Starting phenix.real_space_refine on Sun Sep 13 18:44:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xm0_22253/09_2026/6xm0_22253.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xm0_22253/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6xm0_22253/09_2026/6xm0_22253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xm0_22253/09_2026/6xm0_22253.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xm0_22253/09_2026/6xm0_22253.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xm0_22253/09_2026/6xm0_22253.cif" model { file = "/net/cci-nas-00/data/ceres_data/6xm0_22253/09_2026/6xm0_22253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xm0_22253/09_2026/6xm0_22253.cif" } 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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 8 Time building chain proxies: 6.82, per 1000 atoms: 0.27 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: 2.06 Conformation dependent library (CDL) restraints added in 1.3 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: 0.85 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: 6.27 Time building geometry restraints manager: 2.72 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: 13274 17.77 - 35.53: 1323 35.53 - 53.30: 232 53.30 - 71.07: 37 71.07 - 88.84: 29 Dihedral angle restraints: 14895 sinusoidal: 5784 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 14892 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: 9.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.020 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:10.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 : 14.698 88.835 8910 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/Z covalent geometry : bond 0.01027 / 0.44 (25759) covalent geometry : angle 1.11555 / 0.60 (35068) SS BOND : bond 0.00709 / 0.47 ( 39) SS BOND : angle 2.79932 / 1.72 ( 78) hydrogen bonds : bond 0.30970 / 20.44 ( 843) hydrogen bonds : angle 9.42667 / 6.50 ( 2370) link_BETA1-4 : bond 0.01073 / 0.70 ( 14) link_BETA1-4 : angle 2.70516 / 1.70 ( 42) link_NAG-ASN : bond 0.00556 / 0.30 ( 42) link_NAG-ASN : angle 3.76079 / 2.53 ( 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 : 0.947 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: 0.5746 time to fit residues: 181.6774 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 : 0.938 ------------------------------------------------------------------------------- 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: 0.6980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4191 r_free = 0.4191 target = 0.201557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.153441 restraints weight = 33349.296| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.17 r_work: 0.3328 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 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 = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1256 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= 0.140 Angle : 0.717 13.550 35314 Z= 0.363 Chirality : 0.047 0.506 4162 Planarity : 0.006 0.093 4464 Dihedral : 6.173 49.317 3355 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.52 % Favored : 94.41 % Rotamer: Outliers : 1.57 % Allowed : 9.77 % Favored : 88.66 % 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: -2.57 (0.13), residues: 3080 helix: -1.18 (0.18), residues: 677 sheet: -0.43 (0.20), residues: 633 loop : -2.52 (0.12), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 237 TYR 0.024 0.001 TYR B 904 PHE 0.022 0.001 PHE A 32 TRP 0.020 0.002 TRP A 886 HIS 0.013 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (25759) covalent geometry : angle 0.68938 / 0.36 (35068) SS BOND : bond 0.00568 / 0.34 ( 39) SS BOND : angle 1.71979 / 1.04 ( 78) hydrogen bonds : bond 0.07499 / 4.93 ( 843) hydrogen bonds : angle 5.71344 / 3.91 ( 2370) link_BETA1-4 : bond 0.00393 / 0.25 ( 14) link_BETA1-4 : angle 1.31924 / 0.83 ( 42) link_NAG-ASN : bond 0.00336 / 0.22 ( 42) link_NAG-ASN : angle 3.08484 / 2.12 ( 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 268 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9008 (tpt) cc_final: 0.8779 (ttm) REVERT: A 1038 LYS cc_start: 0.8939 (mmtm) cc_final: 0.8661 (mptt) REVERT: A 1101 HIS cc_start: 0.8420 (t70) cc_final: 0.8216 (t-170) REVERT: B 271 GLN cc_start: 0.7663 (mt0) cc_final: 0.7179 (mp10) REVERT: C 52 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7858 (tm-30) REVERT: C 410 ILE cc_start: 0.8126 (mm) cc_final: 0.7919 (mm) REVERT: C 592 PHE cc_start: 0.8491 (p90) cc_final: 0.8261 (p90) REVERT: C 616 ASN cc_start: 0.8191 (t0) cc_final: 0.7868 (m-40) REVERT: C 983 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6956 (ttp-110) outliers start: 43 outliers final: 26 residues processed: 250 average time/residue: 0.5247 time to fit residues: 157.5166 Evaluate side-chains 230 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 319 ARG 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 983 ARG 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: 0.9980 chunk 110 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 chunk 279 optimal weight: 0.3980 chunk 114 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 271 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 360 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN C 164 ASN C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4195 r_free = 0.4195 target = 0.201937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.148764 restraints weight = 26064.621| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.02 r_work: 0.3304 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25854 Z= 0.133 Angle : 0.664 12.639 35314 Z= 0.332 Chirality : 0.047 0.404 4162 Planarity : 0.005 0.077 4464 Dihedral : 5.607 43.802 3353 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.30 % Favored : 93.67 % Rotamer: Outliers : 2.30 % Allowed : 10.79 % Favored : 86.91 % 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: -1.65 (0.14), residues: 3080 helix: 0.51 (0.21), residues: 679 sheet: -0.05 (0.20), residues: 650 loop : -2.30 (0.13), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.028 0.001 TYR B1138 PHE 0.022 0.001 PHE A 32 TRP 0.014 0.001 TRP A 886 HIS 0.013 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (25759) covalent geometry : angle 0.64335 / 0.33 (35068) SS BOND : bond 0.00329 / 0.22 ( 39) SS BOND : angle 1.61235 / 0.96 ( 78) hydrogen bonds : bond 0.06569 / 4.33 ( 843) hydrogen bonds : angle 5.32275 / 3.63 ( 2370) link_BETA1-4 : bond 0.00451 / 0.28 ( 14) link_BETA1-4 : angle 1.17449 / 0.73 ( 42) link_NAG-ASN : bond 0.00289 / 0.18 ( 42) link_NAG-ASN : angle 2.49262 / 1.78 ( 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 271 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1038 LYS cc_start: 0.8935 (mmtm) cc_final: 0.8652 (mptt) REVERT: A 1101 HIS cc_start: 0.8465 (t70) cc_final: 0.8248 (t-170) REVERT: B 118 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7469 (mm) REVERT: B 271 GLN cc_start: 0.7603 (mt0) cc_final: 0.7018 (mp10) REVERT: B 500 THR cc_start: 0.3204 (OUTLIER) cc_final: 0.2980 (m) REVERT: B 531 THR cc_start: 0.7659 (m) cc_final: 0.7445 (p) REVERT: B 921 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8167 (mptt) REVERT: B 1017 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7312 (tp30) REVERT: C 52 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7860 (tm-30) REVERT: C 189 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.5880 (tt) REVERT: C 191 GLU cc_start: 0.7549 (mp0) cc_final: 0.7271 (mp0) REVERT: C 616 ASN cc_start: 0.8239 (t0) cc_final: 0.7886 (m-40) outliers start: 63 outliers final: 31 residues processed: 249 average time/residue: 0.5012 time to fit residues: 150.5932 Evaluate side-chains 230 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 A residue 878 LEU Chi-restraints excluded: chain B residue 118 LEU 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 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 500 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 878 LEU Chi-restraints excluded: chain B residue 921 LYS 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 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 407 VAL Chi-restraints excluded: chain C residue 540 ASN 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 983 ARG 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: 3.9990 chunk 111 optimal weight: 7.9990 chunk 126 optimal weight: 0.5980 chunk 134 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 207 HIS A 360 ASN A 540 ASN B 125 ASN B 164 ASN B 207 HIS B 607 GLN B1010 GLN C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 501 ASN C 935 GLN C1010 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.200336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.146973 restraints weight = 34904.185| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.34 r_work: 0.3234 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 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 = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 25854 Z= 0.190 Angle : 0.719 13.150 35314 Z= 0.362 Chirality : 0.050 0.371 4162 Planarity : 0.005 0.076 4464 Dihedral : 5.661 45.724 3350 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.43 % Favored : 93.54 % Rotamer: Outliers : 2.89 % Allowed : 11.38 % Favored : 85.74 % 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: -1.57 (0.14), residues: 3080 helix: 0.68 (0.21), residues: 677 sheet: 0.04 (0.20), residues: 620 loop : -2.27 (0.13), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.029 0.002 TYR B 904 PHE 0.026 0.002 PHE A 592 TRP 0.011 0.002 TRP A 886 HIS 0.012 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (25759) covalent geometry : angle 0.69819 / 0.36 (35068) SS BOND : bond 0.00349 / 0.23 ( 39) SS BOND : angle 1.80370 / 1.08 ( 78) hydrogen bonds : bond 0.07556 / 4.98 ( 843) hydrogen bonds : angle 5.33823 / 3.65 ( 2370) link_BETA1-4 : bond 0.00418 / 0.25 ( 14) link_BETA1-4 : angle 1.27078 / 0.80 ( 42) link_NAG-ASN : bond 0.00321 / 0.19 ( 42) link_NAG-ASN : angle 2.60996 / 1.85 ( 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 279 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 200 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1038 LYS cc_start: 0.8986 (mmtm) cc_final: 0.8695 (mptt) REVERT: B 271 GLN cc_start: 0.7710 (mt0) cc_final: 0.7104 (mp10) REVERT: B 319 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7997 (ttm170) REVERT: B 425 LEU cc_start: 0.2074 (OUTLIER) cc_final: 0.1097 (mp) REVERT: B 500 THR cc_start: 0.3242 (OUTLIER) cc_final: 0.3023 (m) REVERT: B 531 THR cc_start: 0.7796 (m) cc_final: 0.7343 (p) REVERT: B 921 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8315 (mptt) REVERT: B 1017 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7456 (tp30) REVERT: C 52 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7813 (tm-30) REVERT: C 189 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6076 (tt) REVERT: C 616 ASN cc_start: 0.8285 (t0) cc_final: 0.7927 (m-40) REVERT: C 904 TYR cc_start: 0.8013 (p90) cc_final: 0.7656 (p90) outliers start: 79 outliers final: 45 residues processed: 257 average time/residue: 0.4842 time to fit residues: 151.7456 Evaluate side-chains 246 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 195 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 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 B residue 48 LEU Chi-restraints excluded: chain B residue 130 VAL 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 500 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 904 TYR 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 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 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 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 878 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR 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: 0.8980 chunk 206 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 273 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 207 HIS A 360 ASN A 540 ASN B 607 GLN B 613 GLN C 540 ASN C 935 GLN C1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.199472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.144221 restraints weight = 27729.050| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.02 r_work: 0.3255 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 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 = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 25854 Z= 0.210 Angle : 0.742 13.687 35314 Z= 0.373 Chirality : 0.051 0.348 4162 Planarity : 0.005 0.078 4464 Dihedral : 5.743 48.284 3350 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.76 % Favored : 93.21 % Rotamer: Outliers : 3.04 % Allowed : 12.22 % Favored : 84.75 % 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: -1.55 (0.14), residues: 3080 helix: 0.68 (0.21), residues: 679 sheet: 0.05 (0.20), residues: 611 loop : -2.24 (0.13), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1039 TYR 0.031 0.002 TYR B 904 PHE 0.027 0.002 PHE B 559 TRP 0.010 0.002 TRP A 886 HIS 0.013 0.002 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.21 (25759) covalent geometry : angle 0.72036 / 0.37 (35068) SS BOND : bond 0.00341 / 0.23 ( 39) SS BOND : angle 1.95790 / 1.17 ( 78) hydrogen bonds : bond 0.07870 / 5.19 ( 843) hydrogen bonds : angle 5.34902 / 3.65 ( 2370) link_BETA1-4 : bond 0.00418 / 0.25 ( 14) link_BETA1-4 : angle 1.33087 / 0.84 ( 42) link_NAG-ASN : bond 0.00343 / 0.20 ( 42) link_NAG-ASN : angle 2.64277 / 1.87 ( 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 277 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 194 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8695 (tt0) cc_final: 0.8167 (tm-30) REVERT: A 1010 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8562 (mt0) REVERT: A 1038 LYS cc_start: 0.8976 (mmtm) cc_final: 0.8700 (mptt) REVERT: B 242 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5635 (pp) REVERT: B 271 GLN cc_start: 0.7698 (mt0) cc_final: 0.7094 (mp10) REVERT: B 319 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7925 (ttm170) REVERT: B 500 THR cc_start: 0.3181 (OUTLIER) cc_final: 0.2966 (m) REVERT: B 921 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8333 (mptt) REVERT: B 1017 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7440 (tp30) REVERT: C 52 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7843 (tm-30) REVERT: C 189 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.5981 (tt) REVERT: C 616 ASN cc_start: 0.8276 (t0) cc_final: 0.7934 (m-40) outliers start: 83 outliers final: 50 residues processed: 253 average time/residue: 0.4965 time to fit residues: 152.5222 Evaluate side-chains 247 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 190 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 382 VAL 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 A residue 1010 GLN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 242 LEU 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 500 THR Chi-restraints excluded: chain B residue 599 THR 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 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 1017 GLU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1114 ILE 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 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 654 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1002 GLN 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: 3.9990 chunk 95 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 360 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 501 ASN B 519 HIS B 613 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4179 r_free = 0.4179 target = 0.200465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.152659 restraints weight = 28228.752| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.05 r_work: 0.3348 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1743 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= 0.161 Angle : 0.683 13.242 35314 Z= 0.343 Chirality : 0.048 0.264 4162 Planarity : 0.005 0.079 4464 Dihedral : 5.525 47.706 3350 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.17 % Favored : 93.80 % Rotamer: Outliers : 3.18 % Allowed : 12.58 % Favored : 84.24 % 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: -1.39 (0.14), residues: 3080 helix: 0.92 (0.21), residues: 673 sheet: 0.13 (0.20), residues: 613 loop : -2.17 (0.13), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.030 0.002 TYR B 904 PHE 0.023 0.002 PHE C 32 TRP 0.011 0.002 TRP B 64 HIS 0.013 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (25759) covalent geometry : angle 0.66281 / 0.34 (35068) SS BOND : bond 0.00313 / 0.21 ( 39) SS BOND : angle 1.76768 / 1.05 ( 78) hydrogen bonds : bond 0.06997 / 4.61 ( 843) hydrogen bonds : angle 5.20859 / 3.55 ( 2370) link_BETA1-4 : bond 0.00417 / 0.25 ( 14) link_BETA1-4 : angle 1.19437 / 0.75 ( 42) link_NAG-ASN : bond 0.00294 / 0.18 ( 42) link_NAG-ASN : angle 2.49826 / 1.78 ( 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 281 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 194 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8612 (tt0) cc_final: 0.8141 (tm-30) REVERT: A 1002 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8642 (tm-30) REVERT: A 1038 LYS cc_start: 0.8929 (mmtm) cc_final: 0.8636 (mptt) REVERT: B 134 GLN cc_start: 0.3678 (OUTLIER) cc_final: 0.2645 (pp30) REVERT: B 271 GLN cc_start: 0.7670 (mt0) cc_final: 0.7118 (mp10) REVERT: B 319 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7875 (ttm170) REVERT: B 425 LEU cc_start: 0.2084 (OUTLIER) cc_final: 0.1226 (tp) REVERT: B 500 THR cc_start: 0.3148 (OUTLIER) cc_final: 0.2920 (m) REVERT: B 531 THR cc_start: 0.7808 (m) cc_final: 0.7395 (p) REVERT: B 921 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8296 (mptt) REVERT: B 1017 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7343 (tp30) REVERT: C 52 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7853 (tm-30) REVERT: C 117 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6256 (tt) REVERT: C 189 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.5926 (tt) REVERT: C 616 ASN cc_start: 0.8209 (t0) cc_final: 0.7918 (m-40) REVERT: C 904 TYR cc_start: 0.7953 (p90) cc_final: 0.7426 (p90) outliers start: 87 outliers final: 51 residues processed: 256 average time/residue: 0.4785 time to fit residues: 149.0690 Evaluate side-chains 249 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 189 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 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 A residue 1002 GLN Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 227 VAL 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 500 THR 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 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 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 569 ILE 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 723 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 983 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 256 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 304 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 360 ASN B 370 ASN 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 = 0.4172 r_free = 0.4172 target = 0.199822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.149616 restraints weight = 25729.683| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.04 r_work: 0.3306 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 25854 Z= 0.196 Angle : 0.724 13.291 35314 Z= 0.364 Chirality : 0.050 0.518 4162 Planarity : 0.005 0.079 4464 Dihedral : 5.619 48.793 3350 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.76 % Favored : 93.21 % Rotamer: Outliers : 3.15 % Allowed : 12.95 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.41 (0.14), residues: 3080 helix: 0.76 (0.21), residues: 685 sheet: 0.20 (0.21), residues: 594 loop : -2.15 (0.13), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1039 TYR 0.031 0.002 TYR B 904 PHE 0.029 0.002 PHE A 855 TRP 0.013 0.002 TRP B 64 HIS 0.013 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (25759) covalent geometry : angle 0.70207 / 0.36 (35068) SS BOND : bond 0.00324 / 0.22 ( 39) SS BOND : angle 1.97275 / 1.16 ( 78) hydrogen bonds : bond 0.07547 / 4.98 ( 843) hydrogen bonds : angle 5.25110 / 3.59 ( 2370) link_BETA1-4 : bond 0.00429 / 0.25 ( 14) link_BETA1-4 : angle 1.26160 / 0.79 ( 42) link_NAG-ASN : bond 0.00329 / 0.20 ( 42) link_NAG-ASN : angle 2.63078 / 1.86 ( 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 280 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 194 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1038 LYS cc_start: 0.8909 (mmtm) cc_final: 0.8612 (mptt) REVERT: B 134 GLN cc_start: 0.3686 (OUTLIER) cc_final: 0.2656 (pp30) REVERT: B 271 GLN cc_start: 0.7626 (mt0) cc_final: 0.7091 (mp10) REVERT: B 319 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7861 (ttm170) REVERT: B 425 LEU cc_start: 0.1945 (OUTLIER) cc_final: 0.1115 (tp) REVERT: B 531 THR cc_start: 0.7861 (m) cc_final: 0.7418 (p) REVERT: B 854 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7685 (mmpt) REVERT: B 921 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8314 (mptt) REVERT: B 1017 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7286 (tp30) REVERT: C 52 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7872 (tm-30) REVERT: C 117 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6228 (tt) REVERT: C 189 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.5973 (tt) REVERT: C 616 ASN cc_start: 0.8237 (t0) cc_final: 0.7941 (m-40) REVERT: C 904 TYR cc_start: 0.7917 (p90) cc_final: 0.7392 (p90) outliers start: 86 outliers final: 58 residues processed: 255 average time/residue: 0.4820 time to fit residues: 149.5701 Evaluate side-chains 252 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 187 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 336 CYS 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 34 ARG Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 227 VAL 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 500 THR 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 1002 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 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 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 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1002 GLN 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: 1.9990 chunk 106 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 165 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 269 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 207 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.201125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.142233 restraints weight = 28247.716| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.01 r_work: 0.2945 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 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 = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25854 Z= 0.144 Angle : 0.686 15.795 35314 Z= 0.342 Chirality : 0.052 1.353 4162 Planarity : 0.005 0.078 4464 Dihedral : 5.455 48.004 3350 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.98 % Favored : 93.99 % Rotamer: Outliers : 2.74 % Allowed : 13.50 % Favored : 83.76 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.25 (0.14), residues: 3080 helix: 1.00 (0.21), residues: 679 sheet: 0.25 (0.20), residues: 631 loop : -2.11 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.028 0.001 TYR B 904 PHE 0.024 0.002 PHE C 32 TRP 0.015 0.001 TRP B 64 HIS 0.014 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (25759) covalent geometry : angle 0.65924 / 0.34 (35068) SS BOND : bond 0.00328 / 0.22 ( 39) SS BOND : angle 1.79677 / 1.05 ( 78) hydrogen bonds : bond 0.06569 / 4.33 ( 843) hydrogen bonds : angle 5.12703 / 3.50 ( 2370) link_BETA1-4 : bond 0.00414 / 0.25 ( 14) link_BETA1-4 : angle 1.14006 / 0.71 ( 42) link_NAG-ASN : bond 0.00659 / 0.43 ( 42) link_NAG-ASN : angle 2.94244 / 2.14 ( 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 269 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 194 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8760 (tt0) cc_final: 0.7986 (tm-30) REVERT: A 360 ASN cc_start: 0.6273 (t0) cc_final: 0.6048 (m-40) REVERT: A 516 GLU cc_start: 0.7385 (tm-30) cc_final: 0.7054 (pp20) REVERT: A 1038 LYS cc_start: 0.9076 (mmtm) cc_final: 0.8825 (mptt) REVERT: B 271 GLN cc_start: 0.7572 (mt0) cc_final: 0.6564 (mp10) REVERT: B 286 THR cc_start: 0.7634 (OUTLIER) cc_final: 0.7425 (p) REVERT: B 319 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7912 (ttm170) REVERT: B 425 LEU cc_start: 0.0799 (OUTLIER) cc_final: 0.0162 (tp) REVERT: B 531 THR cc_start: 0.6906 (m) cc_final: 0.6149 (p) REVERT: B 921 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8162 (mptt) REVERT: B 1017 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7559 (tp30) REVERT: C 52 GLN cc_start: 0.8445 (tm-30) cc_final: 0.7804 (tm-30) REVERT: C 117 LEU cc_start: 0.5405 (OUTLIER) cc_final: 0.5078 (tt) REVERT: C 189 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5433 (tt) REVERT: C 190 ARG cc_start: 0.6229 (ttt180) cc_final: 0.5516 (ttm110) REVERT: C 410 ILE cc_start: 0.7673 (mm) cc_final: 0.7441 (mm) REVERT: C 616 ASN cc_start: 0.8307 (t0) cc_final: 0.7852 (m-40) REVERT: C 904 TYR cc_start: 0.8232 (p90) cc_final: 0.7728 (p90) REVERT: C 983 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7088 (ttp-110) outliers start: 75 outliers final: 50 residues processed: 247 average time/residue: 0.4873 time to fit residues: 146.0965 Evaluate side-chains 246 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 336 CYS 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 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 227 VAL 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 500 THR 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 840 CYS 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 1002 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1128 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 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 569 ILE Chi-restraints excluded: chain C residue 581 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 983 ARG 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: 0.2980 chunk 43 optimal weight: 1.9990 chunk 233 optimal weight: 0.2980 chunk 302 optimal weight: 0.0060 chunk 166 optimal weight: 1.9990 chunk 128 optimal weight: 0.0030 chunk 135 optimal weight: 20.0000 chunk 295 optimal weight: 0.0770 chunk 191 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 360 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.204681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.150929 restraints weight = 28437.472| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.07 r_work: 0.3289 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 25854 Z= 0.110 Angle : 0.628 18.865 35314 Z= 0.313 Chirality : 0.046 0.442 4162 Planarity : 0.004 0.075 4464 Dihedral : 4.946 43.486 3350 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.67 % Rotamer: Outliers : 1.43 % Allowed : 14.92 % Favored : 83.65 % Cbeta Deviations : 0.03 % 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: -0.95 (0.15), residues: 3080 helix: 1.38 (0.21), residues: 680 sheet: 0.39 (0.20), residues: 629 loop : -1.96 (0.13), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.020 0.001 TYR B 904 PHE 0.018 0.001 PHE A 32 TRP 0.017 0.001 TRP B 64 HIS 0.014 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (25759) covalent geometry : angle 0.61101 / 0.31 (35068) SS BOND : bond 0.00295 / 0.20 ( 39) SS BOND : angle 1.35647 / 0.80 ( 78) hydrogen bonds : bond 0.04770 / 3.13 ( 843) hydrogen bonds : angle 4.90161 / 3.34 ( 2370) link_BETA1-4 : bond 0.00422 / 0.25 ( 14) link_BETA1-4 : angle 0.99919 / 0.62 ( 42) link_NAG-ASN : bond 0.00965 / 0.64 ( 42) link_NAG-ASN : angle 2.27003 / 1.64 ( 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 248 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8659 (tt0) cc_final: 0.8130 (tm-30) REVERT: A 540 ASN cc_start: 0.8025 (m-40) cc_final: 0.7756 (m110) REVERT: A 1038 LYS cc_start: 0.8927 (mmtm) cc_final: 0.8693 (mptt) REVERT: A 1101 HIS cc_start: 0.8389 (t70) cc_final: 0.8166 (t-170) REVERT: B 134 GLN cc_start: 0.3426 (OUTLIER) cc_final: 0.2593 (pp30) REVERT: B 271 GLN cc_start: 0.7618 (mt0) cc_final: 0.6985 (mp10) REVERT: B 319 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7801 (ttm170) REVERT: B 425 LEU cc_start: 0.1616 (OUTLIER) cc_final: 0.0942 (tp) REVERT: B 500 THR cc_start: 0.3287 (OUTLIER) cc_final: 0.3062 (m) REVERT: B 531 THR cc_start: 0.7515 (m) cc_final: 0.7245 (p) REVERT: B 921 LYS cc_start: 0.8357 (mmtm) cc_final: 0.8073 (mptt) REVERT: C 52 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7769 (tm-30) REVERT: C 117 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6159 (tt) REVERT: C 190 ARG cc_start: 0.6416 (ttt180) cc_final: 0.6120 (ttm110) REVERT: C 516 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7972 (tt0) REVERT: C 616 ASN cc_start: 0.8220 (t0) cc_final: 0.7928 (m-40) outliers start: 39 outliers final: 20 residues processed: 235 average time/residue: 0.5287 time to fit residues: 149.0915 Evaluate side-chains 210 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 130 VAL Chi-restraints excluded: chain B residue 134 GLN 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 500 THR 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 939 SER Chi-restraints excluded: chain B residue 1002 GLN 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 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 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: 6.9990 chunk 111 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 142 optimal weight: 0.1980 chunk 229 optimal weight: 0.0770 chunk 109 optimal weight: 4.9990 chunk 271 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 12 optimal weight: 0.0670 chunk 275 optimal weight: 1.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** B 613 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.203236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.151971 restraints weight = 29641.174| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.07 r_work: 0.3230 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25854 Z= 0.120 Angle : 0.640 17.760 35314 Z= 0.318 Chirality : 0.048 0.829 4162 Planarity : 0.004 0.075 4464 Dihedral : 4.960 41.927 3350 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.67 % Rotamer: Outliers : 1.43 % Allowed : 15.40 % Favored : 83.17 % 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: -0.82 (0.15), residues: 3080 helix: 1.50 (0.21), residues: 680 sheet: 0.48 (0.20), residues: 634 loop : -1.89 (0.13), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 983 TYR 0.028 0.001 TYR B 904 PHE 0.025 0.001 PHE C 32 TRP 0.016 0.001 TRP B 64 HIS 0.013 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (25759) covalent geometry : angle 0.61463 / 0.31 (35068) SS BOND : bond 0.00300 / 0.20 ( 39) SS BOND : angle 1.66270 / 0.99 ( 78) hydrogen bonds : bond 0.05487 / 3.61 ( 843) hydrogen bonds : angle 4.90792 / 3.34 ( 2370) link_BETA1-4 : bond 0.00398 / 0.25 ( 14) link_BETA1-4 : angle 1.02599 / 0.63 ( 42) link_NAG-ASN : bond 0.00647 / 0.42 ( 42) link_NAG-ASN : angle 2.74267 / 1.99 ( 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 228 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8732 (tt0) cc_final: 0.8176 (tm-30) REVERT: A 516 GLU cc_start: 0.7395 (pp20) cc_final: 0.7149 (tm-30) REVERT: A 540 ASN cc_start: 0.8055 (m-40) cc_final: 0.7786 (m110) REVERT: A 1038 LYS cc_start: 0.8952 (mmtm) cc_final: 0.8728 (mptt) REVERT: A 1101 HIS cc_start: 0.8446 (t70) cc_final: 0.8223 (t-170) REVERT: B 134 GLN cc_start: 0.3470 (OUTLIER) cc_final: 0.2610 (pp30) REVERT: B 271 GLN cc_start: 0.7694 (mt0) cc_final: 0.7073 (mp10) REVERT: B 319 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7838 (ttm170) REVERT: B 425 LEU cc_start: 0.1628 (OUTLIER) cc_final: 0.0956 (tp) REVERT: B 500 THR cc_start: 0.3297 (OUTLIER) cc_final: 0.3054 (m) REVERT: B 531 THR cc_start: 0.7545 (m) cc_final: 0.7285 (p) REVERT: B 921 LYS cc_start: 0.8496 (mmtm) cc_final: 0.8191 (mptt) REVERT: C 52 GLN cc_start: 0.8399 (tm-30) cc_final: 0.7949 (tm-30) REVERT: C 117 LEU cc_start: 0.6587 (OUTLIER) cc_final: 0.6200 (tt) REVERT: C 189 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.5722 (tt) REVERT: C 190 ARG cc_start: 0.6450 (ttt180) cc_final: 0.6097 (ttm110) REVERT: C 516 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8011 (tt0) REVERT: C 616 ASN cc_start: 0.8230 (t0) cc_final: 0.7933 (m-40) outliers start: 39 outliers final: 22 residues processed: 218 average time/residue: 0.5032 time to fit residues: 132.8342 Evaluate side-chains 209 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 GLN 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 500 THR 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 939 SER Chi-restraints excluded: chain B residue 1002 GLN 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 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 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: 0.6980 chunk 38 optimal weight: 0.5980 chunk 240 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 0.0570 chunk 142 optimal weight: 0.0870 chunk 94 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 222 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** B 613 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.203483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.151486 restraints weight = 33416.356| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.15 r_work: 0.3226 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 25854 Z= 0.120 Angle : 0.760 59.199 35314 Z= 0.398 Chirality : 0.048 0.917 4162 Planarity : 0.005 0.110 4464 Dihedral : 4.945 41.644 3350 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.58 % Rotamer: Outliers : 1.32 % Allowed : 15.80 % Favored : 82.88 % 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: -0.80 (0.15), residues: 3080 helix: 1.53 (0.21), residues: 680 sheet: 0.49 (0.20), residues: 634 loop : -1.88 (0.13), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.027 0.001 TYR B 904 PHE 0.019 0.001 PHE A 32 TRP 0.015 0.001 TRP B 64 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (25759) covalent geometry : angle 0.73822 / 0.39 (35068) SS BOND : bond 0.00395 / 0.26 ( 39) SS BOND : angle 2.28364 / 1.35 ( 78) hydrogen bonds : bond 0.05293 / 3.48 ( 843) hydrogen bonds : angle 4.90596 / 3.34 ( 2370) link_BETA1-4 : bond 0.00390 / 0.25 ( 14) link_BETA1-4 : angle 1.01644 / 0.63 ( 42) link_NAG-ASN : bond 0.00391 / 0.25 ( 42) link_NAG-ASN : angle 2.61325 / 1.91 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10508.12 seconds wall clock time: 179 minutes 14.56 seconds (10754.56 seconds total)