Starting phenix.real_space_refine on Fri Mar 6 16:38:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u0p_26262/03_2026/7u0p_26262.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u0p_26262/03_2026/7u0p_26262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u0p_26262/03_2026/7u0p_26262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u0p_26262/03_2026/7u0p_26262.map" model { file = "/net/cci-nas-00/data/ceres_data/7u0p_26262/03_2026/7u0p_26262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u0p_26262/03_2026/7u0p_26262.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.089 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 146 5.16 5 C 20576 2.51 5 N 5345 2.21 5 O 6304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32371 Number of models: 1 Model: "" Number of chains: 15 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: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1684 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "D" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1684 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "I" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1662 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "F" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1662 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "B1" 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: "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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.38, per 1000 atoms: 0.23 Number of scatterers: 32371 At special positions: 0 Unit cell: (172.7, 159.5, 240.9, 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 146 16.00 O 6304 8.00 N 5345 7.00 C 20576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, 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 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 135 " - pdb=" SG CYS I 195 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAGB1 1 " - " NAGB1 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " 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 C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 343 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B 343 " " NAGB1 1 " - " ASN B1134 " Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7662 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 68 sheets defined 20.6% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.572A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.558A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.562A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.952A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.614A pdb=" N GLY A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 removed outlier: 3.552A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.569A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 877 " --> pdb=" O TYR A 873 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.747A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.805A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.807A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 removed outlier: 3.645A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 940 removed outlier: 4.051A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.782A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (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 982 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 992 through 1033 removed outlier: 3.836A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.405A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 336 through 341 removed outlier: 4.412A pdb=" N GLY B 339 " --> pdb=" O CYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.104A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.762A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.769A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.619A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 639 removed outlier: 4.157A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.203A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 771 removed outlier: 3.636A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 783 removed outlier: 4.203A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.870A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.691A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.674A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 890' Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.826A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 918 Processing helix chain 'B' and resid 919 through 938 removed outlier: 3.622A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 4.440A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 967 No H-bonds generated for 'chain 'B' and resid 965 through 967' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.981A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG B1019 " --> pdb=" O ALA B1015 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1149 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.540A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 338 through 343' Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.789A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.538A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.202A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.708A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.164A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.805A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.570A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 855 removed outlier: 3.847A pdb=" N LYS C 854 " --> pdb=" O CYS C 851 " (cutoff:3.500A) removed outlier: 3.506A 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 885 removed outlier: 3.530A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.503A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.608A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.587A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.149A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.629A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.653A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE C1018 " --> pdb=" O ARG C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.381A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 193 through 197 Processing helix chain 'D' and resid 28 through 32 removed outlier: 4.230A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.976A pdb=" N GLN D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.169A pdb=" N THR D 197 " --> pdb=" O SER D 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 129 Processing helix chain 'I' and resid 184 through 190 removed outlier: 3.728A pdb=" N HIS I 190 " --> pdb=" O ASP I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 215 No H-bonds generated for 'chain 'I' and resid 213 through 215' Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.069A pdb=" N ILE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 184 through 190 removed outlier: 3.757A pdb=" N HIS F 190 " --> pdb=" O ASP F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.859A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.468A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.984A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 115 through 121 removed outlier: 3.713A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.960A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 153 removed outlier: 6.394A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.749A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.487A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.811A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.162A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.750A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.453A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 672 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.022A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.714A pdb=" N ARG B 78 " --> pdb=" O HIS B 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 28 removed outlier: 6.386A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 229 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.902A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.408A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER B 155 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS B 146 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.196A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.318A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.537A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.572A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.860A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.868A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.678A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 714 Processing sheet with id=AD4, first strand: chain 'B' and resid 717 through 719 Processing sheet with id=AD5, first strand: chain 'B' and resid 722 through 728 removed outlier: 4.091A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.541A pdb=" N PHE B1121 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B1089 " --> pdb=" O PHE B1121 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.229A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.865A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 104 through 107 Processing sheet with id=AE3, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.804A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 151 through 153 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 354 through 358 removed outlier: 4.354A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.405A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.073A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.626A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.721A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF6, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AF7, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.011A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 127 through 130 removed outlier: 3.808A pdb=" N ASP E 150 " --> pdb=" O TYR E 182 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR E 182 " --> pdb=" O ASP E 150 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 127 through 130 removed outlier: 3.808A pdb=" N ASP E 150 " --> pdb=" O TYR E 182 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR E 182 " --> pdb=" O ASP E 150 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER E 183 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL E 175 " --> pdb=" O SER E 183 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 157 through 160 removed outlier: 4.067A pdb=" N TYR E 200 " --> pdb=" O VAL E 217 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.879A pdb=" N SER D 71 " --> pdb=" O TYR D 80 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.525A pdb=" N GLU D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 127 through 130 Processing sheet with id=AG5, first strand: chain 'D' and resid 127 through 130 removed outlier: 3.595A pdb=" N VAL D 175 " --> pdb=" O SER D 183 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 157 through 160 removed outlier: 4.150A pdb=" N TYR D 200 " --> pdb=" O VAL D 217 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.814A pdb=" N LEU I 11 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 115 through 119 removed outlier: 6.367A pdb=" N TYR I 174 " --> pdb=" O ASN I 139 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 155 through 156 removed outlier: 4.736A pdb=" N TRP I 149 " --> pdb=" O GLN I 156 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AH3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.862A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE F 48 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 115 through 119 removed outlier: 6.151A pdb=" N TYR F 174 " --> pdb=" O ASN F 139 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 154 through 155 1140 hydrogen bonds defined for protein. 3048 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: 8.46 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 1 1.11 - 1.29: 5283 1.29 - 1.47: 13458 1.47 - 1.65: 14195 1.65 - 1.83: 186 Bond restraints: 33123 Sorted by residual: bond pdb=" CB PRO C 209 " pdb=" CG PRO C 209 " ideal model delta sigma weight residual 1.492 0.934 0.558 5.00e-02 4.00e+02 1.25e+02 bond pdb=" CG PRO C 209 " pdb=" CD PRO C 209 " ideal model delta sigma weight residual 1.503 1.190 0.313 3.40e-02 8.65e+02 8.45e+01 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" N PRO C 209 " pdb=" CA PRO C 209 " ideal model delta sigma weight residual 1.469 1.504 -0.035 1.28e-02 6.10e+03 7.51e+00 ... (remaining 33118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.45: 45078 9.45 - 18.90: 1 18.90 - 28.35: 1 28.35 - 37.80: 1 37.80 - 47.26: 1 Bond angle restraints: 45082 Sorted by residual: angle pdb=" N PRO C 209 " pdb=" CD PRO C 209 " pdb=" CG PRO C 209 " ideal model delta sigma weight residual 103.20 76.92 26.28 1.50e+00 4.44e-01 3.07e+02 angle pdb=" CA PRO C 209 " pdb=" CB PRO C 209 " pdb=" CG PRO C 209 " ideal model delta sigma weight residual 104.50 74.41 30.09 1.90e+00 2.77e-01 2.51e+02 angle pdb=" CB PRO C 209 " pdb=" CG PRO C 209 " pdb=" CD PRO C 209 " ideal model delta sigma weight residual 106.10 153.36 -47.26 3.20e+00 9.77e-02 2.18e+02 angle pdb=" CA PRO C 209 " pdb=" N PRO C 209 " pdb=" CD PRO C 209 " ideal model delta sigma weight residual 112.00 101.86 10.14 1.40e+00 5.10e-01 5.24e+01 angle pdb=" CA MET D 101 " pdb=" C MET D 101 " pdb=" N THR D 102 " ideal model delta sigma weight residual 117.92 123.98 -6.06 1.35e+00 5.49e-01 2.02e+01 ... (remaining 45077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.84: 18552 24.84 - 49.68: 1312 49.68 - 74.52: 185 74.52 - 99.36: 67 99.36 - 124.20: 7 Dihedral angle restraints: 20123 sinusoidal: 8194 harmonic: 11929 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -26.40 -59.60 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -28.88 -57.12 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -33.61 -52.39 1 1.00e+01 1.00e-02 3.74e+01 ... (remaining 20120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4079 0.049 - 0.098: 822 0.098 - 0.147: 273 0.147 - 0.196: 0 0.196 - 0.245: 6 Chirality restraints: 5180 Sorted by residual: 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 1.50e+00 chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB THR B 259 " pdb=" CA THR B 259 " pdb=" OG1 THR B 259 " pdb=" CG2 THR B 259 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 5177 not shown) Planarity restraints: 5814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " -0.061 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO C 209 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 791 " -0.037 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 792 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 792 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 792 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO A 987 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.030 5.00e-02 4.00e+02 ... (remaining 5811 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 689 2.69 - 3.24: 28903 3.24 - 3.79: 45061 3.79 - 4.35: 55921 4.35 - 4.90: 97536 Nonbonded interactions: 228110 Sorted by model distance: nonbonded pdb=" OG SER I 63 " pdb=" OG1 THR I 74 " model vdw 2.132 3.040 nonbonded pdb=" O4 NAG C1301 " pdb=" O7 NAG C1301 " model vdw 2.209 3.040 nonbonded pdb=" OE1 GLN I 167 " pdb=" OH TYR I 174 " model vdw 2.213 3.040 nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR A 33 " pdb=" O GLN A 218 " model vdw 2.224 3.040 ... (remaining 228105 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 1303 through 1308)) selection = (chain 'B' and (resid 14 through 617 or resid 641 through 827 or resid 852 throu \ gh 940 or resid 944 through 1146 or resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 675 or resid 690 through 827 or resid 852 throu \ gh 1146 or resid 1303 through 1308)) } ncs_group { reference = chain 'B1' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 31.260 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.558 33178 Z= 0.159 Angle : 0.637 47.256 45224 Z= 0.315 Chirality : 0.044 0.245 5180 Planarity : 0.004 0.087 5787 Dihedral : 17.207 124.198 12392 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.42 % Allowed : 23.41 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 4060 helix: 1.39 (0.22), residues: 667 sheet: 0.81 (0.16), residues: 1061 loop : -1.00 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 18 TYR 0.018 0.001 TYR C 904 PHE 0.012 0.001 PHE A1121 TRP 0.023 0.001 TRP E 160 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00457 (33123) covalent geometry : angle 0.62494 (45082) SS BOND : bond 0.00414 ( 23) SS BOND : angle 1.37976 ( 46) hydrogen bonds : bond 0.12088 ( 1112) hydrogen bonds : angle 5.38466 ( 3048) link_BETA1-4 : bond 0.00429 ( 5) link_BETA1-4 : angle 2.31392 ( 15) link_NAG-ASN : bond 0.00437 ( 27) link_NAG-ASN : angle 2.64253 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 344 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.1327 (tmm) cc_final: -0.1760 (ptm) REVERT: A 392 PHE cc_start: 0.8527 (m-80) cc_final: 0.8112 (m-10) REVERT: A 451 TYR cc_start: 0.7413 (m-80) cc_final: 0.6947 (m-10) REVERT: A 489 TYR cc_start: 0.5184 (m-80) cc_final: 0.4642 (m-10) REVERT: A 1002 GLN cc_start: 0.8398 (tt0) cc_final: 0.8177 (tp40) REVERT: B 88 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8070 (p0) REVERT: B 97 LYS cc_start: 0.8388 (pttm) cc_final: 0.7947 (mmtm) REVERT: B 177 MET cc_start: 0.1758 (tpt) cc_final: 0.1145 (mmt) REVERT: C 138 ASP cc_start: 0.6928 (m-30) cc_final: 0.6633 (m-30) REVERT: C 139 PRO cc_start: 0.7550 (Cg_endo) cc_final: 0.7313 (Cg_exo) REVERT: C 258 TRP cc_start: 0.2981 (m100) cc_final: 0.2753 (m-90) REVERT: C 427 ASP cc_start: 0.8176 (m-30) cc_final: 0.7908 (t0) REVERT: C 988 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8186 (mp0) REVERT: D 109 TRP cc_start: 0.6827 (m100) cc_final: 0.6480 (m100) outliers start: 15 outliers final: 5 residues processed: 357 average time/residue: 0.1993 time to fit residues: 117.0987 Evaluate side-chains 201 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 894 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.0470 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 50.0000 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 7.9990 overall best weight: 3.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 99 ASN A 121 ASN A 122 ASN A 207 HIS A 239 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 935 GLN A1135 ASN B 99 ASN B 115 GLN B 360 ASN B 422 ASN B 563 GLN B 655 HIS B 658 ASN B 774 GLN B 954 GLN B1088 HIS C 207 HIS C 239 GLN C 439 ASN C 493 GLN C 498 GLN C 564 GLN C 901 GLN C 913 GLN C 920 GLN C1101 HIS ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN F 79 GLN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.145978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.109090 restraints weight = 72040.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.099989 restraints weight = 92578.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.098404 restraints weight = 84278.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.097929 restraints weight = 68193.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.098287 restraints weight = 63109.868| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 33178 Z= 0.304 Angle : 0.754 16.004 45224 Z= 0.385 Chirality : 0.050 0.322 5180 Planarity : 0.005 0.070 5787 Dihedral : 8.842 104.534 5078 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.83 % Allowed : 21.48 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.13), residues: 4060 helix: 0.63 (0.21), residues: 677 sheet: 0.60 (0.16), residues: 1090 loop : -1.40 (0.12), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 357 TYR 0.025 0.002 TYR I 91 PHE 0.029 0.002 PHE A 906 TRP 0.022 0.002 TRP I 97 HIS 0.010 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00747 (33123) covalent geometry : angle 0.73730 (45082) SS BOND : bond 0.00702 ( 23) SS BOND : angle 1.91557 ( 46) hydrogen bonds : bond 0.07190 ( 1112) hydrogen bonds : angle 5.30182 ( 3048) link_BETA1-4 : bond 0.00347 ( 5) link_BETA1-4 : angle 2.12927 ( 15) link_NAG-ASN : bond 0.00509 ( 27) link_NAG-ASN : angle 3.39868 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 200 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.1093 (tmm) cc_final: -0.1340 (ptm) REVERT: A 392 PHE cc_start: 0.8540 (m-80) cc_final: 0.8247 (m-80) REVERT: A 985 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7597 (p0) REVERT: A 1018 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8308 (tt) REVERT: A 1029 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.8702 (tpp) REVERT: B 97 LYS cc_start: 0.8405 (pttm) cc_final: 0.7850 (mmtp) REVERT: B 129 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7853 (ptpt) REVERT: B 220 PHE cc_start: 0.6472 (t80) cc_final: 0.6028 (t80) REVERT: B 906 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8090 (t80) REVERT: B 1010 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7766 (mm-40) REVERT: C 65 PHE cc_start: 0.7128 (m-80) cc_final: 0.6830 (m-80) REVERT: C 534 VAL cc_start: 0.9173 (OUTLIER) cc_final: 0.8972 (m) REVERT: C 906 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.7515 (t80) REVERT: C 968 SER cc_start: 0.9320 (OUTLIER) cc_final: 0.9032 (m) REVERT: I 147 VAL cc_start: 0.1606 (OUTLIER) cc_final: 0.1389 (m) outliers start: 209 outliers final: 111 residues processed: 390 average time/residue: 0.1765 time to fit residues: 116.1581 Evaluate side-chains 288 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 167 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 387 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 121 optimal weight: 9.9990 chunk 304 optimal weight: 0.9990 chunk 42 optimal weight: 30.0000 chunk 191 optimal weight: 0.8980 chunk 218 optimal weight: 8.9990 chunk 382 optimal weight: 30.0000 chunk 52 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 245 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 907 ASN B 125 ASN B 658 ASN C 564 GLN C 901 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.148018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.109186 restraints weight = 71810.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100368 restraints weight = 81003.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.099378 restraints weight = 75018.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.098961 restraints weight = 57357.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.099240 restraints weight = 51383.051| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 33178 Z= 0.147 Angle : 0.598 13.694 45224 Z= 0.302 Chirality : 0.045 0.267 5180 Planarity : 0.004 0.059 5787 Dihedral : 7.858 99.291 5075 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.27 % Allowed : 23.10 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.13), residues: 4060 helix: 0.94 (0.21), residues: 657 sheet: 0.67 (0.16), residues: 1070 loop : -1.33 (0.12), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.025 0.001 TYR C 369 PHE 0.016 0.001 PHE A 133 TRP 0.015 0.001 TRP C 64 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00349 (33123) covalent geometry : angle 0.57836 (45082) SS BOND : bond 0.00461 ( 23) SS BOND : angle 2.20308 ( 46) hydrogen bonds : bond 0.05280 ( 1112) hydrogen bonds : angle 4.93325 ( 3048) link_BETA1-4 : bond 0.00313 ( 5) link_BETA1-4 : angle 2.10800 ( 15) link_NAG-ASN : bond 0.00367 ( 27) link_NAG-ASN : angle 3.17043 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 182 time to evaluate : 1.221 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 153 MET cc_start: 0.7412 (pmm) cc_final: 0.6782 (pmm) REVERT: A 177 MET cc_start: -0.1117 (OUTLIER) cc_final: -0.1327 (ptm) REVERT: A 189 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6340 (mm) REVERT: A 392 PHE cc_start: 0.8554 (m-80) cc_final: 0.8065 (m-10) REVERT: A 733 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7822 (ptpt) REVERT: A 1029 MET cc_start: 0.9398 (OUTLIER) cc_final: 0.8847 (tpp) REVERT: B 97 LYS cc_start: 0.8455 (pttm) cc_final: 0.7850 (mmtt) REVERT: B 129 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.8004 (ptpt) REVERT: B 133 PHE cc_start: 0.7247 (m-80) cc_final: 0.6225 (m-80) REVERT: B 220 PHE cc_start: 0.6493 (t80) cc_final: 0.6182 (t80) REVERT: B 906 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8330 (t80) REVERT: C 65 PHE cc_start: 0.6990 (m-80) cc_final: 0.6755 (m-80) REVERT: C 191 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7810 (tt0) REVERT: C 906 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.7746 (t80) REVERT: E 51 ILE cc_start: 0.8364 (pt) cc_final: 0.7983 (mt) REVERT: D 48 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6421 (ptm) outliers start: 153 outliers final: 93 residues processed: 316 average time/residue: 0.1841 time to fit residues: 96.7380 Evaluate side-chains 259 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 158 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 130 optimal weight: 10.0000 chunk 137 optimal weight: 0.8980 chunk 255 optimal weight: 6.9990 chunk 375 optimal weight: 9.9990 chunk 296 optimal weight: 0.9990 chunk 219 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 283 optimal weight: 6.9990 chunk 319 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 293 optimal weight: 0.0980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN B1010 GLN D 111 GLN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.148202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.108954 restraints weight = 71787.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.099367 restraints weight = 77256.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.099057 restraints weight = 66998.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.099294 restraints weight = 47945.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.099316 restraints weight = 41422.663| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 33178 Z= 0.130 Angle : 0.579 13.612 45224 Z= 0.290 Chirality : 0.045 0.252 5180 Planarity : 0.004 0.054 5787 Dihedral : 7.302 91.148 5075 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.19 % Allowed : 22.96 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.13), residues: 4060 helix: 1.12 (0.21), residues: 654 sheet: 0.64 (0.16), residues: 1083 loop : -1.31 (0.12), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 158 TYR 0.018 0.001 TYR C1067 PHE 0.035 0.001 PHE A 133 TRP 0.014 0.001 TRP C 64 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00305 (33123) covalent geometry : angle 0.55866 (45082) SS BOND : bond 0.00442 ( 23) SS BOND : angle 2.08154 ( 46) hydrogen bonds : bond 0.04927 ( 1112) hydrogen bonds : angle 4.77926 ( 3048) link_BETA1-4 : bond 0.00315 ( 5) link_BETA1-4 : angle 2.07149 ( 15) link_NAG-ASN : bond 0.00348 ( 27) link_NAG-ASN : angle 3.14909 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 172 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7396 (pmm) cc_final: 0.6997 (pmm) REVERT: A 189 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6254 (mm) REVERT: A 237 ARG cc_start: 0.6655 (mtm-85) cc_final: 0.6340 (mpt180) REVERT: A 392 PHE cc_start: 0.8529 (m-80) cc_final: 0.8110 (m-10) REVERT: A 733 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7776 (ptpt) REVERT: A 1018 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8547 (tt) REVERT: A 1029 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.8500 (tpp) REVERT: B 97 LYS cc_start: 0.8342 (pttm) cc_final: 0.7809 (mmtt) REVERT: B 129 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.8011 (ptpt) REVERT: B 133 PHE cc_start: 0.6964 (m-80) cc_final: 0.6004 (m-80) REVERT: B 220 PHE cc_start: 0.6431 (t80) cc_final: 0.6094 (t80) REVERT: B 505 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7263 (t80) REVERT: B 781 VAL cc_start: 0.8698 (t) cc_final: 0.8441 (t) REVERT: B 906 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8376 (t80) REVERT: C 58 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7521 (m-80) REVERT: C 65 PHE cc_start: 0.6937 (m-80) cc_final: 0.6648 (m-80) REVERT: C 94 SER cc_start: 0.7823 (OUTLIER) cc_final: 0.7619 (p) REVERT: C 191 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7800 (tt0) REVERT: C 231 ILE cc_start: 0.6293 (OUTLIER) cc_final: 0.5950 (mp) REVERT: C 427 ASP cc_start: 0.7970 (m-30) cc_final: 0.7607 (t0) REVERT: C 906 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7686 (t80) REVERT: E 51 ILE cc_start: 0.8322 (pt) cc_final: 0.8039 (mt) REVERT: D 82 GLN cc_start: 0.7880 (mt0) cc_final: 0.7210 (mp-120) outliers start: 150 outliers final: 109 residues processed: 309 average time/residue: 0.1734 time to fit residues: 92.1942 Evaluate side-chains 275 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 155 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 292 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 256 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 47 optimal weight: 0.0070 chunk 267 optimal weight: 9.9990 chunk 374 optimal weight: 6.9990 chunk 378 optimal weight: 20.0000 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.151026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.116374 restraints weight = 73884.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.113484 restraints weight = 114514.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.111102 restraints weight = 92849.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.110362 restraints weight = 90349.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.109061 restraints weight = 80914.768| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 33178 Z= 0.328 Angle : 0.743 14.715 45224 Z= 0.382 Chirality : 0.050 0.275 5180 Planarity : 0.005 0.124 5787 Dihedral : 7.668 84.210 5075 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 5.72 % Allowed : 21.65 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 4060 helix: 0.55 (0.21), residues: 657 sheet: 0.31 (0.16), residues: 1109 loop : -1.57 (0.12), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 18 TYR 0.025 0.002 TYR C1067 PHE 0.033 0.002 PHE A 133 TRP 0.022 0.002 TRP I 97 HIS 0.010 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00808 (33123) covalent geometry : angle 0.72216 (45082) SS BOND : bond 0.00728 ( 23) SS BOND : angle 2.89819 ( 46) hydrogen bonds : bond 0.07249 ( 1112) hydrogen bonds : angle 5.25861 ( 3048) link_BETA1-4 : bond 0.00351 ( 5) link_BETA1-4 : angle 2.41310 ( 15) link_NAG-ASN : bond 0.00545 ( 27) link_NAG-ASN : angle 3.51072 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 164 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7160 (pmm) cc_final: 0.6798 (pmm) REVERT: A 223 LEU cc_start: 0.5316 (OUTLIER) cc_final: 0.5028 (mt) REVERT: A 733 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7909 (ptpt) REVERT: A 985 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7726 (p0) REVERT: A 1029 MET cc_start: 0.9320 (OUTLIER) cc_final: 0.8511 (tpp) REVERT: B 220 PHE cc_start: 0.6446 (t80) cc_final: 0.6221 (t80) REVERT: B 505 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7234 (t80) REVERT: B 906 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8194 (t80) REVERT: C 58 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7325 (m-80) REVERT: C 231 ILE cc_start: 0.6502 (OUTLIER) cc_final: 0.6156 (mp) REVERT: C 534 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8959 (m) REVERT: C 655 HIS cc_start: 0.7611 (OUTLIER) cc_final: 0.7342 (p90) REVERT: C 906 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.7568 (t80) REVERT: D 46 GLU cc_start: 0.7606 (mp0) cc_final: 0.7289 (mp0) REVERT: D 82 GLN cc_start: 0.7966 (mt0) cc_final: 0.7611 (mp10) REVERT: I 2 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8415 (mm) REVERT: I 147 VAL cc_start: 0.1879 (OUTLIER) cc_final: 0.1463 (p) outliers start: 205 outliers final: 154 residues processed: 356 average time/residue: 0.1705 time to fit residues: 104.4439 Evaluate side-chains 314 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 147 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 117 PHE Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 364 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 201 optimal weight: 0.6980 chunk 225 optimal weight: 8.9990 chunk 349 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 171 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN B 196 ASN C 409 GLN C 901 GLN D 28 ASN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.142878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.106275 restraints weight = 72905.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.099070 restraints weight = 100843.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.096528 restraints weight = 85999.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097040 restraints weight = 76811.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.096850 restraints weight = 67599.414| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33178 Z= 0.124 Angle : 0.612 17.127 45224 Z= 0.305 Chirality : 0.045 0.260 5180 Planarity : 0.004 0.055 5787 Dihedral : 7.128 78.137 5075 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.38 % Allowed : 23.27 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 4060 helix: 0.87 (0.21), residues: 659 sheet: 0.35 (0.15), residues: 1129 loop : -1.39 (0.12), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 457 TYR 0.022 0.001 TYR C 369 PHE 0.032 0.001 PHE C 133 TRP 0.019 0.001 TRP C 104 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00283 (33123) covalent geometry : angle 0.58827 (45082) SS BOND : bond 0.00504 ( 23) SS BOND : angle 2.88269 ( 46) hydrogen bonds : bond 0.05052 ( 1112) hydrogen bonds : angle 4.89169 ( 3048) link_BETA1-4 : bond 0.00312 ( 5) link_BETA1-4 : angle 2.36262 ( 15) link_NAG-ASN : bond 0.00414 ( 27) link_NAG-ASN : angle 3.25960 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 166 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7294 (pmm) cc_final: 0.6862 (pmm) REVERT: A 189 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6013 (mm) REVERT: A 223 LEU cc_start: 0.5527 (OUTLIER) cc_final: 0.5209 (mt) REVERT: A 236 THR cc_start: 0.7307 (OUTLIER) cc_final: 0.6881 (p) REVERT: A 733 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7876 (ptpt) REVERT: A 1018 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8251 (tt) REVERT: A 1029 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.8281 (tpp) REVERT: B 97 LYS cc_start: 0.7004 (mmtt) cc_final: 0.5824 (mmtm) REVERT: B 220 PHE cc_start: 0.6418 (t80) cc_final: 0.6119 (t80) REVERT: B 238 PHE cc_start: 0.5866 (p90) cc_final: 0.5536 (p90) REVERT: B 505 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7331 (t80) REVERT: B 906 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8300 (t80) REVERT: C 58 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7332 (m-80) REVERT: C 231 ILE cc_start: 0.6342 (OUTLIER) cc_final: 0.5989 (mp) REVERT: C 408 ARG cc_start: 0.8652 (ppt170) cc_final: 0.8387 (ppt170) REVERT: C 655 HIS cc_start: 0.7527 (OUTLIER) cc_final: 0.7269 (p90) REVERT: C 906 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.7776 (t80) REVERT: C 923 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8895 (mm) REVERT: D 28 ASN cc_start: 0.6705 (t0) cc_final: 0.6364 (t0) REVERT: D 46 GLU cc_start: 0.7671 (mp0) cc_final: 0.7215 (mp0) REVERT: D 48 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6626 (ptm) REVERT: D 82 GLN cc_start: 0.8136 (mt0) cc_final: 0.7506 (mp10) outliers start: 157 outliers final: 116 residues processed: 309 average time/residue: 0.1742 time to fit residues: 92.4089 Evaluate side-chains 280 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 150 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 117 PHE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 229 optimal weight: 5.9990 chunk 9 optimal weight: 0.4980 chunk 205 optimal weight: 0.5980 chunk 324 optimal weight: 10.0000 chunk 370 optimal weight: 20.0000 chunk 295 optimal weight: 1.9990 chunk 386 optimal weight: 30.0000 chunk 207 optimal weight: 2.9990 chunk 384 optimal weight: 20.0000 chunk 367 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.143516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.107218 restraints weight = 73399.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.100891 restraints weight = 107786.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.098812 restraints weight = 84479.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.098567 restraints weight = 74580.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.098569 restraints weight = 67077.489| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33178 Z= 0.153 Angle : 0.615 14.049 45224 Z= 0.307 Chirality : 0.045 0.248 5180 Planarity : 0.004 0.055 5787 Dihedral : 6.930 72.066 5073 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.77 % Allowed : 23.41 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 4060 helix: 0.98 (0.22), residues: 659 sheet: 0.33 (0.16), residues: 1118 loop : -1.41 (0.12), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 237 TYR 0.030 0.001 TYR A 160 PHE 0.036 0.001 PHE C 133 TRP 0.018 0.001 TRP C 104 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00367 (33123) covalent geometry : angle 0.59264 (45082) SS BOND : bond 0.00493 ( 23) SS BOND : angle 2.71307 ( 46) hydrogen bonds : bond 0.05299 ( 1112) hydrogen bonds : angle 4.86158 ( 3048) link_BETA1-4 : bond 0.00207 ( 5) link_BETA1-4 : angle 2.35179 ( 15) link_NAG-ASN : bond 0.00387 ( 27) link_NAG-ASN : angle 3.24324 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 159 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7398 (pmm) cc_final: 0.6920 (pmm) REVERT: A 189 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.5891 (mm) REVERT: A 223 LEU cc_start: 0.5530 (OUTLIER) cc_final: 0.5193 (mt) REVERT: A 697 MET cc_start: 0.8348 (mmm) cc_final: 0.8103 (tpp) REVERT: A 733 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7888 (ptpt) REVERT: A 1018 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8482 (tt) REVERT: A 1029 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8083 (tpp) REVERT: B 97 LYS cc_start: 0.6882 (mmtt) cc_final: 0.5791 (mmtm) REVERT: B 200 TYR cc_start: 0.7458 (m-80) cc_final: 0.7172 (t80) REVERT: B 220 PHE cc_start: 0.6426 (t80) cc_final: 0.6107 (t80) REVERT: B 238 PHE cc_start: 0.6044 (p90) cc_final: 0.5640 (p90) REVERT: B 505 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7367 (t80) REVERT: B 675 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7233 (pp30) REVERT: B 906 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8215 (t80) REVERT: B 973 ILE cc_start: 0.8950 (mt) cc_final: 0.8740 (mt) REVERT: C 58 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7300 (m-80) REVERT: C 231 ILE cc_start: 0.6386 (OUTLIER) cc_final: 0.6038 (mp) REVERT: C 408 ARG cc_start: 0.8647 (ppt170) cc_final: 0.8406 (ppt170) REVERT: C 655 HIS cc_start: 0.7516 (OUTLIER) cc_final: 0.7294 (p90) REVERT: C 906 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.7612 (t80) REVERT: C 923 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8891 (mm) REVERT: D 28 ASN cc_start: 0.6950 (t0) cc_final: 0.6627 (t0) REVERT: D 46 GLU cc_start: 0.7707 (mp0) cc_final: 0.7338 (mp0) REVERT: D 48 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6573 (ptm) REVERT: D 82 GLN cc_start: 0.8160 (mt0) cc_final: 0.7517 (mp10) REVERT: I 147 VAL cc_start: 0.2078 (OUTLIER) cc_final: 0.1676 (p) outliers start: 171 outliers final: 136 residues processed: 317 average time/residue: 0.1607 time to fit residues: 88.0813 Evaluate side-chains 304 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 153 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 117 PHE Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 93 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 357 optimal weight: 20.0000 chunk 384 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 405 optimal weight: 20.0000 chunk 101 optimal weight: 0.4980 chunk 380 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 394 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 ASN ** F 101 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 = 0.4166 r_free = 0.4166 target = 0.142790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.106925 restraints weight = 72988.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.100102 restraints weight = 97291.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.097024 restraints weight = 97737.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.097627 restraints weight = 76169.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.097848 restraints weight = 61953.682| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33178 Z= 0.137 Angle : 0.601 16.273 45224 Z= 0.298 Chirality : 0.045 0.254 5180 Planarity : 0.004 0.055 5787 Dihedral : 6.708 63.828 5073 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.11 % Allowed : 23.16 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.13), residues: 4060 helix: 1.07 (0.22), residues: 654 sheet: 0.35 (0.16), residues: 1117 loop : -1.39 (0.12), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 237 TYR 0.024 0.001 TYR A 160 PHE 0.043 0.001 PHE C 133 TRP 0.019 0.001 TRP C 104 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00327 (33123) covalent geometry : angle 0.57875 (45082) SS BOND : bond 0.00439 ( 23) SS BOND : angle 2.51203 ( 46) hydrogen bonds : bond 0.04960 ( 1112) hydrogen bonds : angle 4.77184 ( 3048) link_BETA1-4 : bond 0.00255 ( 5) link_BETA1-4 : angle 2.37479 ( 15) link_NAG-ASN : bond 0.00379 ( 27) link_NAG-ASN : angle 3.21554 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 160 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.5569 (OUTLIER) cc_final: 0.5229 (mt) REVERT: A 697 MET cc_start: 0.8345 (mmm) cc_final: 0.7983 (tpp) REVERT: A 733 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7918 (ptpt) REVERT: A 1018 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8311 (tt) REVERT: A 1029 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.8270 (tpp) REVERT: B 97 LYS cc_start: 0.6806 (mmtt) cc_final: 0.5701 (mmtm) REVERT: B 200 TYR cc_start: 0.7469 (m-80) cc_final: 0.7093 (t80) REVERT: B 220 PHE cc_start: 0.6491 (t80) cc_final: 0.6207 (t80) REVERT: B 238 PHE cc_start: 0.6007 (p90) cc_final: 0.5592 (p90) REVERT: B 505 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7301 (t80) REVERT: B 675 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7199 (pp30) REVERT: B 781 VAL cc_start: 0.8696 (t) cc_final: 0.8432 (t) REVERT: B 906 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8280 (t80) REVERT: C 58 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: C 177 MET cc_start: 0.3701 (mmt) cc_final: 0.2382 (mmt) REVERT: C 231 ILE cc_start: 0.6370 (OUTLIER) cc_final: 0.6024 (mp) REVERT: C 655 HIS cc_start: 0.7532 (OUTLIER) cc_final: 0.7302 (p90) REVERT: C 906 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.7716 (t80) REVERT: C 923 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8933 (mm) REVERT: D 28 ASN cc_start: 0.6920 (t0) cc_final: 0.6594 (t0) REVERT: D 46 GLU cc_start: 0.7641 (mp0) cc_final: 0.7327 (mp0) REVERT: D 48 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6702 (ptm) REVERT: D 82 GLN cc_start: 0.8162 (mt0) cc_final: 0.7541 (mp10) outliers start: 183 outliers final: 147 residues processed: 327 average time/residue: 0.1668 time to fit residues: 94.6208 Evaluate side-chains 311 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 151 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 117 PHE Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 88 optimal weight: 0.0370 chunk 129 optimal weight: 0.9980 chunk 283 optimal weight: 0.8980 chunk 284 optimal weight: 0.0970 chunk 267 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 141 optimal weight: 7.9990 chunk 393 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 196 optimal weight: 0.5980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.156931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.117211 restraints weight = 72943.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.110429 restraints weight = 88180.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.107576 restraints weight = 66318.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.107099 restraints weight = 64029.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.107795 restraints weight = 53385.737| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33178 Z= 0.103 Angle : 0.594 16.666 45224 Z= 0.290 Chirality : 0.044 0.239 5180 Planarity : 0.004 0.054 5787 Dihedral : 6.401 58.650 5073 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.52 % Allowed : 24.47 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.13), residues: 4060 helix: 1.26 (0.22), residues: 656 sheet: 0.41 (0.16), residues: 1112 loop : -1.28 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 18 TYR 0.041 0.001 TYR A 160 PHE 0.053 0.001 PHE C 133 TRP 0.020 0.001 TRP C 104 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00227 (33123) covalent geometry : angle 0.57366 (45082) SS BOND : bond 0.00417 ( 23) SS BOND : angle 2.21375 ( 46) hydrogen bonds : bond 0.04135 ( 1112) hydrogen bonds : angle 4.62139 ( 3048) link_BETA1-4 : bond 0.00343 ( 5) link_BETA1-4 : angle 2.34310 ( 15) link_NAG-ASN : bond 0.00434 ( 27) link_NAG-ASN : angle 3.12556 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 161 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.5665 (OUTLIER) cc_final: 0.5332 (mt) REVERT: A 697 MET cc_start: 0.8444 (mmm) cc_final: 0.8018 (tpp) REVERT: A 1029 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8212 (tpp) REVERT: B 200 TYR cc_start: 0.8039 (m-80) cc_final: 0.7468 (t80) REVERT: B 220 PHE cc_start: 0.6444 (t80) cc_final: 0.6049 (t80) REVERT: B 505 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7410 (t80) REVERT: B 675 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7154 (pp30) REVERT: B 906 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8261 (t80) REVERT: C 58 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7408 (m-80) REVERT: C 190 ARG cc_start: 0.5607 (ttm170) cc_final: 0.5326 (ttm170) REVERT: C 231 ILE cc_start: 0.6075 (OUTLIER) cc_final: 0.5757 (mp) REVERT: C 906 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.7728 (t80) REVERT: C 923 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8864 (mm) REVERT: D 28 ASN cc_start: 0.6636 (t0) cc_final: 0.6256 (t0) REVERT: D 46 GLU cc_start: 0.7756 (mp0) cc_final: 0.7338 (mp0) REVERT: D 48 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6730 (ptm) REVERT: D 82 GLN cc_start: 0.8144 (mt0) cc_final: 0.7340 (mp10) REVERT: D 93 MET cc_start: 0.6665 (tpt) cc_final: 0.5994 (tpt) outliers start: 126 outliers final: 104 residues processed: 273 average time/residue: 0.1614 time to fit residues: 76.1846 Evaluate side-chains 267 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 153 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain I residue 117 PHE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 139 optimal weight: 6.9990 chunk 188 optimal weight: 0.6980 chunk 275 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 223 optimal weight: 0.0470 chunk 117 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 208 optimal weight: 0.4980 chunk 338 optimal weight: 50.0000 chunk 72 optimal weight: 0.4980 chunk 354 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 394 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 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 = 0.4206 r_free = 0.4206 target = 0.146143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.107521 restraints weight = 74505.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.101527 restraints weight = 96882.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.098903 restraints weight = 78293.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.099658 restraints weight = 65358.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.099425 restraints weight = 61916.915| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33178 Z= 0.101 Angle : 0.577 17.099 45224 Z= 0.282 Chirality : 0.044 0.237 5180 Planarity : 0.004 0.054 5787 Dihedral : 6.189 58.387 5073 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.21 % Allowed : 24.97 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.13), residues: 4060 helix: 1.39 (0.22), residues: 658 sheet: 0.57 (0.16), residues: 1055 loop : -1.25 (0.12), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1107 TYR 0.037 0.001 TYR A 160 PHE 0.022 0.001 PHE A 201 TRP 0.019 0.001 TRP I 149 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00227 (33123) covalent geometry : angle 0.55815 (45082) SS BOND : bond 0.00369 ( 23) SS BOND : angle 2.03851 ( 46) hydrogen bonds : bond 0.03962 ( 1112) hydrogen bonds : angle 4.54202 ( 3048) link_BETA1-4 : bond 0.00330 ( 5) link_BETA1-4 : angle 2.30507 ( 15) link_NAG-ASN : bond 0.00425 ( 27) link_NAG-ASN : angle 3.07615 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 162 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.5636 (OUTLIER) cc_final: 0.5289 (mt) REVERT: A 508 TYR cc_start: 0.7386 (m-80) cc_final: 0.7063 (m-80) REVERT: A 697 MET cc_start: 0.8408 (mmm) cc_final: 0.7946 (tpp) REVERT: A 1029 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.7803 (tpp) REVERT: B 200 TYR cc_start: 0.7752 (m-80) cc_final: 0.7225 (t80) REVERT: B 220 PHE cc_start: 0.6417 (t80) cc_final: 0.6090 (t80) REVERT: B 505 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7337 (t80) REVERT: B 906 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8021 (t80) REVERT: C 58 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: C 231 ILE cc_start: 0.6270 (OUTLIER) cc_final: 0.5914 (mp) REVERT: C 740 MET cc_start: 0.7822 (tpt) cc_final: 0.7611 (tpt) REVERT: C 906 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.7621 (t80) REVERT: C 923 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8817 (mm) REVERT: D 28 ASN cc_start: 0.6736 (t0) cc_final: 0.6337 (t0) REVERT: D 48 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6688 (ptm) REVERT: D 82 GLN cc_start: 0.8150 (mt0) cc_final: 0.7488 (mp10) REVERT: D 93 MET cc_start: 0.6692 (tpt) cc_final: 0.6007 (tpt) REVERT: I 147 VAL cc_start: 0.2009 (OUTLIER) cc_final: 0.1630 (p) outliers start: 115 outliers final: 95 residues processed: 261 average time/residue: 0.1731 time to fit residues: 77.8025 Evaluate side-chains 257 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 152 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 117 PHE Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain F residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 14 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 341 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 365 optimal weight: 30.0000 chunk 51 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN B 928 ASN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.145641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.107929 restraints weight = 73657.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.099135 restraints weight = 87773.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097848 restraints weight = 69087.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.097285 restraints weight = 57690.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.097463 restraints weight = 55393.087| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.468 33178 Z= 0.290 Angle : 0.725 59.200 45224 Z= 0.397 Chirality : 0.051 0.921 5180 Planarity : 0.004 0.091 5787 Dihedral : 6.193 58.460 5073 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.21 % Allowed : 25.08 % Favored : 71.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.13), residues: 4060 helix: 1.30 (0.22), residues: 658 sheet: 0.56 (0.16), residues: 1066 loop : -1.25 (0.12), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.102 0.002 TYR A 160 PHE 0.088 0.002 PHE C 133 TRP 0.016 0.001 TRP C 104 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00681 (33123) covalent geometry : angle 0.71013 (45082) SS BOND : bond 0.00539 ( 23) SS BOND : angle 2.07531 ( 46) hydrogen bonds : bond 0.04443 ( 1112) hydrogen bonds : angle 4.54736 ( 3048) link_BETA1-4 : bond 0.00586 ( 5) link_BETA1-4 : angle 2.37091 ( 15) link_NAG-ASN : bond 0.00453 ( 27) link_NAG-ASN : angle 3.07763 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5345.72 seconds wall clock time: 93 minutes 30.72 seconds (5610.72 seconds total)