Starting phenix.real_space_refine on Thu Mar 5 20:29:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xm0_22253/03_2026/6xm0_22253.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xm0_22253/03_2026/6xm0_22253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xm0_22253/03_2026/6xm0_22253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xm0_22253/03_2026/6xm0_22253.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xm0_22253/03_2026/6xm0_22253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xm0_22253/03_2026/6xm0_22253.map" } resolution = 2.7 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= 0.002 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 108 5.16 5 C 16037 2.51 5 N 4118 2.21 5 O 4938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25201 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8109 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1037, 8103 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 51, 'TRANS': 985} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1037, 8103 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 51, 'TRANS': 985} Chain breaks: 7 bond proxies already assigned to first conformer: 8280 Chain: "B" Number of atoms: 8242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8242 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 52, 'TRANS': 1003} Chain breaks: 6 Chain: "C" Number of atoms: 8066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8066 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 52, 'TRANS': 979} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.39, per 1000 atoms: 0.29 Number of scatterers: 25201 At special positions: 0 Unit cell: (139.4, 136, 198.05, 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 108 16.00 O 4938 8.00 N 4118 7.00 C 16037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C1134 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.4 seconds 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5868 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 44 sheets defined 23.6% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.548A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.794A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.668A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.960A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.738A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.739A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.517A 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: 3.894A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.547A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.523A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.526A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.848A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.698A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.212A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.676A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.576A pdb=" N GLY B 744 " --> pdb=" O MET B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.641A 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: 3.640A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 832 through 842 removed outlier: 3.509A pdb=" N CYS B 840 " --> pdb=" O GLN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.521A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.521A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.978A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.560A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.326A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.544A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.802A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.702A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 390' Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.917A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 443' Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 632 through 636 removed outlier: 4.053A pdb=" N VAL C 635 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 757 Processing helix chain 'C' and resid 759 through 783 removed outlier: 3.551A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.512A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.562A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.145A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.510A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.030A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.641A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 981' Processing helix chain 'C' and resid 989 through 1032 removed outlier: 3.717A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.299A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.547A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.961A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.973A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.621A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.560A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.710A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.722A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.722A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.537A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.790A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.422A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.597A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.722A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 453 through 454 removed outlier: 3.837A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.512A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.529A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.708A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.615A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.515A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.521A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.523A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.534A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AD4, first strand: chain 'C' and resid 117 through 118 removed outlier: 3.766A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.041A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.577A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.167A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.727A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 538 through 539 removed outlier: 5.487A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.409A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.660A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.660A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.585A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.450A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 867 hydrogen bonds defined for protein. 2370 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.58 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7024 1.33 - 1.47: 7519 1.47 - 1.60: 11084 1.60 - 1.74: 2 1.74 - 1.87: 130 Bond restraints: 25759 Sorted by residual: bond pdb=" N ASN B 657 " pdb=" CA ASN B 657 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.32e-02 5.74e+03 1.23e+01 bond pdb=" N ALA B 520 " pdb=" CA ALA B 520 " ideal model delta sigma weight residual 1.456 1.489 -0.032 9.40e-03 1.13e+04 1.19e+01 bond pdb=" N LEU B 244 " pdb=" CA LEU B 244 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.21e-02 6.83e+03 1.12e+01 bond pdb=" N HIS B 245 " pdb=" CA HIS B 245 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N VAL C 320 " pdb=" CA VAL C 320 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.27e-02 6.20e+03 1.01e+01 ... (remaining 25754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 34094 2.89 - 5.77: 851 5.77 - 8.66: 94 8.66 - 11.54: 24 11.54 - 14.43: 5 Bond angle restraints: 35068 Sorted by residual: angle pdb=" C SER A 31 " pdb=" N PHE A 32 " pdb=" CA PHE A 32 " ideal model delta sigma weight residual 121.54 134.02 -12.48 1.91e+00 2.74e-01 4.27e+01 angle pdb=" C GLN C 321 " pdb=" CA GLN C 321 " pdb=" CB GLN C 321 " ideal model delta sigma weight residual 108.86 118.00 -9.14 1.44e+00 4.82e-01 4.03e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.88 -7.18 1.22e+00 6.72e-01 3.47e+01 angle pdb=" C ALA A 522 " pdb=" N THR A 523 " pdb=" CA THR A 523 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.46e+01 angle pdb=" CA TYR B 904 " pdb=" CB TYR B 904 " pdb=" CG TYR B 904 " ideal model delta sigma weight residual 113.90 123.98 -10.08 1.80e+00 3.09e-01 3.13e+01 ... (remaining 35063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 14342 17.77 - 35.53: 1375 35.53 - 53.30: 268 53.30 - 71.07: 57 71.07 - 88.84: 29 Dihedral angle restraints: 16071 sinusoidal: 6960 harmonic: 9111 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 11.96 81.04 1 1.00e+01 1.00e-02 8.10e+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 93.00 165.65 -72.65 1 1.00e+01 1.00e-02 6.74e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -155.37 69.37 1 1.00e+01 1.00e-02 6.22e+01 ... (remaining 16068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 3543 0.096 - 0.192: 568 0.192 - 0.287: 38 0.287 - 0.383: 9 0.383 - 0.479: 4 Chirality restraints: 4162 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" CB VAL B 130 " pdb=" CA VAL B 130 " pdb=" CG1 VAL B 130 " pdb=" CG2 VAL B 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CB THR A 95 " pdb=" CA THR A 95 " pdb=" OG1 THR A 95 " pdb=" CG2 THR A 95 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.40 2.00e-01 2.50e+01 3.90e+00 ... (remaining 4159 not shown) Planarity restraints: 4506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " -0.338 2.00e-02 2.50e+03 2.88e-01 1.03e+03 pdb=" C7 NAG B1307 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " -0.169 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " 0.507 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " -0.323 2.00e-02 2.50e+03 2.75e-01 9.42e+02 pdb=" C7 NAG A1305 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " 0.480 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " 0.315 2.00e-02 2.50e+03 2.62e-01 8.57e+02 pdb=" C7 NAG A1306 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " 0.202 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " -0.442 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " 0.014 2.00e-02 2.50e+03 ... (remaining 4503 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4006 2.76 - 3.30: 20382 3.30 - 3.83: 39468 3.83 - 4.37: 47055 4.37 - 4.90: 81810 Nonbonded interactions: 192721 Sorted by model distance: nonbonded pdb=" OH TYR A 91 " pdb=" OE2 GLU A 191 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR B 449 " pdb=" O PHE B 497 " model vdw 2.281 3.040 nonbonded pdb=" O GLN C 134 " pdb=" OH TYR C 160 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR C1138 " pdb=" OE2 GLU C1144 " model vdw 2.320 3.040 nonbonded pdb=" OE2 GLU A 619 " pdb=" NH2 ARG B 847 " model vdw 2.326 3.120 ... (remaining 192716 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 27 through 172 or resid 186 through 250 or resid 265 throu \ gh 612 or resid 614 through 827 or resid 853 through 1308)) selection = (chain 'B' and (resid 27 through 250 or resid 265 through 612 or resid 614 throu \ gh 827 or resid 853 through 1308)) selection = (chain 'C' and (resid 27 through 250 or resid 265 through 612 or resid 614 throu \ gh 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 8.040 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 29.460 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.010 0.112 25854 Z= 0.443 Angle : 1.146 14.429 35314 Z= 0.606 Chirality : 0.070 0.479 4162 Planarity : 0.011 0.288 4464 Dihedral : 14.511 88.835 10086 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.25 % Favored : 91.52 % Rotamer: Outliers : 0.55 % Allowed : 5.85 % Favored : 93.60 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.12), residues: 3080 helix: -4.44 (0.08), residues: 681 sheet: -1.13 (0.20), residues: 621 loop : -2.89 (0.11), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 34 TYR 0.040 0.004 TYR A 873 PHE 0.051 0.004 PHE B 559 TRP 0.039 0.004 TRP A 886 HIS 0.016 0.002 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.01027 (25759) covalent geometry : angle 1.11555 (35068) SS BOND : bond 0.00709 ( 39) SS BOND : angle 2.79932 ( 78) hydrogen bonds : bond 0.30970 ( 843) hydrogen bonds : angle 9.42667 ( 2370) link_BETA1-4 : bond 0.01073 ( 14) link_BETA1-4 : angle 2.70516 ( 42) link_NAG-ASN : bond 0.00556 ( 42) link_NAG-ASN : angle 3.76079 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 253 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 765 ARG cc_start: 0.8213 (ptp90) cc_final: 0.7913 (ptp-170) REVERT: B 271 GLN cc_start: 0.7455 (mt0) cc_final: 0.7015 (mp10) REVERT: B 616 ASN cc_start: 0.6899 (m-40) cc_final: 0.6631 (t0) REVERT: C 616 ASN cc_start: 0.8036 (t0) cc_final: 0.7707 (m-40) outliers start: 15 outliers final: 8 residues processed: 266 average time/residue: 0.5540 time to fit residues: 173.4621 Evaluate side-chains 214 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 206 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 581 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 173 GLN A 207 HIS A 460 ASN A 544 ASN A 804 GLN A 901 GLN A 955 ASN B 66 HIS B 239 GLN B 245 HIS B 437 ASN B 474 GLN B 804 GLN B 853 GLN B 901 GLN C 49 HIS C 321 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 804 GLN C 901 GLN C 935 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.201465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.153389 restraints weight = 33338.643| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.16 r_work: 0.3318 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25854 Z= 0.141 Angle : 0.718 13.516 35314 Z= 0.364 Chirality : 0.048 0.479 4162 Planarity : 0.006 0.093 4464 Dihedral : 7.889 57.425 4531 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.55 % Favored : 94.38 % Rotamer: Outliers : 1.61 % Allowed : 9.77 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.13), residues: 3080 helix: -1.28 (0.18), residues: 677 sheet: -0.44 (0.20), residues: 633 loop : -2.52 (0.12), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 237 TYR 0.024 0.001 TYR B 904 PHE 0.022 0.001 PHE A 32 TRP 0.019 0.002 TRP A 886 HIS 0.013 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00308 (25759) covalent geometry : angle 0.68953 (35068) SS BOND : bond 0.00665 ( 39) SS BOND : angle 1.77272 ( 78) hydrogen bonds : bond 0.07691 ( 843) hydrogen bonds : angle 5.73211 ( 2370) link_BETA1-4 : bond 0.00330 ( 14) link_BETA1-4 : angle 1.46247 ( 42) link_NAG-ASN : bond 0.00315 ( 42) link_NAG-ASN : angle 3.09526 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9009 (tpt) cc_final: 0.8783 (ttm) REVERT: A 1038 LYS cc_start: 0.8947 (mmtm) cc_final: 0.8667 (mptt) REVERT: A 1101 HIS cc_start: 0.8420 (t70) cc_final: 0.8215 (t-170) REVERT: B 271 GLN cc_start: 0.7666 (mt0) cc_final: 0.7179 (mp10) REVERT: C 52 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7865 (tm-30) REVERT: C 410 ILE cc_start: 0.8134 (mm) cc_final: 0.7923 (mm) REVERT: C 592 PHE cc_start: 0.8488 (p90) cc_final: 0.8255 (p90) REVERT: C 616 ASN cc_start: 0.8178 (t0) cc_final: 0.7855 (m-40) outliers start: 44 outliers final: 25 residues processed: 251 average time/residue: 0.5151 time to fit residues: 154.3122 Evaluate side-chains 228 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 70 optimal weight: 2.9990 chunk 257 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 270 optimal weight: 5.9990 chunk 279 optimal weight: 0.5980 chunk 114 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 271 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 360 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN C 164 ASN C 414 GLN C 540 ASN C 935 GLN C1010 GLN C1011 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.199833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.144376 restraints weight = 25995.097| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.88 r_work: 0.2912 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 25854 Z= 0.187 Angle : 0.735 13.542 35314 Z= 0.370 Chirality : 0.050 0.396 4162 Planarity : 0.005 0.082 4464 Dihedral : 7.429 58.631 4529 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.82 % Favored : 93.15 % Rotamer: Outliers : 2.71 % Allowed : 10.68 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.14), residues: 3080 helix: 0.23 (0.20), residues: 677 sheet: -0.17 (0.20), residues: 634 loop : -2.38 (0.13), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 34 TYR 0.030 0.002 TYR B 904 PHE 0.026 0.002 PHE B 559 TRP 0.015 0.002 TRP A 886 HIS 0.013 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00449 (25759) covalent geometry : angle 0.71172 (35068) SS BOND : bond 0.00355 ( 39) SS BOND : angle 1.84980 ( 78) hydrogen bonds : bond 0.07926 ( 843) hydrogen bonds : angle 5.48398 ( 2370) link_BETA1-4 : bond 0.00430 ( 14) link_BETA1-4 : angle 1.47835 ( 42) link_NAG-ASN : bond 0.00358 ( 42) link_NAG-ASN : angle 2.75765 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 206 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7221 (tm-30) REVERT: A 1010 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8842 (mt0) REVERT: A 1038 LYS cc_start: 0.9078 (mmtm) cc_final: 0.8830 (mptt) REVERT: B 118 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6699 (mm) REVERT: B 202 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7892 (mtmm) REVERT: B 271 GLN cc_start: 0.7574 (mt0) cc_final: 0.6534 (mp10) REVERT: B 613 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7942 (mt0) REVERT: B 921 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8160 (mptt) REVERT: B 1017 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7506 (tp30) REVERT: C 52 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7580 (tm-30) REVERT: C 189 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.5641 (tt) REVERT: C 271 GLN cc_start: 0.7216 (mp10) cc_final: 0.6869 (mp10) REVERT: C 616 ASN cc_start: 0.8299 (t0) cc_final: 0.7789 (m-40) outliers start: 74 outliers final: 41 residues processed: 254 average time/residue: 0.4727 time to fit residues: 145.2878 Evaluate side-chains 249 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 88 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 chunk 6 optimal weight: 0.0000 chunk 106 optimal weight: 0.8980 chunk 118 optimal weight: 0.0770 chunk 201 optimal weight: 1.9990 overall best weight: 0.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 207 HIS A 360 ASN A 540 ASN B 207 HIS ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 540 ASN C1010 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.202682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.155177 restraints weight = 35088.996| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.17 r_work: 0.3359 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25854 Z= 0.114 Angle : 0.633 12.349 35314 Z= 0.316 Chirality : 0.046 0.346 4162 Planarity : 0.004 0.075 4464 Dihedral : 6.739 58.914 4528 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.80 % Rotamer: Outliers : 2.05 % Allowed : 12.14 % Favored : 85.81 % 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: -1.38 (0.14), residues: 3080 helix: 0.96 (0.21), residues: 672 sheet: 0.05 (0.20), residues: 651 loop : -2.18 (0.13), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.026 0.001 TYR B1138 PHE 0.022 0.001 PHE C 32 TRP 0.011 0.001 TRP A 886 HIS 0.013 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00246 (25759) covalent geometry : angle 0.61131 (35068) SS BOND : bond 0.00292 ( 39) SS BOND : angle 1.46914 ( 78) hydrogen bonds : bond 0.05784 ( 843) hydrogen bonds : angle 5.17223 ( 2370) link_BETA1-4 : bond 0.00405 ( 14) link_BETA1-4 : angle 1.21068 ( 42) link_NAG-ASN : bond 0.00284 ( 42) link_NAG-ASN : angle 2.51701 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1038 LYS cc_start: 0.8941 (mmtm) cc_final: 0.8681 (mptt) REVERT: A 1101 HIS cc_start: 0.8442 (t70) cc_final: 0.8222 (t-170) REVERT: B 118 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7444 (mm) REVERT: B 271 GLN cc_start: 0.7627 (mt0) cc_final: 0.7098 (mp10) REVERT: B 319 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7866 (ttm170) REVERT: B 425 LEU cc_start: 0.2060 (OUTLIER) cc_final: 0.1128 (mp) REVERT: B 921 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8176 (mptt) REVERT: B 1017 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: C 52 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7808 (tm-30) REVERT: C 189 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.5838 (tt) REVERT: C 191 GLU cc_start: 0.7511 (mp0) cc_final: 0.7256 (mp0) REVERT: C 616 ASN cc_start: 0.8219 (t0) cc_final: 0.7912 (m-40) outliers start: 56 outliers final: 20 residues processed: 250 average time/residue: 0.4959 time to fit residues: 148.6840 Evaluate side-chains 220 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 137 optimal weight: 20.0000 chunk 175 optimal weight: 0.6980 chunk 206 optimal weight: 3.9990 chunk 141 optimal weight: 0.0010 chunk 136 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 273 optimal weight: 0.5980 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 207 HIS A 360 ASN A 540 ASN B 125 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 613 GLN C 487 ASN C 935 GLN C1010 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.201632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.153743 restraints weight = 27811.947| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.99 r_work: 0.3376 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25854 Z= 0.141 Angle : 0.655 12.410 35314 Z= 0.328 Chirality : 0.047 0.386 4162 Planarity : 0.004 0.074 4464 Dihedral : 6.549 59.767 4526 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.94 % Favored : 94.02 % Rotamer: Outliers : 2.34 % Allowed : 12.47 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.15), residues: 3080 helix: 1.12 (0.21), residues: 674 sheet: 0.12 (0.20), residues: 646 loop : -2.11 (0.13), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.029 0.001 TYR B 904 PHE 0.021 0.001 PHE A 32 TRP 0.010 0.001 TRP B 64 HIS 0.012 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00327 (25759) covalent geometry : angle 0.63184 (35068) SS BOND : bond 0.00306 ( 39) SS BOND : angle 1.63082 ( 78) hydrogen bonds : bond 0.06442 ( 843) hydrogen bonds : angle 5.15028 ( 2370) link_BETA1-4 : bond 0.00402 ( 14) link_BETA1-4 : angle 1.25500 ( 42) link_NAG-ASN : bond 0.00286 ( 42) link_NAG-ASN : angle 2.63678 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 197 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8585 (tt0) cc_final: 0.8098 (tm-30) REVERT: A 1038 LYS cc_start: 0.8901 (mmtm) cc_final: 0.8635 (mptt) REVERT: A 1101 HIS cc_start: 0.8367 (t70) cc_final: 0.8165 (t-170) REVERT: B 271 GLN cc_start: 0.7636 (mt0) cc_final: 0.7112 (mp10) REVERT: B 319 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7821 (ttm170) REVERT: B 921 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8207 (mptt) REVERT: B 1017 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7300 (tp30) REVERT: C 52 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7808 (tm-30) REVERT: C 117 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6265 (tt) REVERT: C 189 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.5867 (tt) REVERT: C 616 ASN cc_start: 0.8202 (t0) cc_final: 0.7913 (m-40) outliers start: 64 outliers final: 36 residues processed: 240 average time/residue: 0.4750 time to fit residues: 137.4178 Evaluate side-chains 231 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 38 optimal weight: 0.0030 chunk 95 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 251 optimal weight: 6.9990 chunk 222 optimal weight: 7.9990 chunk 169 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 195 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 360 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 501 ASN B 613 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.202639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.149548 restraints weight = 28356.749| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.99 r_work: 0.2962 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25854 Z= 0.122 Angle : 0.631 11.977 35314 Z= 0.315 Chirality : 0.047 0.656 4162 Planarity : 0.004 0.075 4464 Dihedral : 6.322 58.471 4526 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.49 % Favored : 94.48 % Rotamer: Outliers : 2.27 % Allowed : 13.09 % Favored : 84.64 % 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: -1.12 (0.15), residues: 3080 helix: 1.28 (0.21), residues: 674 sheet: 0.21 (0.20), residues: 646 loop : -2.06 (0.13), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.024 0.001 TYR B 904 PHE 0.023 0.001 PHE C 32 TRP 0.011 0.001 TRP B 64 HIS 0.013 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00274 (25759) covalent geometry : angle 0.60808 (35068) SS BOND : bond 0.00304 ( 39) SS BOND : angle 1.52363 ( 78) hydrogen bonds : bond 0.05913 ( 843) hydrogen bonds : angle 5.06643 ( 2370) link_BETA1-4 : bond 0.00403 ( 14) link_BETA1-4 : angle 1.19287 ( 42) link_NAG-ASN : bond 0.00290 ( 42) link_NAG-ASN : angle 2.58368 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 198 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8743 (tt0) cc_final: 0.7910 (tm-30) REVERT: A 278 LYS cc_start: 0.8623 (tttt) cc_final: 0.8413 (tttm) REVERT: A 360 ASN cc_start: 0.6298 (OUTLIER) cc_final: 0.6060 (m-40) REVERT: A 661 GLU cc_start: 0.8308 (mp0) cc_final: 0.7902 (mm-30) REVERT: A 1038 LYS cc_start: 0.9096 (mmtm) cc_final: 0.8875 (mptt) REVERT: A 1101 HIS cc_start: 0.8669 (t70) cc_final: 0.8368 (t-170) REVERT: B 118 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6632 (mm) REVERT: B 271 GLN cc_start: 0.7509 (mt0) cc_final: 0.6478 (mp10) REVERT: B 309 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: B 319 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7868 (ttm170) REVERT: B 425 LEU cc_start: 0.1010 (OUTLIER) cc_final: 0.0222 (mp) REVERT: B 921 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8068 (mptt) REVERT: B 1017 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7494 (tp30) REVERT: C 52 GLN cc_start: 0.8379 (tm-30) cc_final: 0.7697 (tm-30) REVERT: C 117 LEU cc_start: 0.5251 (OUTLIER) cc_final: 0.4982 (tt) REVERT: C 189 LEU cc_start: 0.5914 (OUTLIER) cc_final: 0.5161 (tt) REVERT: C 616 ASN cc_start: 0.8255 (t0) cc_final: 0.7795 (m-40) outliers start: 62 outliers final: 34 residues processed: 239 average time/residue: 0.4898 time to fit residues: 141.1112 Evaluate side-chains 230 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 256 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 304 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 422 ASN B 519 HIS B 607 GLN B 613 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.199611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.151543 restraints weight = 25712.699| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.96 r_work: 0.3331 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 25854 Z= 0.219 Angle : 0.734 13.264 35314 Z= 0.370 Chirality : 0.051 0.226 4162 Planarity : 0.005 0.078 4464 Dihedral : 6.639 59.402 4526 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.43 % Favored : 93.54 % Rotamer: Outliers : 2.60 % Allowed : 13.28 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.14), residues: 3080 helix: 0.92 (0.21), residues: 677 sheet: 0.08 (0.20), residues: 620 loop : -2.11 (0.13), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 190 TYR 0.036 0.002 TYR B 904 PHE 0.028 0.002 PHE A 855 TRP 0.010 0.002 TRP B 64 HIS 0.012 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00538 (25759) covalent geometry : angle 0.71194 (35068) SS BOND : bond 0.00350 ( 39) SS BOND : angle 1.96411 ( 78) hydrogen bonds : bond 0.07940 ( 843) hydrogen bonds : angle 5.27790 ( 2370) link_BETA1-4 : bond 0.00421 ( 14) link_BETA1-4 : angle 1.42306 ( 42) link_NAG-ASN : bond 0.00394 ( 42) link_NAG-ASN : angle 2.63294 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 193 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8650 (tt0) cc_final: 0.8164 (tm-30) REVERT: A 1038 LYS cc_start: 0.8898 (mmtm) cc_final: 0.8599 (mptt) REVERT: B 134 GLN cc_start: 0.3737 (OUTLIER) cc_final: 0.2663 (pp30) REVERT: B 271 GLN cc_start: 0.7650 (mt0) cc_final: 0.7097 (mp10) REVERT: B 319 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7795 (ttm170) REVERT: B 425 LEU cc_start: 0.2164 (OUTLIER) cc_final: 0.1286 (tp) REVERT: B 921 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8333 (mptt) REVERT: B 1017 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7332 (tp30) REVERT: C 52 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7868 (tm-30) REVERT: C 117 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6301 (tt) REVERT: C 189 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.5891 (tt) REVERT: C 616 ASN cc_start: 0.8227 (t0) cc_final: 0.7937 (m-40) REVERT: C 904 TYR cc_start: 0.7937 (p90) cc_final: 0.7481 (p90) outliers start: 71 outliers final: 46 residues processed: 245 average time/residue: 0.4647 time to fit residues: 137.6919 Evaluate side-chains 234 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 169 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 165 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 190 optimal weight: 0.2980 chunk 269 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 360 ASN B 30 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 613 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.202620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.154237 restraints weight = 28348.855| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.98 r_work: 0.3318 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25854 Z= 0.117 Angle : 0.620 12.181 35314 Z= 0.312 Chirality : 0.046 0.241 4162 Planarity : 0.004 0.077 4464 Dihedral : 6.072 56.464 4526 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.67 % Rotamer: Outliers : 2.08 % Allowed : 14.26 % Favored : 83.65 % 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: -1.07 (0.15), residues: 3080 helix: 1.25 (0.21), residues: 679 sheet: 0.30 (0.20), residues: 632 loop : -2.00 (0.13), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.021 0.001 TYR B 904 PHE 0.024 0.001 PHE C 32 TRP 0.013 0.001 TRP B 64 HIS 0.013 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00255 (25759) covalent geometry : angle 0.59898 (35068) SS BOND : bond 0.00365 ( 39) SS BOND : angle 1.68774 ( 78) hydrogen bonds : bond 0.05741 ( 843) hydrogen bonds : angle 5.04275 ( 2370) link_BETA1-4 : bond 0.00413 ( 14) link_BETA1-4 : angle 1.16416 ( 42) link_NAG-ASN : bond 0.00286 ( 42) link_NAG-ASN : angle 2.36438 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 191 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8623 (tt0) cc_final: 0.8110 (tm-30) REVERT: A 1038 LYS cc_start: 0.8868 (mmtm) cc_final: 0.8609 (mptt) REVERT: A 1101 HIS cc_start: 0.8351 (t70) cc_final: 0.8139 (t-170) REVERT: B 118 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7527 (mm) REVERT: B 134 GLN cc_start: 0.3622 (OUTLIER) cc_final: 0.2655 (pp30) REVERT: B 271 GLN cc_start: 0.7663 (mt0) cc_final: 0.7082 (mp10) REVERT: B 319 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7773 (ttm170) REVERT: B 425 LEU cc_start: 0.2072 (OUTLIER) cc_final: 0.1190 (mp) REVERT: B 658 ASN cc_start: 0.7564 (m-40) cc_final: 0.7284 (m-40) REVERT: B 921 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8172 (mptt) REVERT: B 1017 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7256 (tp30) REVERT: C 52 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7880 (tm-30) REVERT: C 117 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6229 (tt) REVERT: C 189 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.5844 (tt) REVERT: C 616 ASN cc_start: 0.8194 (t0) cc_final: 0.7933 (m-40) outliers start: 57 outliers final: 39 residues processed: 230 average time/residue: 0.4770 time to fit residues: 132.4978 Evaluate side-chains 239 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 133 optimal weight: 0.0270 chunk 43 optimal weight: 7.9990 chunk 233 optimal weight: 0.0770 chunk 302 optimal weight: 0.0070 chunk 166 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 135 optimal weight: 20.0000 chunk 295 optimal weight: 0.0170 chunk 191 optimal weight: 0.0270 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.0310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 613 GLN B ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN C 422 ASN C 460 ASN C 540 ASN C 935 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.207079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.156856 restraints weight = 28705.370| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.07 r_work: 0.3287 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25854 Z= 0.100 Angle : 0.571 10.908 35314 Z= 0.286 Chirality : 0.044 0.235 4162 Planarity : 0.004 0.071 4464 Dihedral : 5.403 55.829 4526 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.97 % Favored : 95.00 % Rotamer: Outliers : 1.50 % Allowed : 14.92 % Favored : 83.58 % 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: -0.70 (0.15), residues: 3080 helix: 1.68 (0.21), residues: 686 sheet: 0.42 (0.20), residues: 641 loop : -1.81 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.017 0.001 TYR B 904 PHE 0.018 0.001 PHE A 32 TRP 0.015 0.001 TRP B 64 HIS 0.013 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00203 (25759) covalent geometry : angle 0.55492 (35068) SS BOND : bond 0.00265 ( 39) SS BOND : angle 1.20463 ( 78) hydrogen bonds : bond 0.04014 ( 843) hydrogen bonds : angle 4.80814 ( 2370) link_BETA1-4 : bond 0.00465 ( 14) link_BETA1-4 : angle 1.09422 ( 42) link_NAG-ASN : bond 0.00251 ( 42) link_NAG-ASN : angle 2.06625 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 0.923 Fit side-chains REVERT: A 516 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7149 (pp20) REVERT: A 540 ASN cc_start: 0.7931 (m-40) cc_final: 0.7637 (m110) REVERT: A 1038 LYS cc_start: 0.8798 (mmtm) cc_final: 0.8580 (mptt) REVERT: A 1101 HIS cc_start: 0.8445 (t70) cc_final: 0.8222 (t-170) REVERT: B 118 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7424 (mm) REVERT: B 134 GLN cc_start: 0.3375 (OUTLIER) cc_final: 0.2638 (pp30) REVERT: B 271 GLN cc_start: 0.7577 (mt0) cc_final: 0.6844 (mp10) REVERT: B 309 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: B 425 LEU cc_start: 0.1930 (OUTLIER) cc_final: 0.1057 (mp) REVERT: B 921 LYS cc_start: 0.8205 (mmtm) cc_final: 0.7924 (mptt) REVERT: C 52 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7877 (tm-30) REVERT: C 117 LEU cc_start: 0.6328 (OUTLIER) cc_final: 0.6002 (tt) REVERT: C 189 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.5822 (tt) REVERT: C 516 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7864 (tt0) REVERT: C 616 ASN cc_start: 0.8226 (t0) cc_final: 0.7862 (m-40) outliers start: 41 outliers final: 14 residues processed: 242 average time/residue: 0.4680 time to fit residues: 136.7718 Evaluate side-chains 212 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 581 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 229 optimal weight: 0.3980 chunk 109 optimal weight: 5.9990 chunk 271 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 275 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN B ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.201069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.146561 restraints weight = 29542.815| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.06 r_work: 0.3191 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25854 Z= 0.171 Angle : 0.671 12.269 35314 Z= 0.338 Chirality : 0.049 0.239 4162 Planarity : 0.005 0.077 4464 Dihedral : 5.794 57.138 4523 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.98 % Favored : 93.99 % Rotamer: Outliers : 1.21 % Allowed : 15.62 % Favored : 83.17 % 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: -0.91 (0.15), residues: 3080 helix: 1.41 (0.21), residues: 673 sheet: 0.30 (0.20), residues: 637 loop : -1.87 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 190 TYR 0.037 0.002 TYR B 904 PHE 0.023 0.002 PHE C 32 TRP 0.013 0.002 TRP B 64 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00412 (25759) covalent geometry : angle 0.65024 (35068) SS BOND : bond 0.00317 ( 39) SS BOND : angle 1.93885 ( 78) hydrogen bonds : bond 0.06944 ( 843) hydrogen bonds : angle 5.07546 ( 2370) link_BETA1-4 : bond 0.00429 ( 14) link_BETA1-4 : angle 1.26562 ( 42) link_NAG-ASN : bond 0.00328 ( 42) link_NAG-ASN : angle 2.35668 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8814 (tt0) cc_final: 0.8215 (tm-30) REVERT: A 540 ASN cc_start: 0.8003 (m-40) cc_final: 0.7701 (m110) REVERT: A 1101 HIS cc_start: 0.8505 (t70) cc_final: 0.8274 (t-170) REVERT: B 118 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7449 (mm) REVERT: B 134 GLN cc_start: 0.3495 (OUTLIER) cc_final: 0.2658 (pp30) REVERT: B 190 ARG cc_start: 0.7509 (mtm110) cc_final: 0.7232 (ptt180) REVERT: B 271 GLN cc_start: 0.7755 (mt0) cc_final: 0.7024 (mp10) REVERT: B 309 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: B 425 LEU cc_start: 0.1809 (OUTLIER) cc_final: 0.0977 (mp) REVERT: B 658 ASN cc_start: 0.7695 (m-40) cc_final: 0.7395 (m-40) REVERT: B 921 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8334 (mptt) REVERT: C 52 GLN cc_start: 0.8459 (tm-30) cc_final: 0.7967 (tm-30) REVERT: C 117 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6164 (tt) REVERT: C 189 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.5794 (tt) REVERT: C 516 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7940 (tt0) REVERT: C 616 ASN cc_start: 0.8288 (t0) cc_final: 0.7976 (m-40) REVERT: C 904 TYR cc_start: 0.8099 (p90) cc_final: 0.7752 (p90) REVERT: C 1010 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8658 (tm-30) outliers start: 33 outliers final: 21 residues processed: 218 average time/residue: 0.4567 time to fit residues: 120.7757 Evaluate side-chains 218 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 276 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 38 optimal weight: 0.0370 chunk 240 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 222 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.203414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.149356 restraints weight = 33472.049| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.25 r_work: 0.3277 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25854 Z= 0.111 Angle : 0.602 11.675 35314 Z= 0.302 Chirality : 0.045 0.238 4162 Planarity : 0.004 0.076 4464 Dihedral : 5.470 55.209 4523 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 1.06 % Allowed : 16.09 % Favored : 82.85 % 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: -0.78 (0.15), residues: 3080 helix: 1.52 (0.21), residues: 681 sheet: 0.40 (0.20), residues: 658 loop : -1.83 (0.13), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 190 TYR 0.021 0.001 TYR B 904 PHE 0.023 0.001 PHE A 855 TRP 0.016 0.001 TRP B 64 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00241 (25759) covalent geometry : angle 0.58360 (35068) SS BOND : bond 0.00252 ( 39) SS BOND : angle 1.66125 ( 78) hydrogen bonds : bond 0.05339 ( 843) hydrogen bonds : angle 4.90640 ( 2370) link_BETA1-4 : bond 0.00409 ( 14) link_BETA1-4 : angle 1.11478 ( 42) link_NAG-ASN : bond 0.00264 ( 42) link_NAG-ASN : angle 2.15370 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10075.04 seconds wall clock time: 171 minutes 27.91 seconds (10287.91 seconds total)