Starting phenix.real_space_refine on Wed Oct 28 05:59:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11ho_75698/10_2026/11ho_75698.cif Found real_map, /net/cci-nas-00/data/ceres_data/11ho_75698/10_2026/11ho_75698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11ho_75698/10_2026/11ho_75698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11ho_75698/10_2026/11ho_75698.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11ho_75698/10_2026/11ho_75698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11ho_75698/10_2026/11ho_75698.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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 112 5.16 5 C 17086 2.51 5 N 4372 2.21 5 O 5186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26756 Number of models: 1 Model: "" Number of chains: 23 Chain: "D" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 941 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "E" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "A" Number of atoms: 8086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8086 Classifications: {'peptide': 1032} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 975} Chain breaks: 6 Chain: "B" Number of atoms: 8086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8086 Classifications: {'peptide': 1032} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 975} Chain breaks: 6 Chain: "C" Number of atoms: 8086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8086 Classifications: {'peptide': 1032} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 975} Chain breaks: 6 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.09, per 1000 atoms: 0.23 Number of scatterers: 26756 At special positions: 0 Unit cell: (138.62, 131.928, 216.056, 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 112 16.00 O 5186 8.00 N 4372 7.00 C 17086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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-ASN " NAG A1301 " - " ASN A 230 " " NAG A1302 " - " ASN A 278 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 354 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 343 " " NAG B1301 " - " ASN B 230 " " NAG B1302 " - " ASN B 278 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 354 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B1074 " " NAG C1301 " - " ASN C 230 " " NAG C1302 " - " ASN C 278 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 354 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C1074 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A 709 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B 717 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN B 709 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C1134 " " NAG T 1 " - " ASN C 709 " NAG-THR " NAG M 1 " - " THR B1100 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 998.3 milliseconds 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6218 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 52 sheets defined 25.9% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.541A pdb=" N PHE E 83 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.815A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.460A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.749A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (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: 3.534A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.585A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.015A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.652A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.958A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.603A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1147 removed outlier: 3.526A pdb=" N LEU A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.571A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 5.454A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.972A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.629A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 627 removed outlier: 3.515A pdb=" N VAL B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.736A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.900A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.722A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.191A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 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 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.687A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1147 removed outlier: 3.844A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 372 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.518A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.517A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.600A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.732A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.287A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.764A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.591A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.540A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.816A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1147 removed outlier: 3.637A pdb=" N LEU C1143 " --> pdb=" O ASP C1139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.968A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP D 58 " --> pdb=" O TYR D 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 5.611A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA7, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.981A pdb=" N ASP A 283 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 63 through 67 removed outlier: 5.941A pdb=" N PHE A 198 " --> pdb=" O ASP A 224 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP A 224 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 200 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 81 through 83 removed outlier: 3.670A pdb=" N LEU A 237 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY A 101 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG A 100 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 114 " --> pdb=" O CYS A 129 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU A 130 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS A 163 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLN A 132 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ASN A 161 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.032A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.215A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.831A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB5, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.750A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.431A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.855A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.855A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC2, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.038A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.919A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC5, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.849A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.791A pdb=" N ASP B 283 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 63 through 67 removed outlier: 3.628A pdb=" N VAL B 223 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N SER B 202 " --> pdb=" O PRO B 221 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 81 through 83 removed outlier: 3.674A pdb=" N LEU B 237 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY B 101 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ARG B 100 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE B 165 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 132 through 133 removed outlier: 7.042A pdb=" N GLN B 132 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.556A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.728A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.525A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 538 through 543 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.996A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.897A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.408A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.863A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.310A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.556A pdb=" N VAL C 47 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP C 283 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 63 through 67 removed outlier: 6.421A pdb=" N PHE C 198 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP C 224 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE C 200 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.298A pdb=" N GLY C 101 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ARG C 100 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS C 129 " --> pdb=" O SER C 114 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 132 through 133 removed outlier: 7.249A pdb=" N GLN C 132 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.941A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.001A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.740A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.581A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.402A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.446A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1096 1091 hydrogen bonds defined for protein. 2925 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8381 1.34 - 1.47: 7001 1.47 - 1.59: 11871 1.59 - 1.71: 0 1.71 - 1.83: 139 Bond restraints: 27392 Sorted by residual: bond pdb=" CA PHE B 802 " pdb=" C PHE B 802 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.66e-02 3.63e+03 4.48e+00 bond pdb=" C1 NAG B1307 " pdb=" C2 NAG B1307 " ideal model delta sigma weight residual 1.532 1.565 -0.033 2.00e-02 2.50e+03 2.79e+00 bond pdb=" CB ASN A 79 " pdb=" CG ASN A 79 " ideal model delta sigma weight residual 1.516 1.557 -0.041 2.50e-02 1.60e+03 2.67e+00 bond pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " ideal model delta sigma weight residual 1.808 1.759 0.049 3.30e-02 9.18e+02 2.20e+00 bond pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " ideal model delta sigma weight residual 1.808 1.760 0.048 3.30e-02 9.18e+02 2.13e+00 ... (remaining 27387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 36605 1.92 - 3.85: 580 3.85 - 5.77: 78 5.77 - 7.69: 16 7.69 - 9.61: 6 Bond angle restraints: 37285 Sorted by residual: angle pdb=" N VAL D 103 " pdb=" CA VAL D 103 " pdb=" C VAL D 103 " ideal model delta sigma weight residual 112.29 108.65 3.64 9.40e-01 1.13e+00 1.50e+01 angle pdb=" CA LYS C 378 " pdb=" CB LYS C 378 " pdb=" CG LYS C 378 " ideal model delta sigma weight residual 114.10 121.02 -6.92 2.00e+00 2.50e-01 1.20e+01 angle pdb=" CA ASN A 79 " pdb=" CB ASN A 79 " pdb=" CG ASN A 79 " ideal model delta sigma weight residual 112.60 116.02 -3.42 1.00e+00 1.00e+00 1.17e+01 angle pdb=" N PRO E 94A" pdb=" CA PRO E 94A" pdb=" C PRO E 94A" ideal model delta sigma weight residual 110.70 114.76 -4.06 1.22e+00 6.72e-01 1.11e+01 angle pdb=" N ILE B 666 " pdb=" CA ILE B 666 " pdb=" C ILE B 666 " ideal model delta sigma weight residual 111.67 108.61 3.06 9.50e-01 1.11e+00 1.04e+01 ... (remaining 37280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 15206 17.87 - 35.73: 1325 35.73 - 53.60: 316 53.60 - 71.46: 72 71.46 - 89.33: 28 Dihedral angle restraints: 16947 sinusoidal: 7274 harmonic: 9673 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 -166.50 80.50 1 1.00e+01 1.00e-02 8.02e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -151.47 65.47 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -148.85 62.85 1 1.00e+01 1.00e-02 5.22e+01 ... (remaining 16944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 4327 0.133 - 0.266: 22 0.266 - 0.398: 0 0.398 - 0.531: 1 0.531 - 0.664: 1 Chirality restraints: 4351 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.04e+00 chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.25 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 4348 not shown) Planarity restraints: 4774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " 0.005 2.00e-02 2.50e+03 1.99e-02 4.96e+00 pdb=" CG ASN B1074 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " -0.014 2.00e-02 2.50e+03 pdb=" C1 NAG B1307 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 79 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ASN B 79 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN B 79 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO B 80 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 745 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.56e+00 pdb=" CG ASP B 745 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP B 745 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP B 745 " -0.013 2.00e-02 2.50e+03 ... (remaining 4771 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 11708 2.93 - 3.42: 25507 3.42 - 3.91: 43774 3.91 - 4.41: 49050 4.41 - 4.90: 83835 Nonbonded interactions: 213874 Sorted by model distance: nonbonded pdb=" O ASN B 79 " pdb=" OD1 ASN B 79 " model vdw 2.433 3.040 nonbonded pdb=" O VAL A 570 " pdb=" OD1 ASP A 571 " model vdw 2.476 3.040 nonbonded pdb=" O ASN A 79 " pdb=" OD1 ASN A 79 " model vdw 2.506 3.040 nonbonded pdb=" O ASP B 195 " pdb=" OD1 ASP B 195 " model vdw 2.511 3.040 nonbonded pdb=" N GLU B 309 " pdb=" OE1 GLU B 309 " model vdw 2.521 3.120 ... (remaining 213869 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.860 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 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 : 0.004 0.049 27484 Z= 0.166 Angle : 0.669 19.071 37519 Z= 0.340 Chirality : 0.046 0.664 4351 Planarity : 0.004 0.050 4739 Dihedral : 14.503 89.326 10606 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.57 % Favored : 96.40 % Rotamer: Outliers : 1.07 % Allowed : 15.15 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.15), residues: 3279 helix: 1.87 (0.20), residues: 720 sheet: 0.04 (0.18), residues: 821 loop : -0.66 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 346 TYR 0.023 0.001 TYR C 904 PHE 0.035 0.001 PHE B 375 TRP 0.029 0.002 TRP E 94 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (27392) covalent geometry : angle 0.61775 / 0.33 (37285) SS BOND : bond 0.00329 / 0.18 ( 41) SS BOND : angle 1.58022 / 1.13 ( 82) hydrogen bonds : bond 0.16609 / 10.85 ( 1086) hydrogen bonds : angle 7.51140 / 5.23 ( 2925) link_BETA1-4 : bond 0.00309 / 0.19 ( 15) link_BETA1-4 : angle 1.33690 / 0.86 ( 45) link_NAG-ASN : bond 0.00630 / 0.43 ( 35) link_NAG-ASN : angle 4.62452 / 3.08 ( 105) link_NAG-THR : bond 0.00801 / 0.42 ( 1) link_NAG-THR : angle 2.92636 / 1.54 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 35 TRP cc_start: 0.7730 (m100) cc_final: 0.6060 (m-10) REVERT: A 129 CYS cc_start: 0.4218 (t) cc_final: 0.3873 (m) REVERT: A 265 TYR cc_start: 0.8516 (m-80) cc_final: 0.7744 (m-80) REVERT: A 421 TYR cc_start: 0.8729 (m-10) cc_final: 0.8270 (m-10) REVERT: A 627 ASP cc_start: 0.8991 (t0) cc_final: 0.8511 (t0) REVERT: A 1010 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7717 (mp10) REVERT: B 113 GLN cc_start: 0.7926 (mp10) cc_final: 0.7093 (mm-40) REVERT: B 436 TRP cc_start: 0.8815 (p90) cc_final: 0.8079 (p90) REVERT: B 523 THR cc_start: 0.8922 (p) cc_final: 0.8654 (p) REVERT: B 574 ASP cc_start: 0.8740 (t70) cc_final: 0.8272 (t0) REVERT: B 586 ASP cc_start: 0.8069 (t0) cc_final: 0.7845 (t0) REVERT: B 868 GLU cc_start: 0.8428 (tp30) cc_final: 0.8014 (tp30) REVERT: B 985 ASP cc_start: 0.8109 (m-30) cc_final: 0.7498 (m-30) REVERT: B 990 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8064 (mp0) REVERT: C 364 ASP cc_start: 0.9144 (t0) cc_final: 0.8875 (t0) REVERT: C 636 TYR cc_start: 0.8256 (t80) cc_final: 0.8028 (t80) outliers start: 31 outliers final: 27 residues processed: 253 average time/residue: 0.1524 time to fit residues: 64.4132 Evaluate side-chains 240 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN A 193 ASN A 417 ASN A 762 GLN B 79 ASN B 235 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.109141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.072048 restraints weight = 55950.974| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.10 r_work: 0.2794 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.0616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27484 Z= 0.184 Angle : 0.626 18.998 37519 Z= 0.304 Chirality : 0.046 0.653 4351 Planarity : 0.004 0.040 4739 Dihedral : 6.912 57.200 4674 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.10 % Allowed : 13.91 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 3279 helix: 1.89 (0.19), residues: 723 sheet: 0.14 (0.18), residues: 835 loop : -0.66 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 346 TYR 0.020 0.001 TYR D 81 PHE 0.024 0.001 PHE B 429 TRP 0.015 0.002 TRP E 94 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (27392) covalent geometry : angle 0.57615 / 0.29 (37285) SS BOND : bond 0.00345 / 0.19 ( 41) SS BOND : angle 1.48095 / 1.07 ( 82) hydrogen bonds : bond 0.04040 / 2.65 ( 1086) hydrogen bonds : angle 5.74939 / 4.00 ( 2925) link_BETA1-4 : bond 0.00278 / 0.17 ( 15) link_BETA1-4 : angle 1.32288 / 0.84 ( 45) link_NAG-ASN : bond 0.00556 / 0.36 ( 35) link_NAG-ASN : angle 4.41633 / 2.99 ( 105) link_NAG-THR : bond 0.00782 / 0.41 ( 1) link_NAG-THR : angle 2.84117 / 1.52 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 230 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.8507 (m-80) cc_final: 0.7598 (m-80) REVERT: A 339 HIS cc_start: 0.8365 (OUTLIER) cc_final: 0.7828 (t70) REVERT: A 421 TYR cc_start: 0.8790 (m-10) cc_final: 0.8304 (m-10) REVERT: A 429 PHE cc_start: 0.8257 (t80) cc_final: 0.8046 (t80) REVERT: A 452 TRP cc_start: 0.9053 (m100) cc_final: 0.8432 (m100) REVERT: A 627 ASP cc_start: 0.8989 (t0) cc_final: 0.8515 (t0) REVERT: A 1010 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7658 (mp10) REVERT: B 113 GLN cc_start: 0.7969 (mp10) cc_final: 0.7298 (mm-40) REVERT: B 436 TRP cc_start: 0.8755 (p90) cc_final: 0.8218 (p90) REVERT: B 523 THR cc_start: 0.8890 (p) cc_final: 0.8667 (p) REVERT: B 574 ASP cc_start: 0.8724 (t70) cc_final: 0.8321 (t0) REVERT: B 619 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: B 868 GLU cc_start: 0.8448 (tp30) cc_final: 0.8073 (tp30) REVERT: B 900 MET cc_start: 0.9136 (mtp) cc_final: 0.8909 (mtp) REVERT: B 985 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: C 364 ASP cc_start: 0.9159 (t0) cc_final: 0.8827 (t0) REVERT: C 516 GLU cc_start: 0.8232 (pt0) cc_final: 0.7984 (pm20) REVERT: C 636 TYR cc_start: 0.8295 (t80) cc_final: 0.8038 (t80) outliers start: 90 outliers final: 53 residues processed: 302 average time/residue: 0.1520 time to fit residues: 75.9932 Evaluate side-chains 273 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 216 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [187, 153, 142, 184, 97, 89, 314, 94, 292, 250, 27] chunk 187 optimal weight: 0.5980 chunk 153 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 184 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 314 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 292 optimal weight: 0.9980 chunk 250 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 3 GLN A 79 ASN A 762 GLN B 79 ASN B 409 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.110545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.073994 restraints weight = 55804.523| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.20 r_work: 0.2835 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27484 Z= 0.111 Angle : 0.584 18.451 37519 Z= 0.281 Chirality : 0.045 0.624 4351 Planarity : 0.003 0.039 4739 Dihedral : 6.623 57.336 4659 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.51 % Allowed : 14.56 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3279 helix: 2.04 (0.20), residues: 720 sheet: 0.35 (0.18), residues: 814 loop : -0.64 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.017 0.001 TYR D 81 PHE 0.016 0.001 PHE B 515 TRP 0.014 0.001 TRP E 94 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (27392) covalent geometry : angle 0.53535 / 0.27 (37285) SS BOND : bond 0.00556 / 0.29 ( 41) SS BOND : angle 1.58470 / 1.10 ( 82) hydrogen bonds : bond 0.03626 / 2.40 ( 1086) hydrogen bonds : angle 5.35692 / 3.72 ( 2925) link_BETA1-4 : bond 0.00350 / 0.20 ( 15) link_BETA1-4 : angle 1.25338 / 0.78 ( 45) link_NAG-ASN : bond 0.00568 / 0.37 ( 35) link_NAG-ASN : angle 4.11696 / 2.80 ( 105) link_NAG-THR : bond 0.01812 / 0.95 ( 1) link_NAG-THR : angle 4.64981 / 2.45 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 254 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 55 ASP cc_start: 0.9092 (t0) cc_final: 0.8661 (t0) REVERT: D 56 ASP cc_start: 0.9315 (OUTLIER) cc_final: 0.8980 (m-30) REVERT: D 106 TRP cc_start: 0.7759 (m100) cc_final: 0.7484 (m100) REVERT: A 265 TYR cc_start: 0.8514 (m-80) cc_final: 0.7909 (m-80) REVERT: A 378 LYS cc_start: 0.8468 (ptmm) cc_final: 0.8219 (ptmt) REVERT: A 421 TYR cc_start: 0.8801 (m-10) cc_final: 0.7679 (m-10) REVERT: A 452 TRP cc_start: 0.9035 (m100) cc_final: 0.8480 (m100) REVERT: A 627 ASP cc_start: 0.8966 (t0) cc_final: 0.8490 (t0) REVERT: A 1010 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: B 113 GLN cc_start: 0.8066 (mp10) cc_final: 0.7485 (mm-40) REVERT: B 436 TRP cc_start: 0.8717 (p90) cc_final: 0.8265 (p90) REVERT: B 523 THR cc_start: 0.8807 (p) cc_final: 0.8554 (p) REVERT: B 574 ASP cc_start: 0.8794 (t70) cc_final: 0.8258 (t0) REVERT: B 868 GLU cc_start: 0.8393 (tp30) cc_final: 0.7985 (tp30) REVERT: B 985 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: B 990 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8144 (mp0) REVERT: C 364 ASP cc_start: 0.9150 (t0) cc_final: 0.8840 (t0) REVERT: C 390 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9436 (pt) REVERT: C 498 ARG cc_start: 0.8849 (mmt90) cc_final: 0.8555 (mmt90) REVERT: C 636 TYR cc_start: 0.8276 (t80) cc_final: 0.8027 (t80) REVERT: C 994 ASP cc_start: 0.8894 (t0) cc_final: 0.8663 (m-30) outliers start: 73 outliers final: 42 residues processed: 310 average time/residue: 0.1488 time to fit residues: 76.9929 Evaluate side-chains 276 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [233, 230, 105, 110, 118, 240, 170, 232, 247, 109, 103] chunk 233 optimal weight: 6.9990 chunk 230 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 232 optimal weight: 0.9980 chunk 247 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 3 GLN A 762 GLN B 79 ASN B 762 GLN C 907 ASN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.107433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.069179 restraints weight = 56189.823| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.82 r_work: 0.2786 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 27484 Z= 0.253 Angle : 0.646 19.220 37519 Z= 0.313 Chirality : 0.047 0.622 4351 Planarity : 0.004 0.038 4739 Dihedral : 6.747 58.424 4655 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.37 % Allowed : 14.73 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3279 helix: 1.84 (0.19), residues: 720 sheet: 0.22 (0.18), residues: 817 loop : -0.68 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.025 0.001 TYR B 380 PHE 0.024 0.002 PHE B 429 TRP 0.016 0.001 TRP E 94 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.25 (27392) covalent geometry : angle 0.60070 / 0.30 (37285) SS BOND : bond 0.00407 / 0.22 ( 41) SS BOND : angle 1.83186 / 1.33 ( 82) hydrogen bonds : bond 0.04002 / 2.65 ( 1086) hydrogen bonds : angle 5.36091 / 3.72 ( 2925) link_BETA1-4 : bond 0.00230 / 0.16 ( 15) link_BETA1-4 : angle 1.33646 / 0.87 ( 45) link_NAG-ASN : bond 0.00534 / 0.32 ( 35) link_NAG-ASN : angle 4.17008 / 2.85 ( 105) link_NAG-THR : bond 0.01234 / 0.65 ( 1) link_NAG-THR : angle 3.44678 / 1.81 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 229 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.9119 (mm) REVERT: A 265 TYR cc_start: 0.8640 (m-80) cc_final: 0.7830 (m-80) REVERT: A 339 HIS cc_start: 0.8486 (OUTLIER) cc_final: 0.7970 (t70) REVERT: A 378 LYS cc_start: 0.8599 (ptmm) cc_final: 0.8350 (ptmt) REVERT: A 627 ASP cc_start: 0.9144 (t0) cc_final: 0.8716 (t0) REVERT: A 661 GLU cc_start: 0.8614 (tp30) cc_final: 0.8397 (tp30) REVERT: A 1010 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7838 (mp10) REVERT: B 378 LYS cc_start: 0.8558 (ttmm) cc_final: 0.8042 (ptmt) REVERT: B 429 PHE cc_start: 0.9113 (t80) cc_final: 0.8858 (t80) REVERT: B 436 TRP cc_start: 0.8792 (p90) cc_final: 0.8465 (p90) REVERT: B 574 ASP cc_start: 0.8968 (t70) cc_final: 0.8431 (t0) REVERT: B 619 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8239 (mp0) REVERT: B 868 GLU cc_start: 0.8824 (tp30) cc_final: 0.8492 (tp30) REVERT: B 985 ASP cc_start: 0.8080 (m-30) cc_final: 0.7619 (m-30) REVERT: C 364 ASP cc_start: 0.9245 (t0) cc_final: 0.8952 (t0) REVERT: C 390 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9464 (pt) REVERT: C 568 ASP cc_start: 0.8944 (t70) cc_final: 0.8567 (t70) REVERT: C 636 TYR cc_start: 0.8458 (t80) cc_final: 0.8168 (t80) REVERT: C 661 GLU cc_start: 0.8508 (tp30) cc_final: 0.8278 (tp30) outliers start: 98 outliers final: 69 residues processed: 312 average time/residue: 0.1509 time to fit residues: 78.3175 Evaluate side-chains 287 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 213 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [100, 36, 296, 87, 154, 327, 56, 99, 304, 216, 241] chunk 100 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 296 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 327 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 304 optimal weight: 1.9990 chunk 216 optimal weight: 0.5980 chunk 241 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 3 GLN A 79 ASN A 762 GLN B 79 ASN C 762 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.109629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.071517 restraints weight = 55470.087| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.86 r_work: 0.2827 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 27484 Z= 0.111 Angle : 0.576 18.281 37519 Z= 0.278 Chirality : 0.045 0.602 4351 Planarity : 0.003 0.039 4739 Dihedral : 6.579 59.033 4653 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.93 % Allowed : 15.42 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 3279 helix: 2.04 (0.20), residues: 717 sheet: 0.35 (0.18), residues: 799 loop : -0.64 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1107 TYR 0.017 0.001 TYR C1067 PHE 0.020 0.001 PHE C 823 TRP 0.023 0.001 TRP D 106 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (27392) covalent geometry : angle 0.53285 / 0.27 (37285) SS BOND : bond 0.00333 / 0.16 ( 41) SS BOND : angle 1.43251 / 1.05 ( 82) hydrogen bonds : bond 0.03500 / 2.32 ( 1086) hydrogen bonds : angle 5.15133 / 3.58 ( 2925) link_BETA1-4 : bond 0.00306 / 0.18 ( 15) link_BETA1-4 : angle 1.25591 / 0.79 ( 45) link_NAG-ASN : bond 0.00535 / 0.33 ( 35) link_NAG-ASN : angle 3.92694 / 2.67 ( 105) link_NAG-THR : bond 0.00717 / 0.38 ( 1) link_NAG-THR : angle 3.00606 / 1.58 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 244 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 51 ILE cc_start: 0.8145 (pt) cc_final: 0.7730 (mt) REVERT: D 55 ASP cc_start: 0.8999 (t0) cc_final: 0.8491 (t0) REVERT: D 56 ASP cc_start: 0.9321 (t0) cc_final: 0.8998 (m-30) REVERT: A 265 TYR cc_start: 0.8509 (m-80) cc_final: 0.7974 (m-80) REVERT: A 378 LYS cc_start: 0.8449 (ptmm) cc_final: 0.8210 (ptmt) REVERT: A 421 TYR cc_start: 0.8679 (m-10) cc_final: 0.8447 (m-10) REVERT: A 425 LEU cc_start: 0.9402 (tp) cc_final: 0.9096 (tp) REVERT: A 627 ASP cc_start: 0.8900 (t0) cc_final: 0.8444 (t0) REVERT: A 1010 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7587 (mp10) REVERT: B 113 GLN cc_start: 0.8088 (mp10) cc_final: 0.7482 (mm-40) REVERT: B 429 PHE cc_start: 0.9022 (t80) cc_final: 0.8430 (t80) REVERT: B 436 TRP cc_start: 0.8754 (p90) cc_final: 0.8431 (p90) REVERT: B 574 ASP cc_start: 0.8684 (t70) cc_final: 0.8386 (t0) REVERT: B 868 GLU cc_start: 0.8367 (tp30) cc_final: 0.8042 (tm-30) REVERT: B 985 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7346 (m-30) REVERT: C 364 ASP cc_start: 0.9042 (t0) cc_final: 0.8809 (t0) REVERT: C 636 TYR cc_start: 0.8237 (t80) cc_final: 0.8008 (t80) outliers start: 85 outliers final: 55 residues processed: 308 average time/residue: 0.1495 time to fit residues: 76.4374 Evaluate side-chains 281 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [225, 297, 245, 234, 135, 38, 328, 14, 198, 292, 170] chunk 225 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 234 optimal weight: 0.9980 chunk 135 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 chunk 14 optimal weight: 30.0000 chunk 198 optimal weight: 4.9990 chunk 292 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN A 762 GLN B 79 ASN B 235 GLN B 784 GLN C 907 ASN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.107117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.068940 restraints weight = 56144.468| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.85 r_work: 0.2776 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 27484 Z= 0.229 Angle : 0.630 18.978 37519 Z= 0.306 Chirality : 0.047 0.607 4351 Planarity : 0.004 0.040 4739 Dihedral : 6.676 59.073 4653 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.37 % Allowed : 15.15 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.15), residues: 3279 helix: 1.86 (0.20), residues: 720 sheet: 0.27 (0.18), residues: 813 loop : -0.69 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1107 TYR 0.022 0.001 TYR C 904 PHE 0.022 0.001 PHE B 392 TRP 0.039 0.002 TRP D 106 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (27392) covalent geometry : angle 0.58721 / 0.30 (37285) SS BOND : bond 0.00427 / 0.22 ( 41) SS BOND : angle 1.75196 / 1.23 ( 82) hydrogen bonds : bond 0.03914 / 2.59 ( 1086) hydrogen bonds : angle 5.22788 / 3.63 ( 2925) link_BETA1-4 : bond 0.00218 / 0.14 ( 15) link_BETA1-4 : angle 1.31456 / 0.85 ( 45) link_NAG-ASN : bond 0.00529 / 0.31 ( 35) link_NAG-ASN : angle 4.02802 / 2.75 ( 105) link_NAG-THR : bond 0.00984 / 0.52 ( 1) link_NAG-THR : angle 2.92294 / 1.56 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 217 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 CYS cc_start: 0.4930 (t) cc_final: 0.4394 (m) REVERT: A 265 TYR cc_start: 0.8524 (m-80) cc_final: 0.7729 (m-80) REVERT: A 339 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.7966 (t70) REVERT: A 378 LYS cc_start: 0.8440 (ptmm) cc_final: 0.8190 (ptmt) REVERT: A 421 TYR cc_start: 0.8634 (m-10) cc_final: 0.8366 (m-10) REVERT: A 661 GLU cc_start: 0.8259 (tp30) cc_final: 0.8003 (tp30) REVERT: A 1010 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: B 429 PHE cc_start: 0.9095 (t80) cc_final: 0.8503 (t80) REVERT: B 436 TRP cc_start: 0.8809 (p90) cc_final: 0.8544 (p90) REVERT: B 574 ASP cc_start: 0.8837 (t70) cc_final: 0.8379 (t0) REVERT: B 619 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: B 868 GLU cc_start: 0.8503 (tp30) cc_final: 0.8170 (tm-30) REVERT: B 990 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8174 (mp0) REVERT: C 364 ASP cc_start: 0.9084 (t0) cc_final: 0.8857 (t0) REVERT: C 636 TYR cc_start: 0.8253 (t80) cc_final: 0.8020 (t80) outliers start: 98 outliers final: 80 residues processed: 301 average time/residue: 0.1502 time to fit residues: 75.1518 Evaluate side-chains 290 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 207 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [287, 233, 148, 53, 140, 325, 49, 37, 129, 66, 224] chunk 287 optimal weight: 1.9990 chunk 233 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 325 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 129 optimal weight: 0.0770 chunk 66 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 3 GLN A 79 ASN A 762 GLN B 79 ASN B 235 GLN C 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.109074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.072334 restraints weight = 55554.189| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.97 r_work: 0.2818 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27484 Z= 0.120 Angle : 0.585 18.182 37519 Z= 0.284 Chirality : 0.045 0.590 4351 Planarity : 0.003 0.040 4739 Dihedral : 6.518 57.557 4652 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.79 % Allowed : 16.35 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 3279 helix: 2.25 (0.20), residues: 693 sheet: 0.32 (0.18), residues: 803 loop : -0.56 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 45 TYR 0.017 0.001 TYR C1067 PHE 0.018 0.001 PHE B 392 TRP 0.062 0.002 TRP D 106 HIS 0.003 0.000 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (27392) covalent geometry : angle 0.54406 / 0.27 (37285) SS BOND : bond 0.00315 / 0.16 ( 41) SS BOND : angle 1.56253 / 1.01 ( 82) hydrogen bonds : bond 0.03462 / 2.29 ( 1086) hydrogen bonds : angle 5.07057 / 3.53 ( 2925) link_BETA1-4 : bond 0.00302 / 0.18 ( 15) link_BETA1-4 : angle 1.22015 / 0.76 ( 45) link_NAG-ASN : bond 0.00521 / 0.32 ( 35) link_NAG-ASN : angle 3.80854 / 2.58 ( 105) link_NAG-THR : bond 0.00560 / 0.29 ( 1) link_NAG-THR : angle 2.77138 / 1.46 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 227 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ARG cc_start: 0.6264 (OUTLIER) cc_final: 0.5394 (tpp80) REVERT: D 56 ASP cc_start: 0.9387 (t0) cc_final: 0.9059 (m-30) REVERT: E 45 ARG cc_start: 0.7982 (mmm-85) cc_final: 0.7537 (tpt170) REVERT: A 265 TYR cc_start: 0.8532 (m-80) cc_final: 0.8175 (m-80) REVERT: A 378 LYS cc_start: 0.8434 (ptmm) cc_final: 0.8166 (ptmt) REVERT: A 421 TYR cc_start: 0.8662 (m-10) cc_final: 0.8387 (m-10) REVERT: A 661 GLU cc_start: 0.8201 (tp30) cc_final: 0.7939 (tp30) REVERT: A 1010 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7548 (mp10) REVERT: B 52 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8040 (tm-30) REVERT: B 113 GLN cc_start: 0.8108 (mp10) cc_final: 0.7534 (mm110) REVERT: B 429 PHE cc_start: 0.9092 (t80) cc_final: 0.8421 (t80) REVERT: B 436 TRP cc_start: 0.8759 (p90) cc_final: 0.8484 (p90) REVERT: B 574 ASP cc_start: 0.8765 (t70) cc_final: 0.8399 (t0) REVERT: B 868 GLU cc_start: 0.8379 (tp30) cc_final: 0.8034 (tm-30) REVERT: C 364 ASP cc_start: 0.9072 (t0) cc_final: 0.8846 (t0) REVERT: C 636 TYR cc_start: 0.8258 (t80) cc_final: 0.8040 (t80) outliers start: 81 outliers final: 65 residues processed: 288 average time/residue: 0.1494 time to fit residues: 71.0673 Evaluate side-chains 284 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 217 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [102, 265, 326, 110, 48, 96, 119, 124, 63, 304, 270] chunk 102 optimal weight: 0.9980 chunk 265 optimal weight: 10.0000 chunk 326 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 96 optimal weight: 0.2980 chunk 119 optimal weight: 0.5980 chunk 124 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 304 optimal weight: 0.0010 chunk 270 optimal weight: 10.0000 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN A 613 GLN A 762 GLN B 79 ASN B 235 GLN B 762 GLN C 762 GLN C 907 ASN C1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.109552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.072996 restraints weight = 55909.591| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.04 r_work: 0.2828 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27484 Z= 0.111 Angle : 0.577 18.073 37519 Z= 0.280 Chirality : 0.045 0.590 4351 Planarity : 0.003 0.039 4739 Dihedral : 6.423 57.386 4652 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.65 % Allowed : 16.66 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 3279 helix: 2.30 (0.20), residues: 693 sheet: 0.40 (0.18), residues: 788 loop : -0.52 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 45 TYR 0.017 0.001 TYR C1067 PHE 0.016 0.001 PHE B 392 TRP 0.048 0.001 TRP D 106 HIS 0.003 0.000 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (27392) covalent geometry : angle 0.53756 / 0.27 (37285) SS BOND : bond 0.00308 / 0.16 ( 41) SS BOND : angle 1.41630 / 0.93 ( 82) hydrogen bonds : bond 0.03346 / 2.21 ( 1086) hydrogen bonds : angle 5.00219 / 3.48 ( 2925) link_BETA1-4 : bond 0.00272 / 0.16 ( 15) link_BETA1-4 : angle 1.24439 / 0.79 ( 45) link_NAG-ASN : bond 0.00525 / 0.32 ( 35) link_NAG-ASN : angle 3.72544 / 2.53 ( 105) link_NAG-THR : bond 0.00638 / 0.34 ( 1) link_NAG-THR : angle 2.61345 / 1.38 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 230 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ARG cc_start: 0.6221 (OUTLIER) cc_final: 0.5876 (tpp80) REVERT: E 45 ARG cc_start: 0.7969 (mmm-85) cc_final: 0.7566 (tpt170) REVERT: A 265 TYR cc_start: 0.8524 (m-80) cc_final: 0.8237 (m-80) REVERT: A 378 LYS cc_start: 0.8432 (ptmm) cc_final: 0.8155 (ptmt) REVERT: A 421 TYR cc_start: 0.8672 (m-10) cc_final: 0.8390 (m-10) REVERT: A 1010 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: B 52 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8076 (tm-30) REVERT: B 113 GLN cc_start: 0.8131 (mp10) cc_final: 0.7579 (mm110) REVERT: B 429 PHE cc_start: 0.9135 (t80) cc_final: 0.8494 (t80) REVERT: B 436 TRP cc_start: 0.8762 (p90) cc_final: 0.8527 (p90) REVERT: B 574 ASP cc_start: 0.8812 (t70) cc_final: 0.8396 (t0) REVERT: B 868 GLU cc_start: 0.8407 (tp30) cc_final: 0.8060 (tm-30) REVERT: C 364 ASP cc_start: 0.9082 (t0) cc_final: 0.8853 (t0) REVERT: C 407 VAL cc_start: 0.8851 (p) cc_final: 0.8634 (t) REVERT: C 636 TYR cc_start: 0.8269 (t80) cc_final: 0.8034 (t80) outliers start: 77 outliers final: 67 residues processed: 289 average time/residue: 0.1461 time to fit residues: 70.0991 Evaluate side-chains 288 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 219 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [138, 137, 91, 303, 195, 45, 107, 84, 85, 236, 48] chunk 138 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 303 optimal weight: 0.7980 chunk 195 optimal weight: 0.7980 chunk 45 optimal weight: 0.0050 chunk 107 optimal weight: 3.9990 chunk 84 optimal weight: 0.0970 chunk 85 optimal weight: 0.9990 chunk 236 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 3 GLN A 762 GLN B 79 ASN B 762 GLN C 762 GLN C 907 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.110246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.073110 restraints weight = 55776.479| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.02 r_work: 0.2836 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 27484 Z= 0.108 Angle : 0.570 18.009 37519 Z= 0.278 Chirality : 0.045 0.586 4351 Planarity : 0.003 0.040 4739 Dihedral : 6.351 57.472 4652 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.62 % Allowed : 16.80 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 3279 helix: 2.32 (0.20), residues: 693 sheet: 0.46 (0.18), residues: 788 loop : -0.49 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 45 TYR 0.019 0.001 TYR E 49 PHE 0.016 0.001 PHE A 371 TRP 0.028 0.001 TRP D 106 HIS 0.003 0.000 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (27392) covalent geometry : angle 0.53290 / 0.27 (37285) SS BOND : bond 0.00286 / 0.15 ( 41) SS BOND : angle 1.32150 / 0.89 ( 82) hydrogen bonds : bond 0.03284 / 2.18 ( 1086) hydrogen bonds : angle 4.94820 / 3.45 ( 2925) link_BETA1-4 : bond 0.00314 / 0.18 ( 15) link_BETA1-4 : angle 1.21898 / 0.77 ( 45) link_NAG-ASN : bond 0.00532 / 0.32 ( 35) link_NAG-ASN : angle 3.64616 / 2.46 ( 105) link_NAG-THR : bond 0.00604 / 0.32 ( 1) link_NAG-THR : angle 2.52501 / 1.33 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 235 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ARG cc_start: 0.6241 (OUTLIER) cc_final: 0.5873 (tpp80) REVERT: E 35 TRP cc_start: 0.7885 (m100) cc_final: 0.7398 (m100) REVERT: E 45 ARG cc_start: 0.7962 (mmm-85) cc_final: 0.7573 (tpt170) REVERT: A 265 TYR cc_start: 0.8521 (m-80) cc_final: 0.8238 (m-80) REVERT: A 378 LYS cc_start: 0.8448 (ptmm) cc_final: 0.8245 (ptmt) REVERT: A 421 TYR cc_start: 0.8690 (m-10) cc_final: 0.8406 (m-10) REVERT: A 661 GLU cc_start: 0.8067 (tp30) cc_final: 0.7817 (tp30) REVERT: A 1010 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7612 (mp10) REVERT: B 52 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8075 (tm-30) REVERT: B 113 GLN cc_start: 0.8042 (mp10) cc_final: 0.7512 (mm110) REVERT: B 429 PHE cc_start: 0.9143 (t80) cc_final: 0.8473 (t80) REVERT: B 436 TRP cc_start: 0.8741 (p90) cc_final: 0.8509 (p90) REVERT: B 574 ASP cc_start: 0.8788 (t70) cc_final: 0.8377 (t0) REVERT: B 868 GLU cc_start: 0.8417 (tp30) cc_final: 0.8063 (tm-30) REVERT: B 869 MET cc_start: 0.9158 (mtm) cc_final: 0.8924 (mtp) REVERT: C 364 ASP cc_start: 0.9071 (t0) cc_final: 0.8839 (t0) REVERT: C 407 VAL cc_start: 0.8843 (p) cc_final: 0.8617 (t) REVERT: C 636 TYR cc_start: 0.8261 (t80) cc_final: 0.8028 (t80) outliers start: 76 outliers final: 66 residues processed: 294 average time/residue: 0.1527 time to fit residues: 74.6851 Evaluate side-chains 294 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 226 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [19, 124, 159, 32, 315, 318, 246, 143, 102, 150, 26] chunk 19 optimal weight: 40.0000 chunk 124 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 315 optimal weight: 0.8980 chunk 318 optimal weight: 1.9990 chunk 246 optimal weight: 0.5980 chunk 143 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 762 GLN C 907 ASN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.111127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.073044 restraints weight = 56191.755| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.99 r_work: 0.2931 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27484 Z= 0.167 Angle : 0.589 18.018 37519 Z= 0.286 Chirality : 0.046 0.589 4351 Planarity : 0.004 0.039 4739 Dihedral : 6.366 58.049 4650 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.51 % Allowed : 17.11 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 3279 helix: 2.27 (0.20), residues: 693 sheet: 0.46 (0.18), residues: 788 loop : -0.51 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 45 TYR 0.030 0.001 TYR B 423 PHE 0.015 0.001 PHE B 392 TRP 0.056 0.002 TRP D 106 HIS 0.006 0.001 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (27392) covalent geometry : angle 0.55202 / 0.28 (37285) SS BOND : bond 0.00325 / 0.17 ( 41) SS BOND : angle 1.44634 / 0.98 ( 82) hydrogen bonds : bond 0.03431 / 2.27 ( 1086) hydrogen bonds : angle 4.98237 / 3.47 ( 2925) link_BETA1-4 : bond 0.00249 / 0.14 ( 15) link_BETA1-4 : angle 1.22776 / 0.78 ( 45) link_NAG-ASN : bond 0.00509 / 0.31 ( 35) link_NAG-ASN : angle 3.67552 / 2.49 ( 105) link_NAG-THR : bond 0.00741 / 0.39 ( 1) link_NAG-THR : angle 2.56836 / 1.36 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 226 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 ARG cc_start: 0.8013 (mmm-85) cc_final: 0.7592 (tpt170) REVERT: A 265 TYR cc_start: 0.8527 (m-80) cc_final: 0.8154 (m-80) REVERT: A 378 LYS cc_start: 0.8327 (ptmm) cc_final: 0.7970 (ptmt) REVERT: A 421 TYR cc_start: 0.8826 (m-10) cc_final: 0.8490 (m-10) REVERT: A 1010 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7697 (mp10) REVERT: B 52 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8179 (tm-30) REVERT: B 113 GLN cc_start: 0.8057 (mp10) cc_final: 0.7450 (mm110) REVERT: B 429 PHE cc_start: 0.9174 (t80) cc_final: 0.8482 (t80) REVERT: B 436 TRP cc_start: 0.8709 (p90) cc_final: 0.8410 (p90) REVERT: B 574 ASP cc_start: 0.8807 (t70) cc_final: 0.8282 (t0) REVERT: B 868 GLU cc_start: 0.8494 (tp30) cc_final: 0.8112 (tp30) REVERT: C 364 ASP cc_start: 0.9186 (t0) cc_final: 0.8938 (t0) REVERT: C 407 VAL cc_start: 0.8750 (p) cc_final: 0.8501 (t) REVERT: C 636 TYR cc_start: 0.8353 (t80) cc_final: 0.8070 (t80) outliers start: 73 outliers final: 71 residues processed: 282 average time/residue: 0.1501 time to fit residues: 69.8887 Evaluate side-chains 292 residues out of total 2905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 220 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [322, 286, 80, 117, 186, 116, 298, 309, 114, 250, 208] chunk 322 optimal weight: 0.8980 chunk 286 optimal weight: 0.0570 chunk 80 optimal weight: 0.0670 chunk 117 optimal weight: 3.9990 chunk 186 optimal weight: 0.0970 chunk 116 optimal weight: 0.7980 chunk 298 optimal weight: 0.5980 chunk 309 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 250 optimal weight: 0.6980 chunk 208 optimal weight: 4.9990 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 3 GLN A 762 GLN C 762 GLN C 907 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.112704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.074856 restraints weight = 55500.164| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.99 r_work: 0.2980 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 27484 Z= 0.102 Angle : 0.571 17.923 37519 Z= 0.278 Chirality : 0.045 0.581 4351 Planarity : 0.003 0.040 4739 Dihedral : 6.314 57.459 4650 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.44 % Allowed : 17.07 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.15), residues: 3279 helix: 2.34 (0.20), residues: 693 sheet: 0.49 (0.18), residues: 788 loop : -0.47 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 45 TYR 0.022 0.001 TYR B 423 PHE 0.017 0.001 PHE A 371 TRP 0.071 0.002 TRP D 106 HIS 0.005 0.000 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (27392) covalent geometry : angle 0.53581 / 0.27 (37285) SS BOND : bond 0.00275 / 0.14 ( 41) SS BOND : angle 1.21561 / 0.82 ( 82) hydrogen bonds : bond 0.03192 / 2.11 ( 1086) hydrogen bonds : angle 4.89462 / 3.42 ( 2925) link_BETA1-4 : bond 0.00325 / 0.19 ( 15) link_BETA1-4 : angle 1.21239 / 0.75 ( 45) link_NAG-ASN : bond 0.00558 / 0.34 ( 35) link_NAG-ASN : angle 3.55202 / 2.40 ( 105) link_NAG-THR : bond 0.00533 / 0.28 ( 1) link_NAG-THR : angle 2.41173 / 1.27 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5785.76 seconds wall clock time: 100 minutes 5.85 seconds (6005.85 seconds total)