Starting phenix.real_space_refine on Fri Mar 6 07:12:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xmz_33308/03_2026/7xmz_33308.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xmz_33308/03_2026/7xmz_33308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xmz_33308/03_2026/7xmz_33308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xmz_33308/03_2026/7xmz_33308.map" model { file = "/net/cci-nas-00/data/ceres_data/7xmz_33308/03_2026/7xmz_33308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xmz_33308/03_2026/7xmz_33308.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.074 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 125 5.16 5 C 18527 2.51 5 N 4830 2.21 5 O 5721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s 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: 29203 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7907 Classifications: {'peptide': 1019} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 53, 'TRANS': 965} Chain breaks: 9 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 7904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7904 Classifications: {'peptide': 1018} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 54, 'TRANS': 963} Chain breaks: 9 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 7814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7814 Classifications: {'peptide': 1009} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 53, 'TRANS': 955} Chain breaks: 9 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 930 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 780 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 930 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 780 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 930 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 780 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 7.09, per 1000 atoms: 0.24 Number of scatterers: 29203 At special positions: 0 Unit cell: (171.69, 179.45, 197.88, 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 125 16.00 O 5721 8.00 N 4830 7.00 C 18527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=1.64 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=1.64 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 89 " 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=3, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A1098 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 234 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B1098 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 234 " " NAG B1310 " - " ASN B 603 " " NAG B1311 " - " ASN B 165 " " NAG C1301 " - " ASN C1098 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 61 " " NAG C1309 " - " ASN C 234 " " NAG C1310 " - " ASN C 603 " " NAG C1311 " - " ASN C 165 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.7 seconds 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6936 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 67 sheets defined 20.6% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.693A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.143A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 568 through 572 removed outlier: 4.280A pdb=" N THR A 572 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.515A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.692A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.956A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 874 removed outlier: 3.936A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 884 removed outlier: 3.848A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 902 through 907 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.536A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.680A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 964 removed outlier: 3.603A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 967 No H-bonds generated for 'chain 'A' and resid 965 through 967' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.686A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 100 removed outlier: 4.476A pdb=" N ASN B 99 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.143A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 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 438 through 443 Processing helix chain 'B' and resid 568 through 572 removed outlier: 4.302A pdb=" N THR B 572 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 623 removed outlier: 3.693A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.519A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (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 783 removed outlier: 3.847A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.916A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 874 removed outlier: 3.910A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 902 Processing helix chain 'B' and resid 902 through 907 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.999A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 965 removed outlier: 3.690A pdb=" N GLN B 954 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.614A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.615A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B1026 " --> pdb=" O ALA B1022 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.142A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.737A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (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: 3.508A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.848A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 874 removed outlier: 3.941A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 907 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.823A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 964 removed outlier: 3.832A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.509A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.408A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA C1026 " --> pdb=" O ALA C1022 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'L' and resid 25 through 32 removed outlier: 3.643A pdb=" N ASP L 31 " --> pdb=" O SER L 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'E' and resid 25 through 32 removed outlier: 3.642A pdb=" N ASP E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'I' and resid 25 through 32 removed outlier: 3.643A pdb=" N ASP I 31 " --> pdb=" O SER I 27 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 8.012A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.687A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.961A 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 removed outlier: 4.053A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 135 removed outlier: 4.317A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.718A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.537A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.603A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 584 through 586 removed outlier: 4.108A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.163A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.743A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.777A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 725 through 728 removed outlier: 3.845A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.735A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.609A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR B 266 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.910A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.558A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.627A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 132 through 135 removed outlier: 3.556A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.767A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.603A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (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 539 through 543 removed outlier: 3.544A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.125A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 722 removed outlier: 6.704A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.805A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.567A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.512A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.275A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.952A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.513A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.708A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 324 through 326 removed outlier: 3.808A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 355 through 358 removed outlier: 3.603A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.057A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.784A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.815A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.558A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.550A pdb=" N MET H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY H 59 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.997A pdb=" N TYR H 112 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.515A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AF7, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF8, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.550A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY D 59 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.996A pdb=" N TYR D 112 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.516A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 9 through 11 Processing sheet with id=AG5, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AG6, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AG7, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.549A pdb=" N MET G 34 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY G 59 " --> pdb=" O GLY G 50 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.996A pdb=" N TYR G 112 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 9 through 11 removed outlier: 6.516A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 9 through 11 Processing sheet with id=AH3, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AH4, first strand: chain 'I' and resid 18 through 23 1067 hydrogen bonds defined for protein. 2814 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: 8.90 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4819 1.30 - 1.43: 8126 1.43 - 1.56: 16742 1.56 - 1.69: 1 1.69 - 1.82: 157 Bond restraints: 29845 Sorted by residual: bond pdb=" N PRO A 600 " pdb=" CD PRO A 600 " ideal model delta sigma weight residual 1.473 1.661 -0.188 1.40e-02 5.10e+03 1.80e+02 bond pdb=" C PRO A 600 " pdb=" O PRO A 600 " ideal model delta sigma weight residual 1.237 1.173 0.064 1.26e-02 6.30e+03 2.57e+01 bond pdb=" C PRO B 807 " pdb=" O PRO B 807 " ideal model delta sigma weight residual 1.233 1.183 0.050 1.16e-02 7.43e+03 1.87e+01 bond pdb=" C PRO C 57 " pdb=" O PRO C 57 " ideal model delta sigma weight residual 1.235 1.183 0.052 1.30e-02 5.92e+03 1.63e+01 bond pdb=" C THR C 723 " pdb=" O THR C 723 " ideal model delta sigma weight residual 1.235 1.182 0.053 1.38e-02 5.25e+03 1.48e+01 ... (remaining 29840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 39710 2.95 - 5.90: 881 5.90 - 8.85: 29 8.85 - 11.80: 10 11.80 - 14.75: 1 Bond angle restraints: 40631 Sorted by residual: angle pdb=" N THR A 602 " pdb=" CA THR A 602 " pdb=" C THR A 602 " ideal model delta sigma weight residual 114.39 99.64 14.75 1.45e+00 4.76e-01 1.04e+02 angle pdb=" C THR B 531 " pdb=" CA THR B 531 " pdb=" CB THR B 531 " ideal model delta sigma weight residual 114.40 103.79 10.61 1.25e+00 6.40e-01 7.21e+01 angle pdb=" C ASP B 808 " pdb=" CA ASP B 808 " pdb=" CB ASP B 808 " ideal model delta sigma weight residual 110.08 100.68 9.40 1.15e+00 7.56e-01 6.68e+01 angle pdb=" C THR A 599 " pdb=" CA THR A 599 " pdb=" CB THR A 599 " ideal model delta sigma weight residual 109.47 100.19 9.28 1.18e+00 7.18e-01 6.19e+01 angle pdb=" N GLY A 601 " pdb=" CA GLY A 601 " pdb=" C GLY A 601 " ideal model delta sigma weight residual 110.69 101.22 9.47 1.33e+00 5.65e-01 5.07e+01 ... (remaining 40626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.16: 17089 22.16 - 44.31: 848 44.31 - 66.47: 149 66.47 - 88.62: 30 88.62 - 110.78: 18 Dihedral angle restraints: 18134 sinusoidal: 7324 harmonic: 10810 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -10.41 -75.59 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -23.91 -62.09 1 1.00e+01 1.00e-02 5.11e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -143.76 57.76 1 1.00e+01 1.00e-02 4.48e+01 ... (remaining 18131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3666 0.083 - 0.167: 841 0.167 - 0.250: 191 0.250 - 0.334: 4 0.334 - 0.417: 2 Chirality restraints: 4704 Sorted by residual: chirality pdb=" CA ASP B 808 " pdb=" N ASP B 808 " pdb=" C ASP B 808 " pdb=" CB ASP B 808 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA THR B 531 " pdb=" N THR B 531 " pdb=" C THR B 531 " pdb=" CB THR B 531 " both_signs ideal model delta sigma weight residual False 2.53 2.83 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 4701 not shown) Planarity restraints: 5273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO B 987 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 599 " 0.051 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO A 600 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 600 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 600 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1302 " 0.026 2.00e-02 2.50e+03 2.13e-02 5.68e+00 pdb=" C7 NAG C1302 " -0.007 2.00e-02 2.50e+03 pdb=" C8 NAG C1302 " 0.020 2.00e-02 2.50e+03 pdb=" N2 NAG C1302 " -0.034 2.00e-02 2.50e+03 pdb=" O7 NAG C1302 " -0.005 2.00e-02 2.50e+03 ... (remaining 5270 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1148 2.72 - 3.26: 27646 3.26 - 3.81: 43901 3.81 - 4.35: 58937 4.35 - 4.90: 99258 Nonbonded interactions: 230890 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.171 3.040 nonbonded pdb=" OE1 GLU A 819 " pdb=" OG SER A1055 " model vdw 2.187 3.040 nonbonded pdb=" OD2 ASP C 578 " pdb=" OG1 THR C 581 " model vdw 2.206 3.040 nonbonded pdb=" OH TYR B 351 " pdb=" NH2 ARG B 454 " model vdw 2.231 2.496 nonbonded pdb=" OH TYR C 351 " pdb=" NH2 ARG C 454 " model vdw 2.231 2.496 ... (remaining 230885 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 26 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 66 or resid 81 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 throug \ h 141 or resid 154 through 170 or (resid 171 and (name N or name CA or name C or \ name O or name CB )) or resid 172 through 189 or (resid 190 and (name N or name \ CA or name C or name O or name CB )) or resid 191 through 243 or resid 264 thro \ ugh 272 or (resid 273 and (name N or name CA or name C or name O or name CB )) o \ r resid 274 through 328 or resid 334 through 645 or (resid 646 through 647 and ( \ name N or name CA or name C or name O or name CB )) or resid 648 through 826 or \ resid 854 or (resid 855 and (name N or name CA or name C or name O or name CB )) \ or resid 856 through 1143 or resid 1301 through 1310)) selection = (chain 'B' and (resid 26 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 95 or (resid 96 through 97 and (na \ me N or name CA or name C or name O or name CB )) or resid 98 through 107 or (re \ sid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 th \ rough 170 or (resid 171 and (name N or name CA or name C or name O or name CB )) \ or resid 172 through 209 or (resid 210 and (name N or name CA or name C or name \ O or name CB )) or resid 211 through 243 or resid 264 through 272 or (resid 273 \ and (name N or name CA or name C or name O or name CB )) or resid 274 through 3 \ 28 or resid 334 through 526 or resid 530 through 645 or (resid 646 through 647 a \ nd (name N or name CA or name C or name O or name CB )) or resid 648 through 810 \ or (resid 811 and (name N or name CA or name C or name O or name CB )) or resid \ 812 through 826 or resid 854 or (resid 855 and (name N or name CA or name C or \ name O or name CB )) or resid 856 through 1143 or resid 1302 through 1311)) selection = (chain 'C' and (resid 26 through 66 or resid 81 through 95 or (resid 96 through \ 97 and (name N or name CA or name C or name O or name CB )) or resid 98 through \ 107 or (resid 108 and (name N or name CA or name C or name O or name CB )) or re \ sid 109 through 133 or (resid 134 through 135 and (name N or name CA or name C o \ r name O or name CB )) or resid 136 through 141 or resid 154 through 209 or (res \ id 210 and (name N or name CA or name C or name O or name CB )) or resid 211 thr \ ough 810 or (resid 811 and (name N or name CA or name C or name O or name CB )) \ or resid 812 through 826 or resid 854 through 1143 or resid 1302 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'L' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.610 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 32.930 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 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 : 0.009 0.387 29921 Z= 0.638 Angle : 1.092 27.717 40809 Z= 0.765 Chirality : 0.072 0.417 4704 Planarity : 0.004 0.081 5241 Dihedral : 13.606 110.779 11075 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.41 % Favored : 95.48 % Rotamer: Outliers : 0.47 % Allowed : 3.13 % Favored : 96.40 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.13), residues: 3673 helix: -1.83 (0.19), residues: 664 sheet: -0.33 (0.17), residues: 972 loop : -0.95 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 815 TYR 0.016 0.001 TYR A 369 PHE 0.017 0.001 PHE C 92 TRP 0.011 0.002 TRP C 886 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00852 (29845) covalent geometry : angle 1.05514 (40631) SS BOND : bond 0.08570 ( 41) SS BOND : angle 5.79639 ( 82) hydrogen bonds : bond 0.25429 ( 1014) hydrogen bonds : angle 10.55149 ( 2814) Misc. bond : bond 0.02977 ( 3) link_NAG-ASN : bond 0.00409 ( 32) link_NAG-ASN : angle 2.65039 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 TYR cc_start: 0.7668 (m-80) cc_final: 0.7109 (m-80) REVERT: B 811 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7909 (mtmm) REVERT: D 34 MET cc_start: 0.1082 (mmm) cc_final: 0.0750 (mtp) REVERT: G 6 GLU cc_start: 0.5551 (OUTLIER) cc_final: 0.3364 (mp0) REVERT: G 7 SER cc_start: 0.6183 (p) cc_final: 0.5982 (t) outliers start: 15 outliers final: 6 residues processed: 216 average time/residue: 0.1856 time to fit residues: 66.7755 Evaluate side-chains 161 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain C residue 57 PRO Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain G residue 6 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.7980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 965 GLN B1010 GLN C 30 ASN C 519 HIS C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.222208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.165509 restraints weight = 34608.943| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 5.48 r_work: 0.3010 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 29921 Z= 0.211 Angle : 0.633 10.891 40809 Z= 0.330 Chirality : 0.047 0.188 4704 Planarity : 0.004 0.067 5241 Dihedral : 8.890 88.548 4695 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.79 % Allowed : 7.46 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.13), residues: 3673 helix: -1.01 (0.19), residues: 681 sheet: -0.17 (0.16), residues: 998 loop : -0.95 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 454 TYR 0.039 0.001 TYR A 265 PHE 0.026 0.002 PHE C 906 TRP 0.010 0.001 TRP A 886 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00515 (29845) covalent geometry : angle 0.61824 (40631) SS BOND : bond 0.00559 ( 41) SS BOND : angle 1.75909 ( 82) hydrogen bonds : bond 0.05434 ( 1014) hydrogen bonds : angle 7.12530 ( 2814) Misc. bond : bond 0.00018 ( 3) link_NAG-ASN : bond 0.00303 ( 32) link_NAG-ASN : angle 2.43086 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6682 (t0) cc_final: 0.6351 (t0) REVERT: A 519 HIS cc_start: 0.2446 (OUTLIER) cc_final: 0.1801 (p-80) REVERT: A 856 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.7743 (p0) REVERT: A 1084 ASP cc_start: 0.8462 (t0) cc_final: 0.8243 (t0) REVERT: A 1144 GLU cc_start: 0.7973 (pt0) cc_final: 0.7707 (pt0) REVERT: B 697 MET cc_start: 0.9063 (ptm) cc_final: 0.8842 (ptp) REVERT: C 64 TRP cc_start: 0.8373 (t60) cc_final: 0.7986 (t60) outliers start: 25 outliers final: 16 residues processed: 185 average time/residue: 0.1753 time to fit residues: 55.2840 Evaluate side-chains 170 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain H residue 89 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 304 optimal weight: 20.0000 chunk 290 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 128 optimal weight: 30.0000 chunk 255 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 81 optimal weight: 0.3980 chunk 84 optimal weight: 0.3980 chunk 38 optimal weight: 0.2980 chunk 258 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 218 GLN A 613 GLN B 675 GLN B 914 ASN B 955 ASN B1010 GLN C 207 HIS D 82 HIS G 82 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.223697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.210227 restraints weight = 34657.208| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 0.61 r_work: 0.3945 rms_B_bonded: 0.72 restraints_weight: 0.5000 r_work: 0.3885 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.3842 rms_B_bonded: 2.05 restraints_weight: 0.1250 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29921 Z= 0.103 Angle : 0.529 8.250 40809 Z= 0.273 Chirality : 0.044 0.193 4704 Planarity : 0.004 0.058 5241 Dihedral : 7.166 68.997 4676 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.39 % Allowed : 9.04 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.14), residues: 3673 helix: -0.17 (0.20), residues: 670 sheet: 0.01 (0.16), residues: 1008 loop : -0.75 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 102 TYR 0.029 0.001 TYR A 265 PHE 0.020 0.001 PHE B 106 TRP 0.013 0.001 TRP G 53 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00232 (29845) covalent geometry : angle 0.51757 (40631) SS BOND : bond 0.00324 ( 41) SS BOND : angle 1.29629 ( 82) hydrogen bonds : bond 0.03867 ( 1014) hydrogen bonds : angle 6.28481 ( 2814) Misc. bond : bond 0.00018 ( 3) link_NAG-ASN : bond 0.00338 ( 32) link_NAG-ASN : angle 2.02311 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 HIS cc_start: 0.2844 (OUTLIER) cc_final: 0.1788 (p-80) REVERT: A 856 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7512 (p0) REVERT: B 269 TYR cc_start: 0.7673 (m-80) cc_final: 0.7310 (m-80) REVERT: C 94 SER cc_start: 0.6846 (m) cc_final: 0.6608 (p) REVERT: C 203 ILE cc_start: 0.8276 (mt) cc_final: 0.7748 (tt) outliers start: 44 outliers final: 22 residues processed: 201 average time/residue: 0.1772 time to fit residues: 60.9914 Evaluate side-chains 173 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 183 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 212 optimal weight: 20.0000 chunk 291 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 302 optimal weight: 30.0000 chunk 220 optimal weight: 10.0000 chunk 257 optimal weight: 0.5980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 239 GLN A1010 GLN B1010 GLN C 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.220476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.160191 restraints weight = 34412.480| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 6.04 r_work: 0.2972 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 29921 Z= 0.224 Angle : 0.612 8.709 40809 Z= 0.312 Chirality : 0.047 0.191 4704 Planarity : 0.004 0.055 5241 Dihedral : 6.680 59.648 4676 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.71 % Allowed : 10.34 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.14), residues: 3673 helix: -0.29 (0.20), residues: 676 sheet: 0.01 (0.16), residues: 1025 loop : -0.79 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 905 TYR 0.036 0.001 TYR A 265 PHE 0.030 0.002 PHE A 65 TRP 0.017 0.001 TRP G 53 HIS 0.008 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00557 (29845) covalent geometry : angle 0.59745 (40631) SS BOND : bond 0.00571 ( 41) SS BOND : angle 1.91924 ( 82) hydrogen bonds : bond 0.04382 ( 1014) hydrogen bonds : angle 6.11968 ( 2814) Misc. bond : bond 0.00029 ( 3) link_NAG-ASN : bond 0.00270 ( 32) link_NAG-ASN : angle 2.17712 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 156 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8740 (tp40) REVERT: A 519 HIS cc_start: 0.2521 (OUTLIER) cc_final: 0.1980 (p-80) REVERT: A 856 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.7955 (p0) REVERT: B 269 TYR cc_start: 0.8156 (m-80) cc_final: 0.7652 (m-80) REVERT: B 569 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8285 (pt) REVERT: B 901 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8661 (tm-30) REVERT: C 873 TYR cc_start: 0.9096 (OUTLIER) cc_final: 0.8215 (m-80) REVERT: C 901 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8933 (tm-30) outliers start: 54 outliers final: 32 residues processed: 196 average time/residue: 0.1708 time to fit residues: 57.4028 Evaluate side-chains 188 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 205 optimal weight: 0.8980 chunk 246 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 312 optimal weight: 50.0000 chunk 150 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.220809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.156450 restraints weight = 34562.824| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 6.60 r_work: 0.3027 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 29921 Z= 0.246 Angle : 0.627 9.425 40809 Z= 0.321 Chirality : 0.048 0.267 4704 Planarity : 0.004 0.053 5241 Dihedral : 6.363 59.878 4676 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.09 % Allowed : 10.81 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3673 helix: -0.42 (0.20), residues: 672 sheet: -0.04 (0.16), residues: 1011 loop : -0.86 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 905 TYR 0.036 0.001 TYR A 265 PHE 0.026 0.002 PHE A 65 TRP 0.027 0.001 TRP G 53 HIS 0.008 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00610 (29845) covalent geometry : angle 0.61236 (40631) SS BOND : bond 0.00579 ( 41) SS BOND : angle 1.99124 ( 82) hydrogen bonds : bond 0.04429 ( 1014) hydrogen bonds : angle 5.97306 ( 2814) Misc. bond : bond 0.00023 ( 3) link_NAG-ASN : bond 0.00283 ( 32) link_NAG-ASN : angle 2.27551 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 158 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8319 (m-30) REVERT: A 314 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8751 (tp40) REVERT: A 519 HIS cc_start: 0.2630 (OUTLIER) cc_final: 0.2057 (p-80) REVERT: A 856 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.7865 (p0) REVERT: A 878 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8619 (tt) REVERT: B 52 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8590 (tm-30) REVERT: B 269 TYR cc_start: 0.8193 (m-80) cc_final: 0.7719 (m-80) REVERT: B 569 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8306 (pt) REVERT: B 878 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8804 (tt) REVERT: B 901 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8634 (tm-30) REVERT: C 873 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: C 901 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8884 (tm-30) outliers start: 66 outliers final: 38 residues processed: 209 average time/residue: 0.1590 time to fit residues: 57.6028 Evaluate side-chains 194 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 105 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 307 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 301 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 292 optimal weight: 0.8980 chunk 243 optimal weight: 30.0000 chunk 167 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 394 ASN A 901 GLN B 334 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.220728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.167208 restraints weight = 34365.041| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 4.85 r_work: 0.2996 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29921 Z= 0.178 Angle : 0.587 21.772 40809 Z= 0.298 Chirality : 0.046 0.288 4704 Planarity : 0.004 0.052 5241 Dihedral : 6.034 58.091 4675 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.37 % Allowed : 11.31 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3673 helix: -0.25 (0.20), residues: 676 sheet: -0.04 (0.16), residues: 999 loop : -0.82 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 905 TYR 0.032 0.001 TYR A 265 PHE 0.021 0.001 PHE A 65 TRP 0.031 0.001 TRP G 53 HIS 0.008 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00438 (29845) covalent geometry : angle 0.57437 (40631) SS BOND : bond 0.00485 ( 41) SS BOND : angle 1.75143 ( 82) hydrogen bonds : bond 0.03960 ( 1014) hydrogen bonds : angle 5.80387 ( 2814) Misc. bond : bond 0.00016 ( 3) link_NAG-ASN : bond 0.00250 ( 32) link_NAG-ASN : angle 2.11047 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 157 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8860 (tp40) REVERT: A 519 HIS cc_start: 0.2547 (OUTLIER) cc_final: 0.1985 (p-80) REVERT: A 856 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.7929 (p0) REVERT: B 52 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8655 (tm-30) REVERT: B 269 TYR cc_start: 0.8200 (m-80) cc_final: 0.7788 (m-80) REVERT: B 569 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8342 (pt) REVERT: B 878 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8772 (tt) REVERT: B 901 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8695 (tm-30) REVERT: C 861 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9090 (mt) REVERT: C 873 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.8333 (m-80) REVERT: C 901 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8870 (tm-30) outliers start: 75 outliers final: 52 residues processed: 218 average time/residue: 0.1646 time to fit residues: 61.6774 Evaluate side-chains 207 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 147 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain G residue 79 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 317 optimal weight: 50.0000 chunk 68 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 320 optimal weight: 50.0000 chunk 364 optimal weight: 5.9990 chunk 338 optimal weight: 10.0000 chunk 240 optimal weight: 50.0000 chunk 10 optimal weight: 3.9990 chunk 303 optimal weight: 40.0000 chunk 221 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B1002 GLN C 914 ASN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.217285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.159716 restraints weight = 34484.076| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 5.37 r_work: 0.2945 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.089 29921 Z= 0.379 Angle : 0.744 15.329 40809 Z= 0.379 Chirality : 0.053 0.302 4704 Planarity : 0.005 0.058 5241 Dihedral : 6.342 59.876 4675 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.75 % Allowed : 11.60 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3673 helix: -0.72 (0.20), residues: 667 sheet: -0.12 (0.16), residues: 1007 loop : -1.02 (0.14), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 905 TYR 0.040 0.002 TYR A 265 PHE 0.031 0.003 PHE B1121 TRP 0.036 0.002 TRP G 53 HIS 0.012 0.002 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00945 (29845) covalent geometry : angle 0.72757 (40631) SS BOND : bond 0.00836 ( 41) SS BOND : angle 2.30360 ( 82) hydrogen bonds : bond 0.05156 ( 1014) hydrogen bonds : angle 6.04326 ( 2814) Misc. bond : bond 0.00030 ( 3) link_NAG-ASN : bond 0.00425 ( 32) link_NAG-ASN : angle 2.60136 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 161 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6931 (t0) cc_final: 0.6700 (t0) REVERT: A 287 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8404 (m-30) REVERT: A 314 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8836 (tp40) REVERT: A 519 HIS cc_start: 0.2600 (OUTLIER) cc_final: 0.2064 (p-80) REVERT: A 856 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8029 (p0) REVERT: A 878 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8643 (tt) REVERT: A 950 ASP cc_start: 0.8743 (t0) cc_final: 0.8397 (t0) REVERT: B 52 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8649 (tm-30) REVERT: B 569 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8376 (pt) REVERT: B 878 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8830 (tt) REVERT: B 901 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8621 (tm-30) REVERT: C 873 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.8362 (m-80) REVERT: C 901 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8724 (tm-30) outliers start: 87 outliers final: 63 residues processed: 233 average time/residue: 0.1714 time to fit residues: 68.7887 Evaluate side-chains 226 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 154 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 300 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 347 optimal weight: 50.0000 chunk 218 optimal weight: 0.8980 chunk 287 optimal weight: 0.0270 chunk 217 optimal weight: 1.9990 chunk 127 optimal weight: 30.0000 chunk 179 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 360 optimal weight: 40.0000 chunk 24 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 218 GLN B 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.221898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.169579 restraints weight = 34598.251| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 4.77 r_work: 0.3059 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 29921 Z= 0.114 Angle : 0.564 16.554 40809 Z= 0.287 Chirality : 0.045 0.271 4704 Planarity : 0.004 0.050 5241 Dihedral : 5.786 55.563 4675 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.83 % Allowed : 12.71 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3673 helix: -0.14 (0.20), residues: 673 sheet: -0.10 (0.16), residues: 1001 loop : -0.82 (0.14), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 646 TYR 0.029 0.001 TYR A 265 PHE 0.016 0.001 PHE A 65 TRP 0.042 0.001 TRP G 53 HIS 0.004 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00270 (29845) covalent geometry : angle 0.55125 (40631) SS BOND : bond 0.00441 ( 41) SS BOND : angle 1.78560 ( 82) hydrogen bonds : bond 0.03521 ( 1014) hydrogen bonds : angle 5.66383 ( 2814) Misc. bond : bond 0.00014 ( 3) link_NAG-ASN : bond 0.00284 ( 32) link_NAG-ASN : angle 1.99226 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 155 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8359 (t0) REVERT: A 314 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8820 (tp40) REVERT: A 519 HIS cc_start: 0.2821 (OUTLIER) cc_final: 0.2190 (p-80) REVERT: A 856 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.8093 (p0) REVERT: A 878 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8412 (tt) REVERT: B 52 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8627 (tm-30) REVERT: B 269 TYR cc_start: 0.8269 (m-80) cc_final: 0.7892 (m-80) REVERT: B 324 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: B 569 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8298 (pt) REVERT: B 878 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8727 (tt) REVERT: C 873 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.8405 (m-80) outliers start: 58 outliers final: 40 residues processed: 201 average time/residue: 0.1646 time to fit residues: 57.4192 Evaluate side-chains 189 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 108 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 270 optimal weight: 0.9980 chunk 360 optimal weight: 50.0000 chunk 114 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN B 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.221856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.169395 restraints weight = 34565.664| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 4.79 r_work: 0.3044 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29921 Z= 0.125 Angle : 0.547 9.144 40809 Z= 0.280 Chirality : 0.045 0.262 4704 Planarity : 0.004 0.049 5241 Dihedral : 5.560 57.037 4675 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.86 % Allowed : 12.93 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3673 helix: 0.08 (0.20), residues: 675 sheet: -0.04 (0.16), residues: 1000 loop : -0.76 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 646 TYR 0.030 0.001 TYR A 265 PHE 0.018 0.001 PHE A 65 TRP 0.042 0.001 TRP G 53 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00304 (29845) covalent geometry : angle 0.53396 (40631) SS BOND : bond 0.00401 ( 41) SS BOND : angle 1.71768 ( 82) hydrogen bonds : bond 0.03507 ( 1014) hydrogen bonds : angle 5.49825 ( 2814) Misc. bond : bond 0.00012 ( 3) link_NAG-ASN : bond 0.00205 ( 32) link_NAG-ASN : angle 1.94256 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 147 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 HIS cc_start: 0.2817 (OUTLIER) cc_final: 0.2226 (p-80) REVERT: A 878 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8423 (tt) REVERT: B 52 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8637 (tm-30) REVERT: B 269 TYR cc_start: 0.8278 (m-80) cc_final: 0.7882 (m-80) REVERT: B 324 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: B 569 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8336 (pt) REVERT: B 878 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8725 (tp) REVERT: C 94 SER cc_start: 0.7696 (m) cc_final: 0.7257 (p) REVERT: C 873 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: D 34 MET cc_start: 0.0805 (mmm) cc_final: 0.0495 (mtp) outliers start: 59 outliers final: 46 residues processed: 196 average time/residue: 0.1693 time to fit residues: 57.4786 Evaluate side-chains 196 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 144 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 359 optimal weight: 40.0000 chunk 217 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 210 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.219741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.165262 restraints weight = 34248.419| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 4.98 r_work: 0.2982 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 29921 Z= 0.226 Angle : 0.622 11.668 40809 Z= 0.317 Chirality : 0.047 0.258 4704 Planarity : 0.004 0.051 5241 Dihedral : 5.703 59.891 4673 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.86 % Allowed : 13.05 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.77 (0.14), residues: 3673 helix: -0.18 (0.20), residues: 673 sheet: -0.05 (0.16), residues: 1000 loop : -0.83 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 646 TYR 0.035 0.001 TYR A 265 PHE 0.022 0.002 PHE B1121 TRP 0.047 0.001 TRP G 53 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00561 (29845) covalent geometry : angle 0.60580 (40631) SS BOND : bond 0.00556 ( 41) SS BOND : angle 2.25106 ( 82) hydrogen bonds : bond 0.04178 ( 1014) hydrogen bonds : angle 5.63021 ( 2814) Misc. bond : bond 0.00016 ( 3) link_NAG-ASN : bond 0.00247 ( 32) link_NAG-ASN : angle 2.17449 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 144 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 HIS cc_start: 0.2850 (OUTLIER) cc_final: 0.2280 (p-80) REVERT: A 878 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8585 (tt) REVERT: A 950 ASP cc_start: 0.8689 (t0) cc_final: 0.8304 (t0) REVERT: B 52 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8648 (tm-30) REVERT: B 269 TYR cc_start: 0.8334 (m-80) cc_final: 0.7949 (m-80) REVERT: B 324 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: B 569 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8313 (pt) REVERT: B 878 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8775 (tt) REVERT: C 94 SER cc_start: 0.7819 (m) cc_final: 0.7346 (p) REVERT: C 873 TYR cc_start: 0.9119 (OUTLIER) cc_final: 0.8364 (m-80) REVERT: C 901 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8891 (tm-30) REVERT: C 934 ILE cc_start: 0.8730 (mm) cc_final: 0.8501 (mm) outliers start: 59 outliers final: 50 residues processed: 194 average time/residue: 0.1660 time to fit residues: 55.6724 Evaluate side-chains 196 residues out of total 3235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 192 optimal weight: 0.2980 chunk 362 optimal weight: 50.0000 chunk 29 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 129 optimal weight: 0.0770 chunk 267 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 259 optimal weight: 0.7980 chunk 39 optimal weight: 30.0000 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 914 ASN C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.223837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.162783 restraints weight = 34551.913| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 6.18 r_work: 0.3057 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 29921 Z= 0.103 Angle : 0.533 11.858 40809 Z= 0.273 Chirality : 0.044 0.256 4704 Planarity : 0.004 0.047 5241 Dihedral : 5.294 54.899 4673 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.80 % Allowed : 13.21 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.14), residues: 3673 helix: 0.23 (0.21), residues: 674 sheet: 0.03 (0.16), residues: 1005 loop : -0.73 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 102 TYR 0.027 0.001 TYR A 265 PHE 0.018 0.001 PHE A 65 TRP 0.047 0.001 TRP G 53 HIS 0.008 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00246 (29845) covalent geometry : angle 0.52129 (40631) SS BOND : bond 0.00336 ( 41) SS BOND : angle 1.65577 ( 82) hydrogen bonds : bond 0.03261 ( 1014) hydrogen bonds : angle 5.41204 ( 2814) Misc. bond : bond 0.00011 ( 3) link_NAG-ASN : bond 0.00265 ( 32) link_NAG-ASN : angle 1.84603 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7143.76 seconds wall clock time: 123 minutes 17.68 seconds (7397.68 seconds total)