Starting phenix.real_space_refine on Sun Sep 13 19:42:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xm4_22255/09_2026/6xm4_22255.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xm4_22255/09_2026/6xm4_22255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6xm4_22255/09_2026/6xm4_22255.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xm4_22255/09_2026/6xm4_22255.cif" model { file = "/net/cci-nas-00/data/ceres_data/6xm4_22255/09_2026/6xm4_22255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xm4_22255/09_2026/6xm4_22255.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xm4_22255/09_2026/6xm4_22255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xm4_22255/09_2026/6xm4_22255.map" } resolution = 2.9 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= -0.001 sd= 0.963 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 110 5.16 5 C 16158 2.51 5 N 4143 2.21 5 O 4987 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.03s 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: 25398 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8103 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 51, 'TRANS': 985} Chain breaks: 7 Chain: "B" Number of atoms: 8259 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1058, 8253 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 52, 'TRANS': 1005} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1058, 8253 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 52, 'TRANS': 1005} Chain breaks: 5 bond proxies already assigned to first conformer: 8435 Chain: "C" Number of atoms: 8182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8182 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 52, 'TRANS': 995} 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: "R" 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: "S" 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: "T" 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: "U" 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: 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 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 7.14, per 1000 atoms: 0.28 Number of scatterers: 25398 At special positions: 0 Unit cell: (138.55, 138.55, 198.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 4987 8.00 N 4143 7.00 C 16158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 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 343 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " 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 331 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 343 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.2 seconds 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5898 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 47 sheets defined 22.7% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.619A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.606A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 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 633 through 637 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 749 through 754 removed outlier: 3.539A 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: 3.778A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.778A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (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: 3.544A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.647A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.619A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.022A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.851A 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 981 removed outlier: 3.571A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 976 through 981' Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.734A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.599A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.608A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.739A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.529A pdb=" N LEU B 629 " --> pdb=" O ALA B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.571A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.519A pdb=" N GLY B 744 " --> pdb=" O MET B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 754 removed outlier: 3.507A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.800A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.640A 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 831 through 839 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.653A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.111A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (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 981 removed outlier: 3.664A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 976 through 981' Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.648A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.608A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.508A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 638 removed outlier: 3.889A pdb=" N SER C 637 " --> pdb=" O ARG C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.702A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.569A pdb=" N GLN C 755 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.823A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 835 through 840 removed outlier: 4.024A pdb=" N ASP C 839 " --> pdb=" O GLN C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.569A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.514A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.057A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 980 removed outlier: 3.657A pdb=" N ILE C 980 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1033 removed outlier: 3.997A pdb=" N ILE C 993 " --> pdb=" O ALA C 989 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.503A 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: 3.516A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.621A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.802A 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 removed outlier: 3.611A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 142 removed outlier: 6.014A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.638A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.303A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.297A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.121A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB2, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.310A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.346A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.643A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.644A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.043A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.874A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.517A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASN B 280 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 285 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.697A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 318 removed outlier: 7.139A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.622A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.630A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.315A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.567A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.676A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.676A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.529A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.583A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.755A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.228A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.590A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 169 through 171 removed outlier: 3.553A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.055A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 325 removed outlier: 7.215A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.597A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.597A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.857A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.229A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 551 through 554 removed outlier: 5.622A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.778A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.605A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.605A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 removed outlier: 3.504A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.905A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 849 hydrogen bonds defined for protein. 2339 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: 6.17 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 7983 1.34 - 1.48: 7186 1.48 - 1.61: 10656 1.61 - 1.75: 1 1.75 - 1.89: 133 Bond restraints: 25959 Sorted by residual: bond pdb=" C GLN A1142 " pdb=" N PRO A1143 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.39e+00 bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.59e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.52e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.35e+00 bond pdb=" C VAL C 620 " pdb=" N PRO C 621 " ideal model delta sigma weight residual 1.337 1.371 -0.033 1.24e-02 6.50e+03 7.26e+00 ... (remaining 25954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 34723 3.09 - 6.18: 539 6.18 - 9.27: 59 9.27 - 12.36: 15 12.36 - 15.45: 4 Bond angle restraints: 35340 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 121.54 134.35 -12.81 1.91e+00 2.74e-01 4.49e+01 angle pdb=" N THR B 415 " pdb=" CA THR B 415 " pdb=" C THR B 415 " ideal model delta sigma weight residual 108.34 115.25 -6.91 1.31e+00 5.83e-01 2.78e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.82 -6.12 1.22e+00 6.72e-01 2.52e+01 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 109.95 117.22 -7.27 1.59e+00 3.96e-01 2.09e+01 angle pdb=" C GLY B 842 " pdb=" N ASP B 843 " pdb=" CA ASP B 843 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 ... (remaining 35335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 13396 17.89 - 35.78: 1285 35.78 - 53.66: 218 53.66 - 71.55: 45 71.55 - 89.44: 28 Dihedral angle restraints: 14972 sinusoidal: 5811 harmonic: 9161 Sorted by residual: 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 93.00 168.42 -75.42 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -161.41 75.41 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 25.49 67.51 1 1.00e+01 1.00e-02 5.93e+01 ... (remaining 14969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3288 0.079 - 0.158: 841 0.158 - 0.237: 62 0.237 - 0.315: 5 0.315 - 0.394: 10 Chirality restraints: 4206 Sorted by residual: chirality pdb=" CB THR A 33 " pdb=" CA THR A 33 " pdb=" OG1 THR A 33 " pdb=" CG2 THR A 33 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.88e+00 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 -2.01 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" C2 NAG B1301 " pdb=" C1 NAG B1301 " pdb=" C3 NAG B1301 " pdb=" N2 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.84e+00 ... (remaining 4203 not shown) Planarity restraints: 4536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " 0.038 2.00e-02 2.50e+03 3.51e-02 1.54e+01 pdb=" CG ASN B 603 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " -0.043 2.00e-02 2.50e+03 pdb=" C1 NAG B1304 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.066 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO C 987 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.058 5.00e-02 4.00e+02 8.61e-02 1.19e+01 pdb=" N PRO A 987 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.049 5.00e-02 4.00e+02 ... (remaining 4533 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3679 2.76 - 3.29: 21028 3.29 - 3.83: 39621 3.83 - 4.36: 46023 4.36 - 4.90: 82215 Nonbonded interactions: 192566 Sorted by model distance: nonbonded pdb=" O GLN B 134 " pdb=" OH TYR B 160 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR A 716 " pdb=" O GLN A1071 " model vdw 2.240 3.040 nonbonded pdb=" OG SER C 349 " pdb=" O LEU C 452 " model vdw 2.257 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.258 3.040 nonbonded pdb=" OG SER A 383 " pdb=" OD1 ASP B 985 " model vdw 2.262 3.040 ... (remaining 192561 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 492 or resid 494 through 828 or resid 850 through 1306)) selection = (chain 'B' and (resid 27 through 250 or resid 265 through 444 or resid 447 throu \ gh 492 or resid 494 through 828 or resid 850 through 1306)) selection = (chain 'C' and (resid 27 through 250 or resid 265 through 492 or resid 494 throu \ gh 828 or resid 834 or resid 851 through 1306)) } 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' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 11.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 27.110 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.011 0.117 26060 Z= 0.440 Angle : 1.109 23.944 35603 Z= 0.583 Chirality : 0.068 0.394 4206 Planarity : 0.008 0.098 4493 Dihedral : 14.551 89.439 8954 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.81 % Favored : 93.09 % Rotamer: Outliers : 0.40 % Allowed : 6.48 % Favored : 93.12 % 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: -3.45 (0.13), residues: 3100 helix: -1.85 (0.17), residues: 681 sheet: -1.32 (0.19), residues: 619 loop : -2.95 (0.12), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1039 TYR 0.031 0.003 TYR B 495 PHE 0.046 0.004 PHE C 329 TRP 0.051 0.005 TRP A 886 HIS 0.010 0.002 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.01071 / 0.44 (25959) covalent geometry : angle 1.06104 / 0.57 (35340) SS BOND : bond 0.00875 / 0.52 ( 40) SS BOND : angle 2.30047 / 1.45 ( 80) hydrogen bonds : bond 0.23277 / 15.39 ( 809) hydrogen bonds : angle 8.06572 / 5.41 ( 2339) link_BETA1-4 : bond 0.01151 / 0.75 ( 18) link_BETA1-4 : angle 3.14704 / 1.94 ( 54) link_NAG-ASN : bond 0.00856 / 0.50 ( 43) link_NAG-ASN : angle 4.87188 / 3.21 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 244 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.6621 (mtm180) cc_final: 0.6255 (mtm-85) REVERT: A 773 GLU cc_start: 0.7604 (tt0) cc_final: 0.7341 (tt0) REVERT: B 324 GLU cc_start: 0.7302 (tt0) cc_final: 0.6981 (mt-10) REVERT: B 869 MET cc_start: 0.8930 (mtt) cc_final: 0.8651 (mtt) REVERT: C 572 THR cc_start: 0.8137 (p) cc_final: 0.7673 (m) REVERT: C 811 LYS cc_start: 0.5932 (ttmt) cc_final: 0.5643 (tppp) REVERT: C 1138 TYR cc_start: 0.8004 (t80) cc_final: 0.7782 (t80) outliers start: 9 outliers final: 4 residues processed: 251 average time/residue: 0.6789 time to fit residues: 197.0178 Evaluate side-chains 167 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 163 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 581 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 779 GLN A 901 GLN A 926 GLN A 955 ASN A1071 GLN A1101 HIS B 66 HIS B 360 ASN B 460 ASN B 613 GLN B 901 GLN B1071 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 409 GLN C 422 ASN C 460 ASN C 498 GLN C 787 GLN C 804 GLN C 901 GLN C 926 GLN C 960 ASN C1101 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.190076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136843 restraints weight = 31064.687| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.11 r_work: 0.3164 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26060 Z= 0.140 Angle : 0.685 18.555 35603 Z= 0.344 Chirality : 0.047 0.273 4206 Planarity : 0.005 0.062 4493 Dihedral : 5.839 41.295 3371 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.58 % Favored : 94.39 % Rotamer: Outliers : 1.82 % Allowed : 9.98 % Favored : 88.20 % 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: -2.32 (0.14), residues: 3100 helix: -0.26 (0.20), residues: 686 sheet: -0.55 (0.20), residues: 596 loop : -2.54 (0.12), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.023 0.001 TYR A 369 PHE 0.022 0.001 PHE A 32 TRP 0.020 0.002 TRP B 886 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (25959) covalent geometry : angle 0.64913 / 0.34 (35340) SS BOND : bond 0.00405 / 0.25 ( 40) SS BOND : angle 1.70508 / 1.09 ( 80) hydrogen bonds : bond 0.06288 / 4.14 ( 809) hydrogen bonds : angle 5.82353 / 3.87 ( 2339) link_BETA1-4 : bond 0.00480 / 0.29 ( 18) link_BETA1-4 : angle 1.42796 / 0.90 ( 54) link_NAG-ASN : bond 0.00483 / 0.26 ( 43) link_NAG-ASN : angle 3.37283 / 2.21 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.6019 (mtm180) cc_final: 0.5451 (mtm-85) REVERT: A 336 CYS cc_start: 0.5655 (OUTLIER) cc_final: 0.5256 (t) REVERT: A 553 THR cc_start: 0.6942 (m) cc_final: 0.6672 (m) REVERT: A 740 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8863 (ttm) REVERT: A 773 GLU cc_start: 0.8447 (tt0) cc_final: 0.8143 (tt0) REVERT: A 1145 LEU cc_start: 0.5397 (OUTLIER) cc_final: 0.5133 (mt) REVERT: B 129 LYS cc_start: 0.7775 (mppt) cc_final: 0.6893 (mmmt) REVERT: B 324 GLU cc_start: 0.7671 (tt0) cc_final: 0.6990 (mt-10) REVERT: B 850 ILE cc_start: 0.7680 (mt) cc_final: 0.7462 (mt) REVERT: C 203 ILE cc_start: 0.7771 (mt) cc_final: 0.7394 (tt) REVERT: C 224 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6115 (mp0) REVERT: C 321 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.6828 (mp10) REVERT: C 448 ASN cc_start: 0.5614 (t0) cc_final: 0.5085 (t0) outliers start: 48 outliers final: 17 residues processed: 218 average time/residue: 0.5584 time to fit residues: 144.8106 Evaluate side-chains 180 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 201 optimal weight: 0.1980 chunk 65 optimal weight: 8.9990 chunk 236 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1010 GLN B 360 ASN B 613 GLN B 675 GLN B1011 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 360 ASN C 409 GLN C 422 ASN C1101 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.193094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148547 restraints weight = 33730.072| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.29 r_work: 0.3173 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 26060 Z= 0.111 Angle : 0.613 18.279 35603 Z= 0.305 Chirality : 0.045 0.267 4206 Planarity : 0.004 0.053 4493 Dihedral : 5.129 26.520 3367 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 2.08 % Allowed : 11.25 % Favored : 86.67 % 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: -1.75 (0.14), residues: 3100 helix: 0.44 (0.21), residues: 689 sheet: -0.22 (0.20), residues: 632 loop : -2.30 (0.13), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.021 0.001 TYR A 369 PHE 0.020 0.001 PHE A 32 TRP 0.011 0.001 TRP B 886 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (25959) covalent geometry : angle 0.57983 / 0.30 (35340) SS BOND : bond 0.00359 / 0.22 ( 40) SS BOND : angle 1.23419 / 0.79 ( 80) hydrogen bonds : bond 0.04993 / 3.29 ( 809) hydrogen bonds : angle 5.31042 / 3.52 ( 2339) link_BETA1-4 : bond 0.00515 / 0.33 ( 18) link_BETA1-4 : angle 1.46785 / 0.94 ( 54) link_NAG-ASN : bond 0.00641 / 0.33 ( 43) link_NAG-ASN : angle 3.13170 / 2.06 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 126 VAL cc_start: 0.8088 (t) cc_final: 0.7673 (p) REVERT: A 190 ARG cc_start: 0.6169 (mtm180) cc_final: 0.5574 (mtm-85) REVERT: A 462 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7640 (mtpt) REVERT: A 553 THR cc_start: 0.6958 (OUTLIER) cc_final: 0.6652 (m) REVERT: A 740 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8619 (tpt) REVERT: A 1145 LEU cc_start: 0.5484 (OUTLIER) cc_final: 0.5227 (mt) REVERT: B 129 LYS cc_start: 0.7990 (mppt) cc_final: 0.7227 (mmmt) REVERT: B 228 ASP cc_start: 0.7766 (t0) cc_final: 0.7476 (t0) REVERT: B 324 GLU cc_start: 0.7542 (tt0) cc_final: 0.6944 (mt-10) REVERT: C 203 ILE cc_start: 0.7748 (mt) cc_final: 0.7395 (tt) REVERT: C 224 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7047 (mt-10) REVERT: C 321 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.6830 (mp10) REVERT: C 1138 TYR cc_start: 0.8270 (t80) cc_final: 0.7988 (t80) outliers start: 55 outliers final: 20 residues processed: 224 average time/residue: 0.5505 time to fit residues: 147.9738 Evaluate side-chains 185 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 46 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 146 optimal weight: 20.0000 chunk 244 optimal weight: 4.9990 chunk 287 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 613 GLN B 675 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 409 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.190258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.137009 restraints weight = 33746.022| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.30 r_work: 0.3136 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26060 Z= 0.145 Angle : 0.628 17.741 35603 Z= 0.313 Chirality : 0.046 0.289 4206 Planarity : 0.004 0.044 4493 Dihedral : 5.024 28.700 3367 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.68 % Rotamer: Outliers : 2.40 % Allowed : 12.24 % Favored : 85.36 % 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: -1.56 (0.14), residues: 3100 helix: 0.61 (0.21), residues: 687 sheet: -0.16 (0.20), residues: 632 loop : -2.16 (0.13), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.023 0.001 TYR A 453 PHE 0.023 0.001 PHE A 32 TRP 0.013 0.001 TRP B 886 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.14 (25959) covalent geometry : angle 0.59703 / 0.31 (35340) SS BOND : bond 0.00319 / 0.18 ( 40) SS BOND : angle 1.42176 / 0.90 ( 80) hydrogen bonds : bond 0.05811 / 3.81 ( 809) hydrogen bonds : angle 5.22899 / 3.47 ( 2339) link_BETA1-4 : bond 0.00458 / 0.30 ( 18) link_BETA1-4 : angle 1.36656 / 0.87 ( 54) link_NAG-ASN : bond 0.00437 / 0.23 ( 43) link_NAG-ASN : angle 3.01489 / 2.00 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 167 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 126 VAL cc_start: 0.7993 (t) cc_final: 0.7615 (p) REVERT: A 190 ARG cc_start: 0.6064 (mtm180) cc_final: 0.5427 (mtm-85) REVERT: A 553 THR cc_start: 0.7206 (OUTLIER) cc_final: 0.6778 (m) REVERT: A 568 ASP cc_start: 0.6764 (p0) cc_final: 0.6514 (p0) REVERT: A 740 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8884 (tpt) REVERT: A 1145 LEU cc_start: 0.5415 (OUTLIER) cc_final: 0.5180 (mt) REVERT: B 129 LYS cc_start: 0.7733 (mppt) cc_final: 0.6926 (mmmt) REVERT: B 324 GLU cc_start: 0.7558 (tt0) cc_final: 0.6812 (mt-10) REVERT: B 581 THR cc_start: 0.7248 (OUTLIER) cc_final: 0.6820 (p) REVERT: C 195 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7687 (ttpt) REVERT: C 224 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: C 237 ARG cc_start: 0.8494 (mtp180) cc_final: 0.8040 (mtp85) REVERT: C 321 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.6935 (mp10) REVERT: C 332 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7049 (mm) REVERT: C 448 ASN cc_start: 0.5392 (t0) cc_final: 0.4915 (t0) REVERT: C 646 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8354 (mtp180) REVERT: C 1138 TYR cc_start: 0.8295 (t80) cc_final: 0.7946 (t80) outliers start: 64 outliers final: 26 residues processed: 213 average time/residue: 0.5117 time to fit residues: 131.8047 Evaluate side-chains 191 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 145 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 139 optimal weight: 30.0000 chunk 131 optimal weight: 9.9990 chunk 137 optimal weight: 0.0370 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 360 ASN B 613 GLN B 625 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 409 GLN C 519 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.188854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.136659 restraints weight = 40934.560| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.47 r_work: 0.3111 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 26060 Z= 0.202 Angle : 0.674 17.402 35603 Z= 0.337 Chirality : 0.049 0.264 4206 Planarity : 0.004 0.044 4493 Dihedral : 5.169 30.384 3367 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.81 % Favored : 94.16 % Rotamer: Outliers : 2.44 % Allowed : 13.29 % Favored : 84.27 % 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: -1.60 (0.14), residues: 3100 helix: 0.43 (0.20), residues: 699 sheet: -0.16 (0.20), residues: 633 loop : -2.14 (0.13), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.026 0.002 TYR A 453 PHE 0.027 0.002 PHE B 559 TRP 0.014 0.002 TRP B 886 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.20 (25959) covalent geometry : angle 0.64388 / 0.33 (35340) SS BOND : bond 0.00422 / 0.24 ( 40) SS BOND : angle 1.55164 / 0.98 ( 80) hydrogen bonds : bond 0.06627 / 4.36 ( 809) hydrogen bonds : angle 5.29469 / 3.51 ( 2339) link_BETA1-4 : bond 0.00452 / 0.29 ( 18) link_BETA1-4 : angle 1.50950 / 0.96 ( 54) link_NAG-ASN : bond 0.00459 / 0.25 ( 43) link_NAG-ASN : angle 3.07529 / 2.03 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 164 time to evaluate : 1.022 Fit side-chains REVERT: A 126 VAL cc_start: 0.8005 (t) cc_final: 0.7601 (p) REVERT: A 132 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6918 (mt-10) REVERT: A 190 ARG cc_start: 0.6085 (mtm180) cc_final: 0.5444 (mtm-85) REVERT: A 462 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7623 (mtpt) REVERT: A 466 ARG cc_start: 0.6955 (ttp-110) cc_final: 0.6445 (ttm170) REVERT: A 553 THR cc_start: 0.7296 (OUTLIER) cc_final: 0.6903 (m) REVERT: A 740 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8738 (tpt) REVERT: A 1145 LEU cc_start: 0.5489 (OUTLIER) cc_final: 0.5232 (mt) REVERT: B 129 LYS cc_start: 0.7806 (mppt) cc_final: 0.7025 (mmmt) REVERT: B 195 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8133 (ptpt) REVERT: B 324 GLU cc_start: 0.7634 (tt0) cc_final: 0.6963 (mt-10) REVERT: B 578 ASP cc_start: 0.8475 (t0) cc_final: 0.8230 (t0) REVERT: B 840 CYS cc_start: 0.3090 (p) cc_final: 0.2846 (p) REVERT: C 195 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7627 (ttpt) REVERT: C 224 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7282 (mt-10) REVERT: C 237 ARG cc_start: 0.8410 (mtp180) cc_final: 0.8002 (mtp85) REVERT: C 321 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.6873 (mp10) REVERT: C 332 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7064 (mm) REVERT: C 646 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8181 (mtp180) REVERT: C 761 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8790 (p) REVERT: C 1138 TYR cc_start: 0.8291 (t80) cc_final: 0.7966 (t80) outliers start: 65 outliers final: 34 residues processed: 215 average time/residue: 0.5450 time to fit residues: 140.8733 Evaluate side-chains 200 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 279 optimal weight: 0.9980 chunk 302 optimal weight: 4.9990 chunk 224 optimal weight: 0.2980 chunk 140 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 208 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 360 ASN B 613 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 409 GLN C1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.191303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.147307 restraints weight = 33063.785| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.24 r_work: 0.3174 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 26060 Z= 0.114 Angle : 0.599 17.124 35603 Z= 0.296 Chirality : 0.045 0.258 4206 Planarity : 0.004 0.044 4493 Dihedral : 4.789 27.205 3367 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.06 % Rotamer: Outliers : 2.51 % Allowed : 13.77 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.15), residues: 3100 helix: 0.89 (0.21), residues: 690 sheet: -0.06 (0.20), residues: 645 loop : -2.00 (0.13), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.024 0.001 TYR A 453 PHE 0.022 0.001 PHE A 32 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.000 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (25959) covalent geometry : angle 0.56574 / 0.29 (35340) SS BOND : bond 0.00427 / 0.26 ( 40) SS BOND : angle 1.39486 / 0.88 ( 80) hydrogen bonds : bond 0.05068 / 3.33 ( 809) hydrogen bonds : angle 5.04945 / 3.35 ( 2339) link_BETA1-4 : bond 0.00464 / 0.29 ( 18) link_BETA1-4 : angle 1.37067 / 0.88 ( 54) link_NAG-ASN : bond 0.00425 / 0.22 ( 43) link_NAG-ASN : angle 3.05444 / 1.98 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 165 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 126 VAL cc_start: 0.8061 (t) cc_final: 0.7678 (p) REVERT: A 132 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6993 (mt-10) REVERT: A 190 ARG cc_start: 0.6084 (mtm180) cc_final: 0.5455 (mtm-85) REVERT: A 237 ARG cc_start: 0.7704 (mtp-110) cc_final: 0.7482 (ttp-110) REVERT: A 360 ASN cc_start: 0.6266 (m-40) cc_final: 0.5321 (t0) REVERT: A 553 THR cc_start: 0.7347 (OUTLIER) cc_final: 0.6908 (m) REVERT: A 568 ASP cc_start: 0.6678 (p0) cc_final: 0.6403 (p0) REVERT: A 1145 LEU cc_start: 0.5437 (OUTLIER) cc_final: 0.5201 (mt) REVERT: B 129 LYS cc_start: 0.7757 (mppt) cc_final: 0.6960 (mmmt) REVERT: B 324 GLU cc_start: 0.7679 (tt0) cc_final: 0.6938 (mt-10) REVERT: B 578 ASP cc_start: 0.8476 (t0) cc_final: 0.8212 (t0) REVERT: B 675 GLN cc_start: 0.7450 (pp30) cc_final: 0.7116 (pp30) REVERT: C 195 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7879 (ttmt) REVERT: C 224 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7210 (mt-10) REVERT: C 237 ARG cc_start: 0.8543 (mtp180) cc_final: 0.8178 (mtp85) REVERT: C 321 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.6987 (mp10) REVERT: C 332 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.7004 (mm) REVERT: C 629 LEU cc_start: 0.2795 (OUTLIER) cc_final: 0.2348 (mp) REVERT: C 646 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8312 (mtp180) REVERT: C 761 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8694 (p) REVERT: C 1138 TYR cc_start: 0.8324 (t80) cc_final: 0.8024 (t80) outliers start: 67 outliers final: 31 residues processed: 218 average time/residue: 0.5732 time to fit residues: 148.9438 Evaluate side-chains 197 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 246 optimal weight: 10.0000 chunk 174 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 213 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 360 ASN B 613 GLN B 628 GLN B 675 GLN C 99 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.189448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.145564 restraints weight = 35157.730| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.27 r_work: 0.3137 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 26060 Z= 0.177 Angle : 0.647 16.649 35603 Z= 0.322 Chirality : 0.047 0.260 4206 Planarity : 0.004 0.044 4493 Dihedral : 4.927 29.437 3367 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.29 % Rotamer: Outliers : 2.37 % Allowed : 14.49 % Favored : 83.14 % 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: -1.35 (0.14), residues: 3100 helix: 0.74 (0.21), residues: 690 sheet: -0.02 (0.20), residues: 635 loop : -2.00 (0.13), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.026 0.002 TYR A 453 PHE 0.023 0.002 PHE B 559 TRP 0.011 0.002 TRP B 886 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 (25959) covalent geometry : angle 0.61587 / 0.32 (35340) SS BOND : bond 0.00514 / 0.32 ( 40) SS BOND : angle 1.56972 / 0.99 ( 80) hydrogen bonds : bond 0.06227 / 4.09 ( 809) hydrogen bonds : angle 5.15561 / 3.42 ( 2339) link_BETA1-4 : bond 0.00449 / 0.28 ( 18) link_BETA1-4 : angle 1.42460 / 0.91 ( 54) link_NAG-ASN : bond 0.00432 / 0.23 ( 43) link_NAG-ASN : angle 3.04916 / 1.99 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 163 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.7998 (m) cc_final: 0.7770 (p) REVERT: A 126 VAL cc_start: 0.8096 (t) cc_final: 0.7696 (p) REVERT: A 132 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7040 (mt-10) REVERT: A 190 ARG cc_start: 0.6115 (mtm180) cc_final: 0.5487 (mtm-85) REVERT: A 360 ASN cc_start: 0.6367 (m-40) cc_final: 0.5320 (t0) REVERT: A 553 THR cc_start: 0.7457 (OUTLIER) cc_final: 0.7004 (m) REVERT: A 568 ASP cc_start: 0.6667 (p0) cc_final: 0.6349 (p0) REVERT: A 1145 LEU cc_start: 0.5463 (OUTLIER) cc_final: 0.5206 (mt) REVERT: B 129 LYS cc_start: 0.7823 (mppt) cc_final: 0.7034 (mmmt) REVERT: B 324 GLU cc_start: 0.7725 (tt0) cc_final: 0.6967 (mt-10) REVERT: B 578 ASP cc_start: 0.8505 (t0) cc_final: 0.8234 (t0) REVERT: C 224 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7409 (mt-10) REVERT: C 237 ARG cc_start: 0.8527 (mtp180) cc_final: 0.8154 (mtp85) REVERT: C 321 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7034 (mp10) REVERT: C 646 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8332 (mtp180) REVERT: C 761 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8830 (p) REVERT: C 1138 TYR cc_start: 0.8397 (t80) cc_final: 0.8095 (t80) outliers start: 63 outliers final: 38 residues processed: 214 average time/residue: 0.5480 time to fit residues: 140.9057 Evaluate side-chains 202 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 136 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 180 optimal weight: 0.2980 chunk 216 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 243 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 46 optimal weight: 0.0970 chunk 207 optimal weight: 5.9990 overall best weight: 3.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 613 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 960 ASN C1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.188253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.144287 restraints weight = 35182.840| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.28 r_work: 0.3109 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 26060 Z= 0.236 Angle : 0.697 16.291 35603 Z= 0.348 Chirality : 0.050 0.260 4206 Planarity : 0.005 0.044 4493 Dihedral : 5.115 30.821 3367 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.10 % Favored : 93.87 % Rotamer: Outliers : 2.33 % Allowed : 14.86 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.14), residues: 3100 helix: 0.52 (0.20), residues: 689 sheet: -0.05 (0.20), residues: 635 loop : -2.06 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.030 0.002 TYR A 508 PHE 0.028 0.002 PHE B 559 TRP 0.013 0.002 TRP B 886 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.24 (25959) covalent geometry : angle 0.66682 / 0.34 (35340) SS BOND : bond 0.00547 / 0.33 ( 40) SS BOND : angle 1.62569 / 1.03 ( 80) hydrogen bonds : bond 0.06959 / 4.58 ( 809) hydrogen bonds : angle 5.27112 / 3.50 ( 2339) link_BETA1-4 : bond 0.00451 / 0.29 ( 18) link_BETA1-4 : angle 1.55896 / 1.00 ( 54) link_NAG-ASN : bond 0.00463 / 0.26 ( 43) link_NAG-ASN : angle 3.08604 / 2.02 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 159 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6890 (mt-10) REVERT: A 190 ARG cc_start: 0.6100 (mtm180) cc_final: 0.5511 (mtm-85) REVERT: A 360 ASN cc_start: 0.6401 (m-40) cc_final: 0.5272 (t0) REVERT: A 466 ARG cc_start: 0.7068 (ttp-110) cc_final: 0.6539 (ttm170) REVERT: A 553 THR cc_start: 0.7452 (OUTLIER) cc_final: 0.7019 (m) REVERT: A 1145 LEU cc_start: 0.5526 (OUTLIER) cc_final: 0.5268 (mt) REVERT: B 129 LYS cc_start: 0.7947 (mppt) cc_final: 0.7199 (mmmt) REVERT: B 578 ASP cc_start: 0.8467 (t0) cc_final: 0.8233 (t0) REVERT: B 675 GLN cc_start: 0.7555 (pp30) cc_final: 0.7287 (pp30) REVERT: B 840 CYS cc_start: 0.3288 (p) cc_final: 0.3033 (p) REVERT: C 224 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: C 237 ARG cc_start: 0.8447 (mtp180) cc_final: 0.8075 (mtp85) REVERT: C 321 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.6974 (mp10) REVERT: C 332 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.6901 (mm) REVERT: C 646 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8239 (mtp180) REVERT: C 761 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8799 (p) REVERT: C 1138 TYR cc_start: 0.8328 (t80) cc_final: 0.8050 (t80) outliers start: 63 outliers final: 37 residues processed: 212 average time/residue: 0.5480 time to fit residues: 139.7028 Evaluate side-chains 200 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 2 optimal weight: 8.9990 chunk 279 optimal weight: 0.1980 chunk 215 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 248 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 310 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 286 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 360 ASN B 613 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.192662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.141132 restraints weight = 39359.634| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.47 r_work: 0.3184 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 26060 Z= 0.100 Angle : 0.573 15.986 35603 Z= 0.285 Chirality : 0.044 0.254 4206 Planarity : 0.004 0.046 4493 Dihedral : 4.546 25.904 3367 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 1.75 % Allowed : 15.44 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.15), residues: 3100 helix: 1.05 (0.21), residues: 693 sheet: 0.14 (0.20), residues: 638 loop : -1.88 (0.13), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1107 TYR 0.026 0.001 TYR A 453 PHE 0.021 0.001 PHE A 32 TRP 0.011 0.001 TRP A 436 HIS 0.002 0.000 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (25959) covalent geometry : angle 0.54579 / 0.28 (35340) SS BOND : bond 0.00457 / 0.30 ( 40) SS BOND : angle 1.18636 / 0.75 ( 80) hydrogen bonds : bond 0.04458 / 2.93 ( 809) hydrogen bonds : angle 4.92646 / 3.27 ( 2339) link_BETA1-4 : bond 0.00469 / 0.31 ( 18) link_BETA1-4 : angle 1.16442 / 0.75 ( 54) link_NAG-ASN : bond 0.00422 / 0.22 ( 43) link_NAG-ASN : angle 2.73130 / 1.80 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 1.084 Fit side-chains REVERT: A 33 THR cc_start: 0.7868 (m) cc_final: 0.7541 (p) REVERT: A 126 VAL cc_start: 0.8011 (t) cc_final: 0.7662 (p) REVERT: A 132 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7049 (mt-10) REVERT: A 190 ARG cc_start: 0.6051 (mtm180) cc_final: 0.5391 (mtm-85) REVERT: A 360 ASN cc_start: 0.6279 (m-40) cc_final: 0.5232 (t0) REVERT: A 553 THR cc_start: 0.7259 (OUTLIER) cc_final: 0.6814 (m) REVERT: A 568 ASP cc_start: 0.6596 (p0) cc_final: 0.6370 (p0) REVERT: A 855 PHE cc_start: 0.8095 (m-10) cc_final: 0.7349 (m-80) REVERT: A 1145 LEU cc_start: 0.5474 (OUTLIER) cc_final: 0.5262 (mt) REVERT: B 129 LYS cc_start: 0.7693 (mppt) cc_final: 0.6900 (mmmt) REVERT: B 578 ASP cc_start: 0.8424 (t0) cc_final: 0.8179 (t0) REVERT: B 581 THR cc_start: 0.7218 (OUTLIER) cc_final: 0.6725 (p) REVERT: B 675 GLN cc_start: 0.7534 (pp30) cc_final: 0.7280 (pp30) REVERT: C 237 ARG cc_start: 0.8452 (mtp180) cc_final: 0.8077 (mtp85) REVERT: C 321 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7024 (mp10) REVERT: C 332 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.6857 (mm) REVERT: C 646 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8315 (mtp180) REVERT: C 761 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8626 (p) REVERT: C 1019 ARG cc_start: 0.8944 (tpt170) cc_final: 0.8624 (ttp-110) REVERT: C 1138 TYR cc_start: 0.8293 (t80) cc_final: 0.8001 (t80) outliers start: 46 outliers final: 24 residues processed: 202 average time/residue: 0.5414 time to fit residues: 131.6707 Evaluate side-chains 187 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 170 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 114 optimal weight: 30.0000 chunk 145 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 chunk 127 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 613 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 409 GLN C1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.191134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.137527 restraints weight = 33232.081| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.19 r_work: 0.3189 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26060 Z= 0.131 Angle : 0.615 15.516 35603 Z= 0.304 Chirality : 0.046 0.259 4206 Planarity : 0.004 0.044 4493 Dihedral : 4.622 29.980 3367 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.10 % Favored : 94.87 % Rotamer: Outliers : 1.53 % Allowed : 16.02 % Favored : 82.45 % 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: -1.06 (0.15), residues: 3100 helix: 1.04 (0.21), residues: 693 sheet: 0.17 (0.20), residues: 635 loop : -1.85 (0.13), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1107 TYR 0.028 0.001 TYR C 904 PHE 0.023 0.001 PHE A 32 TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (25959) covalent geometry : angle 0.57926 / 0.30 (35340) SS BOND : bond 0.00395 / 0.24 ( 40) SS BOND : angle 1.28245 / 0.80 ( 80) hydrogen bonds : bond 0.05247 / 3.45 ( 809) hydrogen bonds : angle 4.95300 / 3.29 ( 2339) link_BETA1-4 : bond 0.00446 / 0.28 ( 18) link_BETA1-4 : angle 1.39629 / 0.90 ( 54) link_NAG-ASN : bond 0.00553 / 0.28 ( 43) link_NAG-ASN : angle 3.24949 / 2.06 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.8001 (t) cc_final: 0.7639 (p) REVERT: A 132 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7070 (mt-10) REVERT: A 190 ARG cc_start: 0.6079 (mtm180) cc_final: 0.5442 (mtm-85) REVERT: A 360 ASN cc_start: 0.6316 (m-40) cc_final: 0.5178 (t0) REVERT: A 553 THR cc_start: 0.7242 (OUTLIER) cc_final: 0.6774 (m) REVERT: A 568 ASP cc_start: 0.6494 (p0) cc_final: 0.6279 (p0) REVERT: A 855 PHE cc_start: 0.8012 (m-10) cc_final: 0.7287 (m-80) REVERT: A 1145 LEU cc_start: 0.5402 (OUTLIER) cc_final: 0.5191 (mt) REVERT: B 129 LYS cc_start: 0.7699 (mppt) cc_final: 0.6912 (mmmt) REVERT: B 578 ASP cc_start: 0.8376 (t0) cc_final: 0.8157 (t0) REVERT: B 581 THR cc_start: 0.7180 (OUTLIER) cc_final: 0.6720 (p) REVERT: B 675 GLN cc_start: 0.7538 (pp30) cc_final: 0.7272 (pp30) REVERT: C 237 ARG cc_start: 0.8431 (mtp180) cc_final: 0.8055 (mtp85) REVERT: C 321 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7071 (mp10) REVERT: C 646 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8275 (mtp180) REVERT: C 761 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8718 (p) REVERT: C 1138 TYR cc_start: 0.8303 (t80) cc_final: 0.8014 (t80) outliers start: 41 outliers final: 29 residues processed: 189 average time/residue: 0.5568 time to fit residues: 126.1048 Evaluate side-chains 187 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 29 optimal weight: 0.0370 chunk 219 optimal weight: 20.0000 chunk 300 optimal weight: 3.9990 chunk 275 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 147 optimal weight: 0.2980 chunk 141 optimal weight: 10.0000 chunk 259 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 613 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 409 GLN C1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.190969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.141342 restraints weight = 46571.240| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.82 r_work: 0.3114 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 26060 Z= 0.152 Angle : 0.740 59.196 35603 Z= 0.396 Chirality : 0.046 0.260 4206 Planarity : 0.004 0.044 4493 Dihedral : 4.631 27.838 3367 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.80 % Rotamer: Outliers : 1.71 % Allowed : 15.84 % Favored : 82.45 % 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: -1.06 (0.15), residues: 3100 helix: 1.04 (0.21), residues: 693 sheet: 0.17 (0.20), residues: 635 loop : -1.85 (0.13), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1107 TYR 0.030 0.001 TYR C 904 PHE 0.022 0.001 PHE A 32 TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (25959) covalent geometry : angle 0.71200 / 0.39 (35340) SS BOND : bond 0.00427 / 0.26 ( 40) SS BOND : angle 1.31995 / 0.82 ( 80) hydrogen bonds : bond 0.05303 / 3.48 ( 809) hydrogen bonds : angle 4.95992 / 3.29 ( 2339) link_BETA1-4 : bond 0.00455 / 0.28 ( 18) link_BETA1-4 : angle 1.38956 / 0.90 ( 54) link_NAG-ASN : bond 0.00495 / 0.26 ( 43) link_NAG-ASN : angle 3.23151 / 2.04 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10188.72 seconds wall clock time: 174 minutes 12.43 seconds (10452.43 seconds total)