Starting phenix.real_space_refine on Mon Aug 25 11:34:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eyg_28686/08_2025/8eyg_28686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eyg_28686/08_2025/8eyg_28686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eyg_28686/08_2025/8eyg_28686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eyg_28686/08_2025/8eyg_28686.map" model { file = "/net/cci-nas-00/data/ceres_data/8eyg_28686/08_2025/8eyg_28686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eyg_28686/08_2025/8eyg_28686.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.020 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 124 5.16 5 C 17484 2.51 5 N 4544 2.21 5 O 5333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27485 Number of models: 1 Model: "" Number of chains: 14 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: "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: "E" 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: "F" 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: "D" 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: "J" 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: "K" 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: "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 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: 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: 7.01, per 1000 atoms: 0.26 Number of scatterers: 27485 At special positions: 0 Unit cell: (162.503, 162.503, 226.649, 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 124 16.00 O 5333 8.00 N 4544 7.00 C 17484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " 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=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " 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 D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 657 " " 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 C1208 " - " ASN C 343 " " NAG D 1 " - " ASN B1134 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B 343 " " NAG K 1 " - " ASN A 343 " Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6442 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 54 sheets defined 20.8% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.862A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.042A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.729A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.504A 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 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.201A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.679A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.563A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.659A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.617A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 989 through 1033 removed outlier: 4.733A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 4.036A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1146' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.669A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 572 removed outlier: 3.539A pdb=" N THR B 572 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 639 removed outlier: 3.833A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 637 " --> pdb=" O TRP B 633 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.688A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.968A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.897A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.513A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.912A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.749A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 Processing helix chain 'B' and resid 939 through 940 No H-bonds generated for 'chain 'B' and resid 939 through 940' Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.753A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.159A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1043 removed outlier: 3.854A pdb=" N PHE B1042 " --> pdb=" O ARG B1039 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N CYS B1043 " --> pdb=" O VAL B1040 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1039 through 1043' Processing helix chain 'B' and resid 1141 through 1149 Processing helix chain 'C' and resid 294 through 303 removed outlier: 4.100A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 removed outlier: 4.773A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 371' Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.603A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 4.086A pdb=" N TYR C 421 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.693A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.556A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.502A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 855 removed outlier: 4.076A pdb=" N LYS C 854 " --> pdb=" O CYS C 851 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE C 855 " --> pdb=" O ALA C 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 851 through 855' Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.656A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.737A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.245A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 4.183A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.021A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 981 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.102A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.737A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.792A 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 'E' and resid 26 through 30 removed outlier: 3.907A pdb=" N SER E 30 " --> pdb=" O GLY E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.969A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.729A pdb=" N LYS F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.342A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP A 64 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE A 92 " --> pdb=" O PHE A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.806A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.743A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 115 through 121 removed outlier: 4.374A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 115 through 121 removed outlier: 3.644A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 156 removed outlier: 6.282A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS A 245 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 195 through 197 removed outlier: 3.535A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.912A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 400 through 402 Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.016A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 642 through 644 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.041A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 719 removed outlier: 7.310A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 722 through 727 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.524A pdb=" N HIS A1083 " --> pdb=" O LYS A1086 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.558A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 53 Processing sheet with id=AC3, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.741A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 144 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER B 155 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 278 through 279 removed outlier: 4.330A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.573A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 400 through 402 removed outlier: 3.588A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC8, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AC9, first strand: chain 'B' and resid 551 through 553 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.955A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 672 " --> pdb=" O ILE B 664 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.610A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 removed outlier: 3.589A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD6, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.099A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.513A pdb=" N PHE C 192 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 104 through 106 Processing sheet with id=AE3, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.725A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 151 through 156 removed outlier: 3.738A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE6, first strand: chain 'C' and resid 398 through 399 removed outlier: 3.524A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE8, first strand: chain 'C' and resid 664 through 667 removed outlier: 3.756A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.471A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.471A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.606A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.773A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF5, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.772A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.789A pdb=" N THR E 111 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR E 94 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL E 113 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 4 through 7 removed outlier: 4.065A pdb=" N VAL F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA F 23 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER F 7 " --> pdb=" O SER F 21 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU F 20 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU F 81 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR F 69 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.575A pdb=" N TYR F 94 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL F 93 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY F 35 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG F 38 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU F 46 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 49 through 51 762 hydrogen bonds defined for protein. 2055 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: 7.12 Time building geometry restraints manager: 3.51 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: 6679 1.33 - 1.45: 6016 1.45 - 1.58: 15264 1.58 - 1.70: 0 1.70 - 1.82: 158 Bond restraints: 28117 Sorted by residual: bond pdb=" C1 NAG A1201 " pdb=" O5 NAG A1201 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" N LEU C 984 " pdb=" CA LEU C 984 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.76e+00 bond pdb=" N SER A 884 " pdb=" CA SER A 884 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.06e-02 8.90e+03 9.75e+00 bond pdb=" N ARG C 983 " pdb=" CA ARG C 983 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.14e-02 7.69e+03 8.29e+00 bond pdb=" C PRO C 986 " pdb=" O PRO C 986 " ideal model delta sigma weight residual 1.240 1.209 0.032 1.12e-02 7.97e+03 7.97e+00 ... (remaining 28112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 37557 2.09 - 4.17: 633 4.17 - 6.26: 60 6.26 - 8.35: 5 8.35 - 10.43: 4 Bond angle restraints: 38259 Sorted by residual: angle pdb=" C ALA A 522 " pdb=" CA ALA A 522 " pdb=" CB ALA A 522 " ideal model delta sigma weight residual 116.54 110.30 6.24 1.15e+00 7.56e-01 2.94e+01 angle pdb=" N LEU C 335 " pdb=" CA LEU C 335 " pdb=" C LEU C 335 " ideal model delta sigma weight residual 110.91 116.28 -5.37 1.17e+00 7.31e-01 2.10e+01 angle pdb=" C ASN C 343 " pdb=" CA ASN C 343 " pdb=" CB ASN C 343 " ideal model delta sigma weight residual 115.79 110.60 5.19 1.19e+00 7.06e-01 1.90e+01 angle pdb=" N ASP C1041 " pdb=" CA ASP C1041 " pdb=" C ASP C1041 " ideal model delta sigma weight residual 110.44 105.39 5.05 1.20e+00 6.94e-01 1.77e+01 angle pdb=" N PHE A 338 " pdb=" CA PHE A 338 " pdb=" C PHE A 338 " ideal model delta sigma weight residual 114.75 109.52 5.23 1.26e+00 6.30e-01 1.72e+01 ... (remaining 38254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.90: 16304 24.90 - 49.79: 659 49.79 - 74.68: 113 74.68 - 99.58: 54 99.58 - 124.47: 26 Dihedral angle restraints: 17156 sinusoidal: 7123 harmonic: 10033 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 31.99 61.01 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual 93.00 52.32 40.68 1 1.00e+01 1.00e-02 2.32e+01 dihedral pdb=" CA ASN C 334 " pdb=" C ASN C 334 " pdb=" N LEU C 335 " pdb=" CA LEU C 335 " ideal model delta harmonic sigma weight residual 180.00 158.40 21.60 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 17153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3557 0.054 - 0.107: 723 0.107 - 0.161: 117 0.161 - 0.215: 11 0.215 - 0.268: 4 Chirality restraints: 4412 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.80e+00 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 -2.16 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 4409 not shown) Planarity restraints: 4952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1209 " 0.294 2.00e-02 2.50e+03 2.48e-01 7.69e+02 pdb=" C7 NAG A1209 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A1209 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG A1209 " -0.425 2.00e-02 2.50e+03 pdb=" O7 NAG A1209 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 336 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO C 337 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO B 987 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.030 5.00e-02 4.00e+02 ... (remaining 4949 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 555 2.67 - 3.23: 26610 3.23 - 3.78: 40648 3.78 - 4.34: 54193 4.34 - 4.90: 88988 Nonbonded interactions: 210994 Sorted by model distance: nonbonded pdb=" OD1 ASP B 53 " pdb=" N LEU B 54 " model vdw 2.112 3.120 nonbonded pdb=" O PRO B 384 " pdb=" OG1 THR B 385 " model vdw 2.190 3.040 nonbonded pdb=" O4 NAG C1201 " pdb=" O7 NAG C1201 " model vdw 2.210 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.223 3.040 ... (remaining 210989 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 1209)) 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 1307)) selection = (chain 'C' and (resid 14 through 675 or resid 690 through 827 or resid 852 throu \ gh 1146 or resid 1203 through 1209)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 6.420 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: 0.050 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.990 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 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 : 0.004 0.069 28172 Z= 0.185 Angle : 0.629 10.435 38405 Z= 0.334 Chirality : 0.045 0.268 4412 Planarity : 0.005 0.248 4922 Dihedral : 15.161 124.475 10657 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.56 % Favored : 90.88 % Rotamer: Outliers : 0.63 % Allowed : 15.98 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.14), residues: 3422 helix: 1.77 (0.22), residues: 573 sheet: -1.46 (0.20), residues: 638 loop : -2.15 (0.12), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1000 TYR 0.017 0.001 TYR B 904 PHE 0.028 0.001 PHE B 486 TRP 0.011 0.001 TRP A 64 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00356 (28117) covalent geometry : angle 0.61901 (38259) SS BOND : bond 0.00209 ( 19) SS BOND : angle 0.92276 ( 38) hydrogen bonds : bond 0.23370 ( 751) hydrogen bonds : angle 8.56041 ( 2055) link_BETA1-4 : bond 0.00628 ( 6) link_BETA1-4 : angle 2.51217 ( 18) link_NAG-ASN : bond 0.00447 ( 30) link_NAG-ASN : angle 2.06576 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 276 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.6797 (mtt90) cc_final: 0.6594 (mtt90) REVERT: B 1135 ASN cc_start: 0.8276 (t0) cc_final: 0.7804 (t0) REVERT: C 725 GLU cc_start: 0.8330 (tt0) cc_final: 0.8094 (tt0) REVERT: F 19 ARG cc_start: 0.7349 (mmm-85) cc_final: 0.6900 (mmm-85) outliers start: 19 outliers final: 11 residues processed: 288 average time/residue: 0.1701 time to fit residues: 82.1998 Evaluate side-chains 275 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 264 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 105 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.0050 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.0040 chunk 298 optimal weight: 0.9980 overall best weight: 0.6008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 901 GLN A1005 GLN B 563 GLN B 764 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 703 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1088 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.258787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.181598 restraints weight = 34662.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.177142 restraints weight = 37553.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.169670 restraints weight = 24442.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.167900 restraints weight = 21545.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.168547 restraints weight = 20132.617| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28172 Z= 0.147 Angle : 0.620 10.854 38405 Z= 0.309 Chirality : 0.046 0.252 4412 Planarity : 0.004 0.065 4922 Dihedral : 10.881 109.493 4501 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.74 % Favored : 90.88 % Rotamer: Outliers : 2.83 % Allowed : 14.45 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.14), residues: 3422 helix: 1.85 (0.22), residues: 586 sheet: -1.50 (0.19), residues: 669 loop : -2.08 (0.12), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.016 0.001 TYR C1067 PHE 0.018 0.001 PHE B1042 TRP 0.016 0.001 TRP B 436 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00334 (28117) covalent geometry : angle 0.61113 (38259) SS BOND : bond 0.00268 ( 19) SS BOND : angle 1.09186 ( 38) hydrogen bonds : bond 0.04483 ( 751) hydrogen bonds : angle 6.16930 ( 2055) link_BETA1-4 : bond 0.00159 ( 6) link_BETA1-4 : angle 2.23516 ( 18) link_NAG-ASN : bond 0.00384 ( 30) link_NAG-ASN : angle 1.92807 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 292 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.0152 (OUTLIER) cc_final: -0.0569 (mt) REVERT: A 559 PHE cc_start: 0.6770 (p90) cc_final: 0.6444 (p90) REVERT: A 614 ASP cc_start: 0.7180 (p0) cc_final: 0.6880 (p0) REVERT: A 983 ARG cc_start: 0.8091 (ptp-170) cc_final: 0.7733 (ptp90) REVERT: B 41 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7657 (mmmt) REVERT: B 177 MET cc_start: 0.5191 (tpt) cc_final: 0.4473 (tpt) REVERT: B 290 ASP cc_start: 0.8435 (t70) cc_final: 0.8205 (t0) REVERT: B 954 GLN cc_start: 0.8013 (mt0) cc_final: 0.7725 (mt0) REVERT: B 1094 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8876 (m) REVERT: C 58 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6362 (m-80) REVERT: C 315 THR cc_start: 0.7161 (p) cc_final: 0.6213 (t) REVERT: C 725 GLU cc_start: 0.8423 (tt0) cc_final: 0.8162 (tt0) REVERT: C 823 PHE cc_start: 0.7855 (t80) cc_final: 0.7622 (t80) REVERT: C 995 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7999 (tpp80) REVERT: E 34 MET cc_start: 0.3737 (pmm) cc_final: 0.2799 (pmm) REVERT: F 19 ARG cc_start: 0.7333 (mmm-85) cc_final: 0.6881 (mmm-85) outliers start: 85 outliers final: 47 residues processed: 360 average time/residue: 0.1630 time to fit residues: 99.4167 Evaluate side-chains 323 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 272 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 105 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 272 optimal weight: 0.3980 chunk 188 optimal weight: 0.9990 chunk 301 optimal weight: 2.9990 chunk 337 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 186 optimal weight: 0.0670 chunk 156 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 341 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 764 ASN B1005 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1088 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.257607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.193990 restraints weight = 34593.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.187204 restraints weight = 55782.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.183402 restraints weight = 43699.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.182073 restraints weight = 41259.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.181025 restraints weight = 32177.875| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28172 Z= 0.136 Angle : 0.581 9.973 38405 Z= 0.290 Chirality : 0.045 0.231 4412 Planarity : 0.004 0.066 4922 Dihedral : 9.042 106.537 4494 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.33 % Favored : 91.23 % Rotamer: Outliers : 3.20 % Allowed : 14.98 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.14), residues: 3422 helix: 1.98 (0.22), residues: 580 sheet: -1.30 (0.19), residues: 677 loop : -2.05 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.019 0.001 TYR B 453 PHE 0.017 0.001 PHE B 192 TRP 0.011 0.001 TRP B 436 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00310 (28117) covalent geometry : angle 0.57139 (38259) SS BOND : bond 0.00289 ( 19) SS BOND : angle 1.12345 ( 38) hydrogen bonds : bond 0.04369 ( 751) hydrogen bonds : angle 5.73765 ( 2055) link_BETA1-4 : bond 0.00608 ( 6) link_BETA1-4 : angle 2.62936 ( 18) link_NAG-ASN : bond 0.00404 ( 30) link_NAG-ASN : angle 1.86786 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 297 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.0346 (OUTLIER) cc_final: -0.0345 (mt) REVERT: A 556 ASN cc_start: 0.7623 (p0) cc_final: 0.7180 (p0) REVERT: A 559 PHE cc_start: 0.7008 (p90) cc_final: 0.6801 (p90) REVERT: A 562 PHE cc_start: 0.8264 (p90) cc_final: 0.7929 (p90) REVERT: A 614 ASP cc_start: 0.7121 (p0) cc_final: 0.6816 (p0) REVERT: A 696 THR cc_start: 0.8773 (t) cc_final: 0.8568 (m) REVERT: A 966 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8628 (mp) REVERT: B 41 LYS cc_start: 0.7868 (mmmt) cc_final: 0.7085 (mmtt) REVERT: B 177 MET cc_start: 0.5182 (tpt) cc_final: 0.4410 (tpt) REVERT: B 281 GLU cc_start: 0.8158 (pp20) cc_final: 0.7700 (pp20) REVERT: B 364 ASP cc_start: 0.7222 (t0) cc_final: 0.6894 (t0) REVERT: B 954 GLN cc_start: 0.7990 (mt0) cc_final: 0.7676 (mt0) REVERT: B 1094 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8894 (m) REVERT: C 58 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6379 (m-80) REVERT: C 315 THR cc_start: 0.7141 (p) cc_final: 0.6176 (t) REVERT: C 725 GLU cc_start: 0.8372 (tt0) cc_final: 0.7990 (tt0) REVERT: C 823 PHE cc_start: 0.7877 (t80) cc_final: 0.7639 (t80) REVERT: C 919 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7105 (p0) REVERT: C 995 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7957 (tpp80) REVERT: E 34 MET cc_start: 0.4201 (pmm) cc_final: 0.3237 (pmm) REVERT: F 19 ARG cc_start: 0.7287 (mmm-85) cc_final: 0.6788 (mmm-85) outliers start: 96 outliers final: 55 residues processed: 369 average time/residue: 0.1647 time to fit residues: 102.1923 Evaluate side-chains 337 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 105 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 94 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 170 optimal weight: 0.5980 chunk 203 optimal weight: 0.4980 chunk 111 optimal weight: 8.9990 chunk 329 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 901 GLN B 764 ASN B1005 GLN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 935 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 = 0.4553 r_free = 0.4553 target = 0.254728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.181590 restraints weight = 34414.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.177169 restraints weight = 49525.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.176104 restraints weight = 46726.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.173126 restraints weight = 33520.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.175195 restraints weight = 30663.827| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28172 Z= 0.160 Angle : 0.598 9.523 38405 Z= 0.298 Chirality : 0.045 0.247 4412 Planarity : 0.004 0.067 4922 Dihedral : 8.392 102.520 4492 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.71 % Favored : 90.88 % Rotamer: Outliers : 3.70 % Allowed : 15.31 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.14), residues: 3422 helix: 1.98 (0.22), residues: 586 sheet: -1.30 (0.19), residues: 674 loop : -2.02 (0.13), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 403 TYR 0.020 0.001 TYR B 421 PHE 0.025 0.001 PHE C 374 TRP 0.026 0.001 TRP F 36 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00375 (28117) covalent geometry : angle 0.58684 (38259) SS BOND : bond 0.00485 ( 19) SS BOND : angle 1.38516 ( 38) hydrogen bonds : bond 0.04190 ( 751) hydrogen bonds : angle 5.54399 ( 2055) link_BETA1-4 : bond 0.00422 ( 6) link_BETA1-4 : angle 2.70192 ( 18) link_NAG-ASN : bond 0.00398 ( 30) link_NAG-ASN : angle 1.95998 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 298 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.2964 (OUTLIER) cc_final: 0.2529 (p90) REVERT: A 556 ASN cc_start: 0.7609 (p0) cc_final: 0.7138 (p0) REVERT: A 614 ASP cc_start: 0.7033 (p0) cc_final: 0.6725 (p0) REVERT: A 966 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8777 (mp) REVERT: B 41 LYS cc_start: 0.7851 (mmmt) cc_final: 0.7624 (mmmt) REVERT: B 177 MET cc_start: 0.5229 (tpt) cc_final: 0.4460 (tpt) REVERT: B 281 GLU cc_start: 0.8084 (pp20) cc_final: 0.7669 (pp20) REVERT: B 364 ASP cc_start: 0.7243 (t0) cc_final: 0.7025 (t0) REVERT: B 918 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7767 (mt-10) REVERT: B 954 GLN cc_start: 0.8020 (mt0) cc_final: 0.7686 (mt0) REVERT: B 1094 VAL cc_start: 0.9153 (OUTLIER) cc_final: 0.8824 (m) REVERT: B 1130 ILE cc_start: 0.8066 (pt) cc_final: 0.7837 (pt) REVERT: B 1135 ASN cc_start: 0.8120 (t0) cc_final: 0.7727 (t0) REVERT: C 58 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6479 (m-80) REVERT: C 315 THR cc_start: 0.7236 (p) cc_final: 0.6270 (t) REVERT: C 537 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8340 (tttm) REVERT: C 725 GLU cc_start: 0.8339 (tt0) cc_final: 0.7955 (tt0) REVERT: C 823 PHE cc_start: 0.7931 (t80) cc_final: 0.7661 (t80) REVERT: C 919 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.7235 (p0) REVERT: C 995 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8005 (tpp80) REVERT: E 34 MET cc_start: 0.4085 (pmm) cc_final: 0.2939 (pmm) REVERT: F 19 ARG cc_start: 0.7269 (mmm-85) cc_final: 0.6794 (mmm-85) outliers start: 111 outliers final: 74 residues processed: 382 average time/residue: 0.1645 time to fit residues: 105.6540 Evaluate side-chains 362 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 281 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 105 PHE Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 263 optimal weight: 8.9990 chunk 258 optimal weight: 0.0770 chunk 63 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 308 optimal weight: 0.9980 chunk 272 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 280 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 332 optimal weight: 0.0870 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 764 ASN B 774 GLN B1005 GLN C 787 GLN ** C 804 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 = 0.4567 r_free = 0.4567 target = 0.256230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.179247 restraints weight = 34469.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.174456 restraints weight = 40730.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.162786 restraints weight = 23760.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.162766 restraints weight = 25482.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.163652 restraints weight = 22983.854| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28172 Z= 0.131 Angle : 0.578 11.326 38405 Z= 0.287 Chirality : 0.045 0.237 4412 Planarity : 0.004 0.062 4922 Dihedral : 7.899 96.511 4492 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.15 % Favored : 91.50 % Rotamer: Outliers : 3.79 % Allowed : 15.78 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.14), residues: 3422 helix: 2.03 (0.22), residues: 592 sheet: -1.21 (0.19), residues: 684 loop : -1.99 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.014 0.001 TYR F 95 PHE 0.028 0.001 PHE A 559 TRP 0.028 0.001 TRP F 36 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00302 (28117) covalent geometry : angle 0.56689 (38259) SS BOND : bond 0.00312 ( 19) SS BOND : angle 1.20539 ( 38) hydrogen bonds : bond 0.03912 ( 751) hydrogen bonds : angle 5.32212 ( 2055) link_BETA1-4 : bond 0.00403 ( 6) link_BETA1-4 : angle 2.82184 ( 18) link_NAG-ASN : bond 0.00379 ( 30) link_NAG-ASN : angle 1.96005 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 297 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.3057 (OUTLIER) cc_final: 0.2505 (p90) REVERT: A 556 ASN cc_start: 0.7783 (OUTLIER) cc_final: 0.7170 (p0) REVERT: A 614 ASP cc_start: 0.7142 (p0) cc_final: 0.6829 (p0) REVERT: A 966 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8729 (mp) REVERT: B 41 LYS cc_start: 0.7849 (mmmt) cc_final: 0.7053 (mmtt) REVERT: B 53 ASP cc_start: 0.7562 (t0) cc_final: 0.7335 (t0) REVERT: B 177 MET cc_start: 0.5283 (tpt) cc_final: 0.4596 (tpt) REVERT: B 281 GLU cc_start: 0.8226 (pp20) cc_final: 0.7812 (pp20) REVERT: B 353 TRP cc_start: 0.7007 (p90) cc_final: 0.6688 (p90) REVERT: B 364 ASP cc_start: 0.7697 (t0) cc_final: 0.7333 (t0) REVERT: B 420 ASP cc_start: 0.8236 (m-30) cc_final: 0.7858 (p0) REVERT: B 752 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8683 (mp) REVERT: B 954 GLN cc_start: 0.7981 (mt0) cc_final: 0.7572 (mt0) REVERT: B 990 GLU cc_start: 0.8050 (tt0) cc_final: 0.7665 (tt0) REVERT: B 1130 ILE cc_start: 0.8053 (pt) cc_final: 0.7820 (pt) REVERT: B 1135 ASN cc_start: 0.8301 (t0) cc_final: 0.7989 (t0) REVERT: C 56 LEU cc_start: 0.2640 (OUTLIER) cc_final: 0.2218 (tp) REVERT: C 58 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6268 (m-80) REVERT: C 315 THR cc_start: 0.7169 (p) cc_final: 0.6226 (t) REVERT: C 537 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8370 (tttm) REVERT: C 725 GLU cc_start: 0.8341 (tt0) cc_final: 0.7873 (tt0) REVERT: C 731 MET cc_start: 0.9075 (ptt) cc_final: 0.8745 (ptt) REVERT: C 919 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.7118 (p0) REVERT: C 995 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8040 (tpp80) REVERT: E 34 MET cc_start: 0.3621 (pmm) cc_final: 0.2635 (pmm) REVERT: F 19 ARG cc_start: 0.7417 (mmm-85) cc_final: 0.6855 (mmm-85) outliers start: 114 outliers final: 75 residues processed: 384 average time/residue: 0.1359 time to fit residues: 88.9056 Evaluate side-chains 368 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 284 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 105 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 46 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 291 optimal weight: 3.9990 chunk 211 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 151 optimal weight: 0.0770 chunk 230 optimal weight: 10.0000 chunk 302 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 315 optimal weight: 0.9980 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 901 GLN B 703 ASN B 764 ASN B 774 GLN B1005 GLN C 282 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.251208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.182535 restraints weight = 34343.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.167103 restraints weight = 57571.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.161096 restraints weight = 38034.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.160042 restraints weight = 32803.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.160523 restraints weight = 25923.075| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28172 Z= 0.211 Angle : 0.655 12.465 38405 Z= 0.324 Chirality : 0.047 0.233 4412 Planarity : 0.004 0.066 4922 Dihedral : 7.701 90.963 4492 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.12 % Favored : 90.53 % Rotamer: Outliers : 4.36 % Allowed : 16.08 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.14), residues: 3422 helix: 1.79 (0.22), residues: 591 sheet: -1.31 (0.19), residues: 693 loop : -2.01 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1000 TYR 0.019 0.001 TYR B 495 PHE 0.024 0.002 PHE C 562 TRP 0.015 0.001 TRP F 36 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00506 (28117) covalent geometry : angle 0.64282 (38259) SS BOND : bond 0.00403 ( 19) SS BOND : angle 1.58055 ( 38) hydrogen bonds : bond 0.04491 ( 751) hydrogen bonds : angle 5.43297 ( 2055) link_BETA1-4 : bond 0.00443 ( 6) link_BETA1-4 : angle 2.98530 ( 18) link_NAG-ASN : bond 0.00403 ( 30) link_NAG-ASN : angle 2.10293 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 289 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 TYR cc_start: 0.2349 (OUTLIER) cc_final: 0.1885 (t80) REVERT: A 266 TYR cc_start: -0.1772 (OUTLIER) cc_final: -0.4082 (t80) REVERT: A 347 PHE cc_start: 0.2954 (OUTLIER) cc_final: 0.2519 (p90) REVERT: A 556 ASN cc_start: 0.7714 (OUTLIER) cc_final: 0.7106 (p0) REVERT: A 586 ASP cc_start: 0.8051 (t0) cc_final: 0.7651 (t0) REVERT: A 614 ASP cc_start: 0.7338 (p0) cc_final: 0.7042 (p0) REVERT: A 756 TYR cc_start: 0.8507 (t80) cc_final: 0.7554 (t80) REVERT: B 41 LYS cc_start: 0.7941 (mmmt) cc_final: 0.7173 (mmtt) REVERT: B 177 MET cc_start: 0.5283 (tpt) cc_final: 0.4919 (tpt) REVERT: B 281 GLU cc_start: 0.8164 (pp20) cc_final: 0.7797 (pp20) REVERT: B 353 TRP cc_start: 0.7198 (p90) cc_final: 0.6863 (p90) REVERT: B 364 ASP cc_start: 0.7772 (t0) cc_final: 0.7454 (t0) REVERT: B 453 TYR cc_start: 0.8274 (p90) cc_final: 0.7963 (p90) REVERT: B 918 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7885 (mt-10) REVERT: B 954 GLN cc_start: 0.8016 (mt0) cc_final: 0.7579 (mt0) REVERT: B 990 GLU cc_start: 0.8164 (tt0) cc_final: 0.7892 (tt0) REVERT: B 1010 GLN cc_start: 0.8493 (tp40) cc_final: 0.8166 (tp40) REVERT: B 1135 ASN cc_start: 0.8338 (t0) cc_final: 0.7858 (t0) REVERT: C 56 LEU cc_start: 0.2930 (OUTLIER) cc_final: 0.2590 (tp) REVERT: C 58 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.6458 (m-80) REVERT: C 537 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8255 (tttm) REVERT: C 725 GLU cc_start: 0.8441 (tt0) cc_final: 0.8066 (tt0) REVERT: C 731 MET cc_start: 0.9169 (ptt) cc_final: 0.8855 (ptt) REVERT: C 995 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8136 (tpp80) REVERT: E 34 MET cc_start: 0.3615 (pmm) cc_final: 0.2715 (pmm) REVERT: F 81 LEU cc_start: 0.4460 (pt) cc_final: 0.3972 (pp) outliers start: 131 outliers final: 87 residues processed: 389 average time/residue: 0.1463 time to fit residues: 96.6235 Evaluate side-chains 376 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 281 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 260 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 223 optimal weight: 0.0470 chunk 124 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 247 optimal weight: 0.6980 chunk 303 optimal weight: 1.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 901 GLN B 764 ASN B 774 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN ** C 804 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 = 0.4531 r_free = 0.4531 target = 0.252073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.182274 restraints weight = 34091.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.177522 restraints weight = 49366.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.176574 restraints weight = 49883.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.173605 restraints weight = 35579.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.174924 restraints weight = 32021.543| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28172 Z= 0.177 Angle : 0.626 13.153 38405 Z= 0.310 Chirality : 0.046 0.236 4412 Planarity : 0.004 0.066 4922 Dihedral : 7.357 84.989 4490 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.36 % Favored : 91.29 % Rotamer: Outliers : 3.93 % Allowed : 16.44 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.14), residues: 3422 helix: 1.77 (0.22), residues: 599 sheet: -1.29 (0.19), residues: 699 loop : -2.02 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 454 TYR 0.029 0.001 TYR B 495 PHE 0.018 0.001 PHE B 192 TRP 0.021 0.001 TRP F 36 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00418 (28117) covalent geometry : angle 0.61275 (38259) SS BOND : bond 0.00335 ( 19) SS BOND : angle 1.53694 ( 38) hydrogen bonds : bond 0.04189 ( 751) hydrogen bonds : angle 5.33564 ( 2055) link_BETA1-4 : bond 0.00379 ( 6) link_BETA1-4 : angle 3.01134 ( 18) link_NAG-ASN : bond 0.00382 ( 30) link_NAG-ASN : angle 2.13866 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 301 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 TYR cc_start: -0.0503 (OUTLIER) cc_final: -0.3617 (t80) REVERT: A 347 PHE cc_start: 0.3028 (OUTLIER) cc_final: 0.2494 (p90) REVERT: A 556 ASN cc_start: 0.7571 (OUTLIER) cc_final: 0.6991 (p0) REVERT: A 558 LYS cc_start: 0.7937 (ttpt) cc_final: 0.7727 (tttm) REVERT: A 586 ASP cc_start: 0.7764 (t0) cc_final: 0.7410 (t0) REVERT: A 614 ASP cc_start: 0.7320 (p0) cc_final: 0.6965 (p0) REVERT: A 756 TYR cc_start: 0.8475 (t80) cc_final: 0.7571 (t80) REVERT: B 41 LYS cc_start: 0.7883 (mmmt) cc_final: 0.7175 (mmtt) REVERT: B 177 MET cc_start: 0.5223 (tpt) cc_final: 0.4797 (tpt) REVERT: B 353 TRP cc_start: 0.7032 (p90) cc_final: 0.6676 (p90) REVERT: B 918 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7890 (mt-10) REVERT: B 954 GLN cc_start: 0.8037 (mt0) cc_final: 0.7590 (mt0) REVERT: B 977 LEU cc_start: 0.7468 (mp) cc_final: 0.7227 (mt) REVERT: B 990 GLU cc_start: 0.8160 (tt0) cc_final: 0.7856 (tt0) REVERT: B 1135 ASN cc_start: 0.8269 (t0) cc_final: 0.7864 (t0) REVERT: C 56 LEU cc_start: 0.2951 (OUTLIER) cc_final: 0.2602 (tp) REVERT: C 58 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.6690 (m-80) REVERT: C 725 GLU cc_start: 0.8297 (tt0) cc_final: 0.7860 (tt0) REVERT: C 731 MET cc_start: 0.9140 (ptt) cc_final: 0.8868 (ptt) REVERT: C 919 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.7319 (p0) REVERT: C 995 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8044 (tpp80) REVERT: E 34 MET cc_start: 0.4114 (pmm) cc_final: 0.3169 (pmm) REVERT: F 81 LEU cc_start: 0.4465 (pt) cc_final: 0.4227 (pp) outliers start: 118 outliers final: 89 residues processed: 395 average time/residue: 0.1629 time to fit residues: 108.1221 Evaluate side-chains 386 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 290 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 135 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 186 optimal weight: 0.0980 chunk 168 optimal weight: 1.9990 chunk 298 optimal weight: 0.5980 chunk 171 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 324 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 255 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 764 ASN C 115 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.248445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.181037 restraints weight = 34203.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.173569 restraints weight = 54947.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.167232 restraints weight = 46504.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.166413 restraints weight = 44760.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.166296 restraints weight = 32717.978| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 28172 Z= 0.240 Angle : 0.685 14.059 38405 Z= 0.341 Chirality : 0.048 0.312 4412 Planarity : 0.005 0.065 4922 Dihedral : 7.404 82.406 4490 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.67 % Favored : 90.01 % Rotamer: Outliers : 3.93 % Allowed : 16.91 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.14), residues: 3422 helix: 1.64 (0.22), residues: 593 sheet: -1.41 (0.19), residues: 711 loop : -2.13 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 34 TYR 0.026 0.002 TYR B 495 PHE 0.025 0.002 PHE C 562 TRP 0.017 0.001 TRP A 64 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00575 (28117) covalent geometry : angle 0.67208 (38259) SS BOND : bond 0.00345 ( 19) SS BOND : angle 1.75714 ( 38) hydrogen bonds : bond 0.04653 ( 751) hydrogen bonds : angle 5.50432 ( 2055) link_BETA1-4 : bond 0.00508 ( 6) link_BETA1-4 : angle 3.01820 ( 18) link_NAG-ASN : bond 0.00410 ( 30) link_NAG-ASN : angle 2.23810 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 304 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 TYR cc_start: -0.1167 (OUTLIER) cc_final: -0.4805 (t80) REVERT: A 347 PHE cc_start: 0.3100 (OUTLIER) cc_final: 0.2567 (p90) REVERT: A 556 ASN cc_start: 0.7407 (OUTLIER) cc_final: 0.6865 (p0) REVERT: A 558 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7797 (tttm) REVERT: A 586 ASP cc_start: 0.7779 (t0) cc_final: 0.7551 (t0) REVERT: A 614 ASP cc_start: 0.7471 (p0) cc_final: 0.7131 (p0) REVERT: A 756 TYR cc_start: 0.8520 (t80) cc_final: 0.7681 (t80) REVERT: A 954 GLN cc_start: 0.8617 (tt0) cc_final: 0.8361 (mt0) REVERT: B 41 LYS cc_start: 0.7944 (mmmt) cc_final: 0.7219 (mmtt) REVERT: B 177 MET cc_start: 0.5305 (tpt) cc_final: 0.4916 (tpt) REVERT: B 281 GLU cc_start: 0.8087 (pp20) cc_final: 0.7854 (pp20) REVERT: B 353 TRP cc_start: 0.7221 (p90) cc_final: 0.6830 (p90) REVERT: B 918 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7949 (mt-10) REVERT: B 1135 ASN cc_start: 0.8294 (t0) cc_final: 0.7883 (t0) REVERT: C 56 LEU cc_start: 0.3363 (OUTLIER) cc_final: 0.3061 (tp) REVERT: C 58 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.6712 (m-80) REVERT: C 725 GLU cc_start: 0.8300 (tt0) cc_final: 0.7886 (tt0) REVERT: C 731 MET cc_start: 0.9144 (ptt) cc_final: 0.8868 (ptt) REVERT: C 919 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.7308 (p0) REVERT: C 995 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8127 (tpp80) REVERT: E 34 MET cc_start: 0.4046 (pmm) cc_final: 0.3090 (pmm) REVERT: F 81 LEU cc_start: 0.4566 (pt) cc_final: 0.4262 (pp) outliers start: 118 outliers final: 93 residues processed: 396 average time/residue: 0.1445 time to fit residues: 96.7402 Evaluate side-chains 388 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 288 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 153 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 233 optimal weight: 8.9990 chunk 288 optimal weight: 0.2980 chunk 200 optimal weight: 0.5980 chunk 195 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 84 optimal weight: 0.0870 chunk 96 optimal weight: 0.4980 chunk 157 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 901 GLN B 764 ASN ** C 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 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 = 0.4534 r_free = 0.4534 target = 0.252447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.188504 restraints weight = 34223.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.181987 restraints weight = 56816.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.177833 restraints weight = 45991.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.177548 restraints weight = 40187.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.176693 restraints weight = 32992.488| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28172 Z= 0.126 Angle : 0.611 14.499 38405 Z= 0.302 Chirality : 0.045 0.241 4412 Planarity : 0.004 0.065 4922 Dihedral : 7.077 76.900 4490 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.07 % Favored : 91.61 % Rotamer: Outliers : 3.00 % Allowed : 17.88 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.14), residues: 3422 helix: 1.79 (0.22), residues: 604 sheet: -1.28 (0.19), residues: 682 loop : -2.05 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 319 TYR 0.034 0.001 TYR B 495 PHE 0.027 0.001 PHE B 497 TRP 0.023 0.001 TRP F 36 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00287 (28117) covalent geometry : angle 0.59779 (38259) SS BOND : bond 0.00261 ( 19) SS BOND : angle 1.48755 ( 38) hydrogen bonds : bond 0.03925 ( 751) hydrogen bonds : angle 5.22189 ( 2055) link_BETA1-4 : bond 0.00505 ( 6) link_BETA1-4 : angle 2.96390 ( 18) link_NAG-ASN : bond 0.00402 ( 30) link_NAG-ASN : angle 2.15417 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 305 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.1798 (OUTLIER) cc_final: 0.1546 (pp) REVERT: A 266 TYR cc_start: -0.1168 (OUTLIER) cc_final: -0.4484 (t80) REVERT: A 347 PHE cc_start: 0.3010 (OUTLIER) cc_final: 0.2456 (p90) REVERT: A 556 ASN cc_start: 0.7515 (OUTLIER) cc_final: 0.6947 (p0) REVERT: A 558 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7702 (tttm) REVERT: A 586 ASP cc_start: 0.7768 (t0) cc_final: 0.7516 (t0) REVERT: A 614 ASP cc_start: 0.7265 (p0) cc_final: 0.6889 (p0) REVERT: A 756 TYR cc_start: 0.8512 (t80) cc_final: 0.7663 (t80) REVERT: A 1122 VAL cc_start: 0.9678 (t) cc_final: 0.9386 (p) REVERT: B 41 LYS cc_start: 0.7873 (mmmt) cc_final: 0.7202 (mmtt) REVERT: B 177 MET cc_start: 0.5289 (tpt) cc_final: 0.4927 (tpt) REVERT: B 281 GLU cc_start: 0.8103 (pp20) cc_final: 0.7872 (pp20) REVERT: B 353 TRP cc_start: 0.7182 (p90) cc_final: 0.6816 (p90) REVERT: B 918 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7877 (mt-10) REVERT: B 954 GLN cc_start: 0.8020 (mt0) cc_final: 0.7546 (mt0) REVERT: B 1135 ASN cc_start: 0.8289 (t0) cc_final: 0.7842 (t0) REVERT: C 58 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.6783 (m-80) REVERT: C 725 GLU cc_start: 0.8242 (tt0) cc_final: 0.7798 (tt0) REVERT: C 731 MET cc_start: 0.9147 (ptt) cc_final: 0.8908 (ptt) REVERT: C 919 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.7229 (p0) REVERT: C 995 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8027 (tpp80) REVERT: E 34 MET cc_start: 0.4062 (pmm) cc_final: 0.3143 (pmm) REVERT: F 81 LEU cc_start: 0.4637 (pt) cc_final: 0.4395 (pp) outliers start: 90 outliers final: 70 residues processed: 374 average time/residue: 0.1522 time to fit residues: 96.4092 Evaluate side-chains 369 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 292 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 252 optimal weight: 4.9990 chunk 320 optimal weight: 6.9990 chunk 249 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 236 optimal weight: 0.0170 chunk 312 optimal weight: 0.7980 chunk 170 optimal weight: 0.0050 chunk 233 optimal weight: 0.6980 chunk 323 optimal weight: 10.0000 chunk 307 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 overall best weight: 0.4232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN B 764 ASN ** C 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.252597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.190993 restraints weight = 34879.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.184060 restraints weight = 57978.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.180289 restraints weight = 48109.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.178852 restraints weight = 45648.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.176996 restraints weight = 35704.659| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28172 Z= 0.124 Angle : 0.610 15.082 38405 Z= 0.300 Chirality : 0.045 0.253 4412 Planarity : 0.004 0.064 4922 Dihedral : 6.881 72.125 4490 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.62 % Favored : 91.06 % Rotamer: Outliers : 2.63 % Allowed : 18.38 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.14), residues: 3422 helix: 1.85 (0.22), residues: 604 sheet: -1.18 (0.19), residues: 668 loop : -2.00 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 319 TYR 0.025 0.001 TYR B 495 PHE 0.020 0.001 PHE F 47 TRP 0.023 0.001 TRP A 64 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00283 (28117) covalent geometry : angle 0.59723 (38259) SS BOND : bond 0.00245 ( 19) SS BOND : angle 1.39654 ( 38) hydrogen bonds : bond 0.03763 ( 751) hydrogen bonds : angle 5.07708 ( 2055) link_BETA1-4 : bond 0.00571 ( 6) link_BETA1-4 : angle 2.92798 ( 18) link_NAG-ASN : bond 0.00401 ( 30) link_NAG-ASN : angle 2.09673 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 299 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.1932 (OUTLIER) cc_final: 0.1693 (pp) REVERT: A 266 TYR cc_start: -0.0621 (OUTLIER) cc_final: -0.4456 (t80) REVERT: A 347 PHE cc_start: 0.2973 (OUTLIER) cc_final: 0.2374 (p90) REVERT: A 556 ASN cc_start: 0.7427 (OUTLIER) cc_final: 0.6860 (p0) REVERT: A 586 ASP cc_start: 0.7799 (t0) cc_final: 0.7587 (t0) REVERT: A 614 ASP cc_start: 0.7334 (p0) cc_final: 0.6921 (p0) REVERT: A 745 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7514 (t0) REVERT: A 756 TYR cc_start: 0.8536 (t80) cc_final: 0.7672 (t80) REVERT: A 983 ARG cc_start: 0.8193 (ptp-110) cc_final: 0.7736 (mtm110) REVERT: A 1122 VAL cc_start: 0.9643 (t) cc_final: 0.9361 (p) REVERT: B 40 ASP cc_start: 0.8040 (t70) cc_final: 0.7487 (p0) REVERT: B 41 LYS cc_start: 0.7750 (mmmt) cc_final: 0.6939 (mmtm) REVERT: B 177 MET cc_start: 0.5306 (tpt) cc_final: 0.4919 (tpt) REVERT: B 281 GLU cc_start: 0.8089 (pp20) cc_final: 0.7869 (pp20) REVERT: B 353 TRP cc_start: 0.7099 (p90) cc_final: 0.6699 (p90) REVERT: B 596 SER cc_start: 0.9414 (m) cc_final: 0.9127 (p) REVERT: B 918 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7785 (mt-10) REVERT: B 954 GLN cc_start: 0.7988 (mt0) cc_final: 0.7526 (mt0) REVERT: B 1135 ASN cc_start: 0.8228 (t0) cc_final: 0.7771 (t0) REVERT: C 58 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.6046 (m-80) REVERT: C 290 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.5961 (m-30) REVERT: C 725 GLU cc_start: 0.8229 (tt0) cc_final: 0.7895 (tt0) REVERT: C 919 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.7065 (p0) REVERT: C 995 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8004 (tpp80) REVERT: E 34 MET cc_start: 0.3995 (pmm) cc_final: 0.2782 (pmm) REVERT: F 81 LEU cc_start: 0.4670 (pt) cc_final: 0.4460 (pp) outliers start: 79 outliers final: 65 residues processed: 362 average time/residue: 0.1648 time to fit residues: 100.2420 Evaluate side-chains 363 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 289 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 56 optimal weight: 0.5980 chunk 280 optimal weight: 0.9980 chunk 318 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 329 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 218 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN B 764 ASN ** C 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.251844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.187721 restraints weight = 34689.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.176669 restraints weight = 58438.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.165924 restraints weight = 51448.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.167170 restraints weight = 43830.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.168194 restraints weight = 29701.913| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.166 28172 Z= 0.158 Angle : 0.730 59.188 38405 Z= 0.394 Chirality : 0.047 0.779 4412 Planarity : 0.004 0.064 4922 Dihedral : 6.888 72.106 4490 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.71 % Favored : 90.97 % Rotamer: Outliers : 2.66 % Allowed : 18.44 % Favored : 78.89 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.14), residues: 3422 helix: 1.82 (0.22), residues: 603 sheet: -1.17 (0.19), residues: 668 loop : -2.00 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 319 TYR 0.026 0.001 TYR B 421 PHE 0.017 0.001 PHE B 456 TRP 0.020 0.001 TRP A 64 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00346 (28117) covalent geometry : angle 0.71872 (38259) SS BOND : bond 0.00469 ( 19) SS BOND : angle 1.71222 ( 38) hydrogen bonds : bond 0.03811 ( 751) hydrogen bonds : angle 5.07750 ( 2055) link_BETA1-4 : bond 0.00991 ( 6) link_BETA1-4 : angle 3.13441 ( 18) link_NAG-ASN : bond 0.00397 ( 30) link_NAG-ASN : angle 2.09686 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4849.19 seconds wall clock time: 84 minutes 47.91 seconds (5087.91 seconds total)