00302 ( 5) link_BETA1-4 : angle 3.39397 ( 15) hydrogen bonds : bond 0.03719 ( 694) hydrogen bonds : angle 5.56269 ( 1956) SS BOND : bond 0.00228 ( 19) SS BOND : angle 1.07666 ( 38) covalent geometry : bond 0.00303 (27189) covalent geometry : angle 0.62476 (37004) *********************** 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 404 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 285 time to evaluate : 2.919 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: 0.5452 (pmm) cc_final: 0.4737 (pmm) REVERT: B 271 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7423 (mm-40) REVERT: B 289 VAL cc_start: 0.9160 (p) cc_final: 0.8894 (m) REVERT: B 568 ASP cc_start: -0.1421 (OUTLIER) cc_final: -0.2378 (t0) REVERT: B 872 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8120 (tp-100) REVERT: B 907 ASN cc_start: 0.7775 (t0) cc_final: 0.7540 (t0) REVERT: B 916 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.6790 (tp) REVERT: B 935 GLN cc_start: 0.8208 (tt0) cc_final: 0.7602 (tt0) REVERT: B 1083 HIS cc_start: 0.6904 (OUTLIER) cc_final: 0.6485 (m-70) REVERT: C 58 PHE cc_start: 0.6214 (OUTLIER) cc_final: 0.4502 (m-80) REVERT: C 78 ARG cc_start: 0.5058 (OUTLIER) cc_final: 0.4364 (ptt-90) REVERT: C 343 ASN cc_start: 0.4441 (OUTLIER) cc_final: 0.4155 (t0) REVERT: C 737 ASP cc_start: 0.5230 (OUTLIER) cc_final: 0.4358 (m-30) REVERT: C 873 TYR cc_start: 0.9099 (OUTLIER) cc_final: 0.7912 (m-10) REVERT: A 52 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: A 175 PHE cc_start: 0.2527 (OUTLIER) cc_final: 0.1665 (p90) REVERT: A 215 ASP cc_start: 0.3645 (OUTLIER) cc_final: 0.3317 (p0) REVERT: A 220 PHE cc_start: 0.1296 (OUTLIER) cc_final: -0.0749 (t80) REVERT: A 660 TYR cc_start: 0.6324 (OUTLIER) cc_final: 0.6103 (m-80) REVERT: A 811 LYS cc_start: 0.7361 (tptp) cc_final: 0.6560 (mmtp) REVERT: A 918 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7809 (mp0) REVERT: A 960 ASN cc_start: 0.8582 (t0) cc_final: 0.8218 (t0) REVERT: A 1089 PHE cc_start: 0.7351 (m-80) cc_final: 0.6790 (m-80) REVERT: A 1092 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6643 (pp20) REVERT: A 1113 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8137 (mm-40) outliers start: 119 outliers final: 97 residues processed: 374 average time/residue: 0.4496 time to fit residues: 291.7143 Evaluate side-chains 392 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 280 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU 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 336 CYS 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 582 LEU 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 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 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 78 ARG 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 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 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 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 727 LEU Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 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 1043 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 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 275 PHE 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 513 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 664 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 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 1092 GLU Chi-restraints excluded: chain A residue 1126 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 302 optimal weight: 0.6980 chunk 182 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 94 optimal weight: 0.3980 chunk 311 optimal weight: 0.5980 chunk 205 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 195 optimal weight: 0.3980 chunk 11 optimal weight: 30.0000 chunk 218 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 784 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.280570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.228172 restraints weight = 36867.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.214946 restraints weight = 53436.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.210058 restraints weight = 42998.164| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27241 Z= 0.144 Angle : 0.667 12.271 37141 Z= 0.320 Chirality : 0.047 0.435 4270 Planarity : 0.005 0.072 4762 Dihedral : 8.023 82.468 4319 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.41 % Favored : 90.29 % Rotamer: Outliers : 3.95 % Allowed : 19.62 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.14), residues: 3306 helix: 0.76 (0.22), residues: 576 sheet: -0.95 (0.21), residues: 579 loop : -2.50 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 436 HIS 0.008 0.001 HIS C 49 PHE 0.022 0.001 PHE A 55 TYR 0.023 0.001 TYR A1067 ARG 0.010 0.000 ARG C 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00710 ( 28) link_NAG-ASN : angle 4.38986 ( 84) link_BETA1-4 : bond 0.00395 ( 5) link_BETA1-4 : angle 3.38822 ( 15) hydrogen bonds : bond 0.03747 ( 694) hydrogen bonds : angle 5.52667 ( 1956) SS BOND : bond 0.00242 ( 19) SS BOND : angle 1.04640 ( 38) covalent geometry : bond 0.00330 (27189) covalent geometry : angle 0.63025 (37004) ********************** 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 399 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 284 time to evaluate : 2.937 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: 0.5049 (pmm) cc_final: 0.4485 (pmm) REVERT: B 271 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7398 (mm-40) REVERT: B 289 VAL cc_start: 0.9202 (p) cc_final: 0.8982 (m) REVERT: B 568 ASP cc_start: -0.0843 (OUTLIER) cc_final: -0.2325 (t0) REVERT: B 907 ASN cc_start: 0.8011 (t0) cc_final: 0.7708 (t0) REVERT: B 916 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.6865 (tp) REVERT: B 935 GLN cc_start: 0.8129 (tt0) cc_final: 0.7507 (tt0) REVERT: B 1083 HIS cc_start: 0.6966 (OUTLIER) cc_final: 0.6565 (m-70) REVERT: B 1092 GLU cc_start: 0.8359 (pt0) cc_final: 0.7936 (pm20) REVERT: C 58 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.4489 (m-80) REVERT: C 565 PHE cc_start: 0.6138 (m-80) cc_final: 0.5854 (m-80) REVERT: C 737 ASP cc_start: 0.5186 (OUTLIER) cc_final: 0.4361 (m-30) REVERT: C 867 ASP cc_start: 0.8198 (m-30) cc_final: 0.7841 (m-30) REVERT: A 52 GLN cc_start: 0.7425 (pm20) cc_final: 0.7031 (tm-30) REVERT: A 175 PHE cc_start: 0.2309 (OUTLIER) cc_final: 0.1520 (p90) REVERT: A 215 ASP cc_start: 0.3807 (OUTLIER) cc_final: 0.3417 (p0) REVERT: A 220 PHE cc_start: 0.1326 (OUTLIER) cc_final: -0.0754 (t80) REVERT: A 811 LYS cc_start: 0.7478 (tptp) cc_final: 0.6735 (mmtp) REVERT: A 918 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7898 (mp0) REVERT: A 960 ASN cc_start: 0.8437 (t0) cc_final: 0.8070 (t0) REVERT: A 1038 LYS cc_start: 0.8179 (mmmt) cc_final: 0.7621 (mptt) REVERT: A 1089 PHE cc_start: 0.7487 (m-80) cc_final: 0.7016 (m-80) REVERT: A 1092 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6487 (pp20) REVERT: A 1113 GLN cc_start: 0.8772 (mm-40) cc_final: 0.7983 (mm-40) outliers start: 115 outliers final: 94 residues processed: 369 average time/residue: 0.3734 time to fit residues: 232.1703 Evaluate side-chains 379 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 276 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 CYS 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 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 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 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 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 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 727 LEU Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 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 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 275 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 664 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 931 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1126 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 269 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 200 optimal weight: 0.2980 chunk 149 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 329 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 237 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** 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 703 ASN ** 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 = 0.4812 r_free = 0.4812 target = 0.281980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.229108 restraints weight = 37006.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.213683 restraints weight = 55500.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.210853 restraints weight = 35397.232| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 27241 Z= 0.155 Angle : 0.772 59.195 37141 Z= 0.408 Chirality : 0.047 0.434 4270 Planarity : 0.004 0.072 4762 Dihedral : 8.011 82.413 4317 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.44 % Favored : 90.26 % Rotamer: Outliers : 3.81 % Allowed : 19.52 % Favored : 76.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.14), residues: 3306 helix: 0.76 (0.22), residues: 576 sheet: -0.95 (0.21), residues: 579 loop : -2.50 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 436 HIS 0.008 0.001 HIS C 49 PHE 0.022 0.001 PHE A 55 TYR 0.022 0.001 TYR A1067 ARG 0.006 0.000 ARG C1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00692 ( 28) link_NAG-ASN : angle 4.39347 ( 84) link_BETA1-4 : bond 0.00583 ( 5) link_BETA1-4 : angle 3.40061 ( 15) hydrogen bonds : bond 0.03759 ( 694) hydrogen bonds : angle 5.53193 ( 1956) SS BOND : bond 0.00247 ( 19) SS BOND : angle 1.06719 ( 38) covalent geometry : bond 0.00347 (27189) covalent geometry : angle 0.74026 (37004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11548.47 seconds wall clock time: 206 minutes 45.97 seconds (12405.97 seconds total)