Starting phenix.real_space_refine on Sun Jul 5 18:35:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8elj_28228/07_2026/8elj_28228.cif Found real_map, /net/cci-nas-00/data/ceres_data/8elj_28228/07_2026/8elj_28228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8elj_28228/07_2026/8elj_28228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8elj_28228/07_2026/8elj_28228.map" model { file = "/net/cci-nas-00/data/ceres_data/8elj_28228/07_2026/8elj_28228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8elj_28228/07_2026/8elj_28228.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8elj_28228/07_2026/8elj_28228.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8elj_28228/07_2026/8elj_28228.cif" } resolution = 3.6 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= 0.011 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 132 5.16 5 C 18732 2.51 5 N 4827 2.21 5 O 5772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29463 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "S" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "T" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "U" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "V" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "W" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "X" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.30, per 1000 atoms: 0.18 Number of scatterers: 29463 At special positions: 0 Unit cell: (136.8, 139.365, 202.635, 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 132 16.00 O 5772 8.00 N 4827 7.00 C 18732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.08 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.07 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.06 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.06 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.06 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.07 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.08 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.07 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.07 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.06 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.05 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.08 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.08 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.05 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.07 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.07 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.07 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.05 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.08 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 90 " distance=2.04 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 90 " distance=2.04 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 96 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 90 " distance=2.04 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=7, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.1 seconds 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6852 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 60 sheets defined 22.1% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.812A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.756A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 759 removed outlier: 7.022A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.529A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.586A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 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: 4.059A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 982 Processing helix chain 'A' and resid 985 through 1031 removed outlier: 4.792A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.810A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.754A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 759 removed outlier: 7.021A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.529A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.548A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.060A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1031 removed outlier: 4.793A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.811A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.755A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 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 759 removed outlier: 7.023A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.529A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.523A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.059A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 982 Processing helix chain 'C' and resid 985 through 1031 removed outlier: 4.792A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.948A pdb=" N TYR S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'T' and resid 81 through 85 Processing helix chain 'U' and resid 28 through 32 removed outlier: 3.949A pdb=" N TYR U 32 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 65 Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'V' and resid 81 through 85 Processing helix chain 'W' and resid 28 through 32 removed outlier: 3.948A pdb=" N TYR W 32 " --> pdb=" O PHE W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 62 through 65 Processing helix chain 'W' and resid 87 through 91 Processing helix chain 'X' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.245A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.657A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.380A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.715A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.491A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.290A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.375A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.758A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.237A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.491A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.315A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.033A 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: 7.037A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.315A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.033A 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: 7.037A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.541A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.239A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.380A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.716A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.482A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.292A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.373A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.758A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.238A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.477A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.538A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.248A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.381A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.715A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.478A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.290A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.757A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.238A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.538A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.656A pdb=" N PHE S 34 " --> pdb=" O TRP S 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TRP S 50 " --> pdb=" O PHE S 34 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP S 36 " --> pdb=" O MET S 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 10 through 11 Processing sheet with id=AF1, first strand: chain 'T' and resid 9 through 12 removed outlier: 6.568A pdb=" N VAL T 10 " --> pdb=" O THR T 108 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP T 37 " --> pdb=" O MET T 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 9 through 12 removed outlier: 6.568A pdb=" N VAL T 10 " --> pdb=" O THR T 108 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 18 through 23 Processing sheet with id=AF4, first strand: chain 'U' and resid 3 through 6 Processing sheet with id=AF5, first strand: chain 'U' and resid 10 through 11 removed outlier: 6.651A pdb=" N PHE U 34 " --> pdb=" O TRP U 50 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TRP U 50 " --> pdb=" O PHE U 34 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP U 36 " --> pdb=" O MET U 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 10 through 11 Processing sheet with id=AF7, first strand: chain 'V' and resid 9 through 12 removed outlier: 6.568A pdb=" N VAL V 10 " --> pdb=" O THR V 108 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP V 37 " --> pdb=" O MET V 49 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 9 through 12 removed outlier: 6.568A pdb=" N VAL V 10 " --> pdb=" O THR V 108 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 18 through 23 Processing sheet with id=AG1, first strand: chain 'W' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'W' and resid 10 through 11 removed outlier: 6.651A pdb=" N PHE W 34 " --> pdb=" O TRP W 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TRP W 50 " --> pdb=" O PHE W 34 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP W 36 " --> pdb=" O MET W 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 10 through 11 Processing sheet with id=AG4, first strand: chain 'X' and resid 9 through 12 removed outlier: 6.569A pdb=" N VAL X 10 " --> pdb=" O THR X 108 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP X 37 " --> pdb=" O MET X 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 9 through 12 removed outlier: 6.569A pdb=" N VAL X 10 " --> pdb=" O THR X 108 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 18 through 23 1216 hydrogen bonds defined for protein. 3204 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: 7.94 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4829 1.32 - 1.45: 9913 1.45 - 1.59: 15219 1.59 - 1.73: 0 1.73 - 1.86: 168 Bond restraints: 30129 Sorted by residual: bond pdb=" CE1 HIS C1048 " pdb=" NE2 HIS C1048 " ideal model delta sigma weight residual 1.321 1.368 -0.047 1.00e-02 1.00e+04 2.19e+01 bond pdb=" C THR C1027 " pdb=" O THR C1027 " ideal model delta sigma weight residual 1.237 1.181 0.055 1.19e-02 7.06e+03 2.16e+01 bond pdb=" CE1 HIS A1048 " pdb=" NE2 HIS A1048 " ideal model delta sigma weight residual 1.321 1.367 -0.046 1.00e-02 1.00e+04 2.11e+01 bond pdb=" CE1 HIS B1048 " pdb=" NE2 HIS B1048 " ideal model delta sigma weight residual 1.321 1.367 -0.046 1.00e-02 1.00e+04 2.08e+01 bond pdb=" C THR B1027 " pdb=" O THR B1027 " ideal model delta sigma weight residual 1.237 1.183 0.053 1.19e-02 7.06e+03 2.00e+01 ... (remaining 30124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 37899 3.19 - 6.39: 2859 6.39 - 9.58: 212 9.58 - 12.78: 25 12.78 - 15.97: 3 Bond angle restraints: 40998 Sorted by residual: angle pdb=" CA PHE B 486 " pdb=" CB PHE B 486 " pdb=" CG PHE B 486 " ideal model delta sigma weight residual 113.80 122.25 -8.45 1.00e+00 1.00e+00 7.15e+01 angle pdb=" CA PHE A 486 " pdb=" CB PHE A 486 " pdb=" CG PHE A 486 " ideal model delta sigma weight residual 113.80 122.22 -8.42 1.00e+00 1.00e+00 7.10e+01 angle pdb=" CA PHE C 486 " pdb=" CB PHE C 486 " pdb=" CG PHE C 486 " ideal model delta sigma weight residual 113.80 122.22 -8.42 1.00e+00 1.00e+00 7.09e+01 angle pdb=" N ILE B 909 " pdb=" CA ILE B 909 " pdb=" C ILE B 909 " ideal model delta sigma weight residual 112.43 105.51 6.92 9.20e-01 1.18e+00 5.66e+01 angle pdb=" N ILE C 909 " pdb=" CA ILE C 909 " pdb=" C ILE C 909 " ideal model delta sigma weight residual 112.43 105.52 6.91 9.20e-01 1.18e+00 5.64e+01 ... (remaining 40993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 16061 17.94 - 35.87: 1036 35.87 - 53.81: 190 53.81 - 71.74: 62 71.74 - 89.68: 39 Dihedral angle restraints: 17388 sinusoidal: 6693 harmonic: 10695 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.68 89.68 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.14 89.14 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.12 89.12 1 1.00e+01 1.00e-02 9.45e+01 ... (remaining 17385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 3009 0.105 - 0.209: 1350 0.209 - 0.314: 346 0.314 - 0.419: 65 0.419 - 0.523: 15 Chirality restraints: 4785 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.32e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.18e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.10e+01 ... (remaining 4782 not shown) Planarity restraints: 5247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " 0.231 2.00e-02 2.50e+03 1.94e-01 4.71e+02 pdb=" C7 NAG J 1 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " 0.160 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " -0.325 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.215 2.00e-02 2.50e+03 1.80e-01 4.06e+02 pdb=" C7 NAG E 1 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.300 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " 0.212 2.00e-02 2.50e+03 1.78e-01 3.97e+02 pdb=" C7 NAG O 1 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " 0.150 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " -0.296 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " -0.008 2.00e-02 2.50e+03 ... (remaining 5244 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.85: 10 1.85 - 2.61: 281 2.61 - 3.37: 36372 3.37 - 4.14: 73090 4.14 - 4.90: 124434 Nonbonded interactions: 234187 Sorted by model distance: nonbonded pdb=" O PHE A 486 " pdb=" OH TYR U 102 " model vdw 1.083 3.040 nonbonded pdb=" O PHE B 486 " pdb=" OH TYR S 102 " model vdw 1.104 3.040 nonbonded pdb=" O PHE C 486 " pdb=" OH TYR W 102 " model vdw 1.109 3.040 nonbonded pdb=" OG1 THR B 912 " pdb=" NE2 GLN B1106 " model vdw 1.809 3.120 nonbonded pdb=" CD1 ILE U 51 " pdb=" CB MET U 70 " model vdw 1.812 3.860 ... (remaining 234182 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'X' } 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 group one per residue 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: 13.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 26.730 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 0.012 0.463 30229 Z= 0.837 Angle : 1.803 15.969 41235 Z= 1.156 Chirality : 0.123 0.523 4785 Planarity : 0.012 0.194 5208 Dihedral : 13.379 87.812 10410 Min Nonbonded Distance : 1.083 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 1.03 % Allowed : 4.19 % Favored : 94.77 % Cbeta Deviations : 1.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.94 (0.13), residues: 3630 helix: -0.55 (0.17), residues: 666 sheet: -0.07 (0.15), residues: 969 loop : -0.89 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.003 ARG B1107 TYR 0.067 0.009 TYR W 102 PHE 0.055 0.010 PHE A 888 TRP 0.051 0.009 TRP S 50 HIS 0.019 0.005 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.01028 / 0.64 (30129) covalent geometry : angle 1.78315 / 1.15 (40998) SS BOND : bond 0.02681 / 1.63 ( 42) SS BOND : angle 2.82716 / 1.78 ( 84) hydrogen bonds : bond 0.21027 / 13.71 ( 1165) hydrogen bonds : angle 7.98400 / 5.52 ( 3204) Misc. bond : bond 0.35514 / 25.01 ( 7) link_BETA1-4 : bond 0.02230 / 1.37 ( 12) link_BETA1-4 : angle 4.43261 / 2.85 ( 36) link_NAG-ASN : bond 0.01407 / 0.88 ( 39) link_NAG-ASN : angle 4.40258 / 3.03 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 411 time to evaluate : 1.119 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: 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 110 LEU cc_start: 0.8160 (mp) cc_final: 0.7854 (mt) REVERT: A 242 LEU cc_start: 0.7676 (mt) cc_final: 0.7227 (mt) REVERT: A 394 ASN cc_start: 0.9154 (m-40) cc_final: 0.8859 (t0) REVERT: A 417 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8805 (mtpt) REVERT: A 979 ASP cc_start: 0.9057 (m-30) cc_final: 0.8640 (t0) REVERT: A 1092 GLU cc_start: 0.9409 (mt-10) cc_final: 0.9009 (pm20) REVERT: B 110 LEU cc_start: 0.8358 (mp) cc_final: 0.8001 (mt) REVERT: B 114 THR cc_start: 0.8889 (t) cc_final: 0.8675 (p) REVERT: B 276 LEU cc_start: 0.9303 (tp) cc_final: 0.9094 (tp) REVERT: B 390 LEU cc_start: 0.8529 (tp) cc_final: 0.8277 (mt) REVERT: B 394 ASN cc_start: 0.9125 (m-40) cc_final: 0.8823 (t0) REVERT: B 979 ASP cc_start: 0.9066 (m-30) cc_final: 0.8629 (t0) REVERT: B 1092 GLU cc_start: 0.9459 (mt-10) cc_final: 0.9168 (pm20) REVERT: C 110 LEU cc_start: 0.8067 (mp) cc_final: 0.7672 (mt) REVERT: C 390 LEU cc_start: 0.8542 (tp) cc_final: 0.8301 (mt) REVERT: C 394 ASN cc_start: 0.9110 (m-40) cc_final: 0.8902 (t0) REVERT: C 417 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8868 (mtpt) REVERT: C 979 ASP cc_start: 0.9114 (m-30) cc_final: 0.8668 (t70) REVERT: C 1092 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9139 (pm20) REVERT: S 89 ASP cc_start: 0.9538 (m-30) cc_final: 0.9254 (p0) REVERT: T 49 MET cc_start: 0.8273 (mmm) cc_final: 0.7920 (mmm) REVERT: U 54 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8914 (mp) REVERT: U 89 ASP cc_start: 0.9545 (m-30) cc_final: 0.9302 (p0) REVERT: V 49 MET cc_start: 0.8202 (mmm) cc_final: 0.7852 (mmm) REVERT: V 63 ARG cc_start: 0.7734 (ptt90) cc_final: 0.7497 (ptt180) REVERT: W 54 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8938 (mp) REVERT: W 89 ASP cc_start: 0.9519 (m-30) cc_final: 0.9281 (p0) REVERT: X 49 MET cc_start: 0.8180 (mmm) cc_final: 0.7803 (mmm) REVERT: X 63 ARG cc_start: 0.7658 (ptt90) cc_final: 0.6732 (ppt170) outliers start: 33 outliers final: 3 residues processed: 434 average time/residue: 0.2104 time to fit residues: 137.8519 Evaluate side-chains 184 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 179 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain W residue 54 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 388 ASN A 474 GLN B 321 GLN B 388 ASN B 474 GLN C 66 HIS C 207 HIS C 474 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 GLN ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 3 GLN ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 GLN ** U 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 41 HIS W 3 GLN ** W 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 GLN ** W 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.083786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053606 restraints weight = 125632.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.055592 restraints weight = 57705.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.056824 restraints weight = 36114.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.057601 restraints weight = 26917.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.058015 restraints weight = 22420.177| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 30229 Z= 0.174 Angle : 0.769 23.876 41235 Z= 0.388 Chirality : 0.048 0.320 4785 Planarity : 0.012 0.446 5208 Dihedral : 6.175 121.803 3967 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.40 % Favored : 97.52 % Rotamer: Outliers : 1.69 % Allowed : 8.36 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.20 (0.13), residues: 3630 helix: 1.22 (0.20), residues: 684 sheet: 0.08 (0.14), residues: 1050 loop : -0.74 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG C 328 TYR 0.046 0.002 TYR U 102 PHE 0.033 0.002 PHE B 486 TRP 0.027 0.002 TRP S 104 HIS 0.013 0.001 HIS U 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (30129) covalent geometry : angle 0.75376 / 0.38 (40998) SS BOND : bond 0.00201 / 0.12 ( 42) SS BOND : angle 1.32163 / 0.82 ( 84) hydrogen bonds : bond 0.06600 / 4.15 ( 1165) hydrogen bonds : angle 6.11921 / 4.18 ( 3204) Misc. bond : bond 0.00581 / 0.29 ( 7) link_BETA1-4 : bond 0.00551 / 0.34 ( 12) link_BETA1-4 : angle 1.63276 / 1.06 ( 36) link_NAG-ASN : bond 0.00492 / 0.30 ( 39) link_NAG-ASN : angle 2.69864 / 1.82 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 201 time to evaluate : 1.008 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7517 (tp) cc_final: 0.7111 (mp) REVERT: A 505 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8429 (t80) REVERT: B 276 LEU cc_start: 0.9377 (tp) cc_final: 0.9173 (tp) REVERT: B 334 ASN cc_start: 0.6668 (OUTLIER) cc_final: 0.6460 (p0) REVERT: B 823 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8391 (t80) REVERT: C 117 LEU cc_start: 0.7627 (tp) cc_final: 0.7173 (mt) REVERT: C 417 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8499 (mtpt) REVERT: C 505 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.8417 (t80) REVERT: C 900 MET cc_start: 0.8533 (mtp) cc_final: 0.8119 (mtm) REVERT: S 70 MET cc_start: 0.6333 (mpp) cc_final: 0.4720 (mmt) REVERT: S 98 ARG cc_start: 0.6502 (tmm-80) cc_final: 0.5827 (tmm160) REVERT: T 38 TYR cc_start: 0.6414 (m-80) cc_final: 0.5997 (m-80) REVERT: U 70 MET cc_start: 0.5517 (mtt) cc_final: 0.4944 (mmt) REVERT: U 101 THR cc_start: 0.7390 (OUTLIER) cc_final: 0.7173 (m) REVERT: V 38 TYR cc_start: 0.6529 (m-80) cc_final: 0.6310 (m-80) REVERT: W 101 THR cc_start: 0.7123 (OUTLIER) cc_final: 0.6872 (m) REVERT: X 38 TYR cc_start: 0.6478 (m-80) cc_final: 0.6134 (m-80) outliers start: 54 outliers final: 16 residues processed: 248 average time/residue: 0.2133 time to fit residues: 79.2637 Evaluate side-chains 146 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain U residue 101 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain W residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 306 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 169 optimal weight: 0.0040 chunk 175 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 94 optimal weight: 0.1980 chunk 39 optimal weight: 0.2980 chunk 235 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 360 ASN C 388 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN ** S 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN ** U 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 52 ASN ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 41 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.082542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.052582 restraints weight = 126119.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.054535 restraints weight = 57403.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.055758 restraints weight = 35849.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.056528 restraints weight = 26730.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.056948 restraints weight = 22223.673| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 30229 Z= 0.136 Angle : 0.651 24.055 41235 Z= 0.330 Chirality : 0.045 0.280 4785 Planarity : 0.011 0.411 5208 Dihedral : 5.857 148.584 3960 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.11 % Rotamer: Outliers : 1.56 % Allowed : 8.95 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.12 (0.14), residues: 3630 helix: 1.91 (0.21), residues: 648 sheet: 0.24 (0.15), residues: 1014 loop : -0.61 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 328 TYR 0.040 0.001 TYR S 102 PHE 0.025 0.001 PHE C 486 TRP 0.044 0.002 TRP S 104 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (30129) covalent geometry : angle 0.64103 / 0.33 (40998) SS BOND : bond 0.00136 / 0.09 ( 42) SS BOND : angle 1.09496 / 0.68 ( 84) hydrogen bonds : bond 0.05775 / 3.62 ( 1165) hydrogen bonds : angle 5.67806 / 3.87 ( 3204) Misc. bond : bond 0.00605 / 0.39 ( 7) link_BETA1-4 : bond 0.00387 / 0.22 ( 12) link_BETA1-4 : angle 1.41562 / 0.93 ( 36) link_NAG-ASN : bond 0.00414 / 0.24 ( 39) link_NAG-ASN : angle 2.01141 / 1.39 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 1.193 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: 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 239 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6179 (tp40) REVERT: A 505 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.8497 (t80) REVERT: C 117 LEU cc_start: 0.7708 (tp) cc_final: 0.7268 (mp) REVERT: C 239 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.5984 (tp40) REVERT: C 505 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.8505 (t80) REVERT: S 3 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8182 (tm-30) REVERT: S 70 MET cc_start: 0.6165 (mpp) cc_final: 0.4410 (mmt) REVERT: U 70 MET cc_start: 0.5482 (mtt) cc_final: 0.4503 (mmt) REVERT: X 63 ARG cc_start: 0.8406 (ptt90) cc_final: 0.7428 (ptt180) outliers start: 50 outliers final: 20 residues processed: 185 average time/residue: 0.2180 time to fit residues: 62.0000 Evaluate side-chains 131 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 150 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 338 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 267 optimal weight: 0.7980 chunk 302 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B 207 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.080779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.050847 restraints weight = 127466.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.052553 restraints weight = 61895.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.053629 restraints weight = 39836.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.054286 restraints weight = 30226.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.054641 restraints weight = 25476.037| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 30229 Z= 0.183 Angle : 0.659 22.792 41235 Z= 0.336 Chirality : 0.045 0.226 4785 Planarity : 0.009 0.414 5208 Dihedral : 5.557 148.409 3960 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 1.78 % Allowed : 9.83 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3630 helix: 1.89 (0.21), residues: 666 sheet: 0.12 (0.15), residues: 1041 loop : -0.75 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG W 72 TYR 0.037 0.002 TYR U 102 PHE 0.029 0.002 PHE A 486 TRP 0.052 0.003 TRP S 104 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (30129) covalent geometry : angle 0.65102 / 0.33 (40998) SS BOND : bond 0.00754 / 0.43 ( 42) SS BOND : angle 1.14761 / 0.71 ( 84) hydrogen bonds : bond 0.05799 / 3.65 ( 1165) hydrogen bonds : angle 5.56417 / 3.80 ( 3204) Misc. bond : bond 0.00760 / 0.57 ( 7) link_BETA1-4 : bond 0.00182 / 0.12 ( 12) link_BETA1-4 : angle 1.34223 / 0.87 ( 36) link_NAG-ASN : bond 0.00383 / 0.24 ( 39) link_NAG-ASN : angle 1.76846 / 1.22 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 127 time to evaluate : 1.232 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: 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 505 TYR cc_start: 0.8840 (OUTLIER) cc_final: 0.8540 (t80) REVERT: A 902 MET cc_start: 0.9203 (tpp) cc_final: 0.8941 (tpt) REVERT: B 117 LEU cc_start: 0.7709 (tp) cc_final: 0.7424 (mp) REVERT: B 403 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8097 (ttm-80) REVERT: C 455 LEU cc_start: 0.9261 (tp) cc_final: 0.9054 (tp) REVERT: C 505 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8545 (t80) REVERT: S 70 MET cc_start: 0.5703 (mpp) cc_final: 0.5020 (mmt) REVERT: V 49 MET cc_start: 0.6397 (ptt) cc_final: 0.6139 (ptt) REVERT: W 70 MET cc_start: 0.5834 (mmt) cc_final: 0.5035 (mmm) outliers start: 57 outliers final: 32 residues processed: 181 average time/residue: 0.2272 time to fit residues: 62.8317 Evaluate side-chains 142 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 22 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 296 optimal weight: 0.0570 chunk 40 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 57 optimal weight: 5.9990 overall best weight: 1.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100 HIS ** U 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 100 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.080874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.050959 restraints weight = 127544.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.052687 restraints weight = 61836.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.053777 restraints weight = 39664.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.054439 restraints weight = 30010.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.054868 restraints weight = 25229.378| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 30229 Z= 0.136 Angle : 0.598 22.598 41235 Z= 0.304 Chirality : 0.045 0.206 4785 Planarity : 0.010 0.434 5208 Dihedral : 5.571 157.164 3960 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.25 % Favored : 96.72 % Rotamer: Outliers : 1.91 % Allowed : 10.23 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3630 helix: 2.11 (0.21), residues: 666 sheet: 0.10 (0.15), residues: 1047 loop : -0.77 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG U 72 TYR 0.033 0.001 TYR W 102 PHE 0.010 0.001 PHE C 543 TRP 0.048 0.002 TRP U 104 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (30129) covalent geometry : angle 0.59004 / 0.30 (40998) SS BOND : bond 0.00140 / 0.10 ( 42) SS BOND : angle 1.08408 / 0.65 ( 84) hydrogen bonds : bond 0.05226 / 3.28 ( 1165) hydrogen bonds : angle 5.30446 / 3.63 ( 3204) Misc. bond : bond 0.00381 / 0.25 ( 7) link_BETA1-4 : bond 0.00448 / 0.26 ( 12) link_BETA1-4 : angle 1.28043 / 0.87 ( 36) link_NAG-ASN : bond 0.00335 / 0.19 ( 39) link_NAG-ASN : angle 1.59732 / 1.12 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 111 time to evaluate : 1.190 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: 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 505 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.8563 (t80) REVERT: B 117 LEU cc_start: 0.7736 (tp) cc_final: 0.7423 (mp) REVERT: B 403 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8023 (ttm-80) REVERT: C 239 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.6914 (tp40) REVERT: C 403 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7959 (ttm-80) REVERT: C 505 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8396 (t80) REVERT: S 19 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7736 (tptp) REVERT: S 70 MET cc_start: 0.6361 (mpp) cc_final: 0.5590 (mmt) REVERT: V 63 ARG cc_start: 0.7956 (ptt180) cc_final: 0.7517 (ptm160) outliers start: 61 outliers final: 31 residues processed: 170 average time/residue: 0.2239 time to fit residues: 59.2654 Evaluate side-chains 143 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 102 TYR Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain W residue 102 TYR Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 27 optimal weight: 4.9990 chunk 302 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 254 optimal weight: 9.9990 chunk 168 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.079949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.049938 restraints weight = 127239.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.051629 restraints weight = 62331.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.052718 restraints weight = 40315.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.053395 restraints weight = 30600.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.053798 restraints weight = 25768.394| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 30229 Z= 0.160 Angle : 0.599 20.769 41235 Z= 0.306 Chirality : 0.044 0.209 4785 Planarity : 0.009 0.356 5208 Dihedral : 5.658 167.155 3960 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.12 % Rotamer: Outliers : 1.88 % Allowed : 10.67 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3630 helix: 2.12 (0.21), residues: 669 sheet: 0.09 (0.15), residues: 1044 loop : -0.83 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG U 72 TYR 0.033 0.001 TYR W 102 PHE 0.011 0.001 PHE C 543 TRP 0.043 0.002 TRP W 104 HIS 0.022 0.001 HIS W 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (30129) covalent geometry : angle 0.59216 / 0.30 (40998) SS BOND : bond 0.00268 / 0.16 ( 42) SS BOND : angle 1.09295 / 0.65 ( 84) hydrogen bonds : bond 0.05294 / 3.33 ( 1165) hydrogen bonds : angle 5.25718 / 3.60 ( 3204) Misc. bond : bond 0.00654 / 0.48 ( 7) link_BETA1-4 : bond 0.00211 / 0.12 ( 12) link_BETA1-4 : angle 1.24385 / 0.82 ( 36) link_NAG-ASN : bond 0.00339 / 0.20 ( 39) link_NAG-ASN : angle 1.56671 / 1.08 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 114 time to evaluate : 1.177 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8537 (t80) REVERT: B 117 LEU cc_start: 0.7849 (tp) cc_final: 0.7510 (mp) REVERT: B 403 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8098 (ttm-80) REVERT: C 403 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7943 (ttm-80) REVERT: C 505 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8367 (t80) REVERT: S 70 MET cc_start: 0.6208 (mpp) cc_final: 0.5394 (mmt) REVERT: T 63 ARG cc_start: 0.7717 (ptm160) cc_final: 0.7393 (ptm160) REVERT: V 63 ARG cc_start: 0.7899 (ptt180) cc_final: 0.7158 (ptm160) outliers start: 60 outliers final: 34 residues processed: 171 average time/residue: 0.2127 time to fit residues: 57.2263 Evaluate side-chains 144 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 241 optimal weight: 1.9990 chunk 328 optimal weight: 7.9990 chunk 184 optimal weight: 0.7980 chunk 318 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 365 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 274 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 262 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100 HIS ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.080233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.050612 restraints weight = 127603.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.052336 restraints weight = 61895.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.053437 restraints weight = 39693.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.054104 restraints weight = 29993.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.054464 restraints weight = 25196.005| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30229 Z= 0.120 Angle : 0.566 19.769 41235 Z= 0.290 Chirality : 0.044 0.193 4785 Planarity : 0.009 0.432 5208 Dihedral : 5.791 165.331 3960 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.25 % Allowed : 11.67 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3630 helix: 2.26 (0.21), residues: 669 sheet: 0.10 (0.15), residues: 1041 loop : -0.81 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.001 ARG U 72 TYR 0.015 0.001 TYR W 33 PHE 0.025 0.001 PHE B 486 TRP 0.048 0.002 TRP U 104 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (30129) covalent geometry : angle 0.55827 / 0.29 (40998) SS BOND : bond 0.00281 / 0.17 ( 42) SS BOND : angle 1.12757 / 0.65 ( 84) hydrogen bonds : bond 0.04854 / 3.03 ( 1165) hydrogen bonds : angle 5.10139 / 3.50 ( 3204) Misc. bond : bond 0.00364 / 0.24 ( 7) link_BETA1-4 : bond 0.00252 / 0.14 ( 12) link_BETA1-4 : angle 1.27506 / 0.85 ( 36) link_NAG-ASN : bond 0.00315 / 0.18 ( 39) link_NAG-ASN : angle 1.46287 / 1.02 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 1.135 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.8495 (t80) REVERT: B 117 LEU cc_start: 0.7834 (tp) cc_final: 0.7520 (mp) REVERT: B 403 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8145 (ttm-80) REVERT: C 403 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7974 (ttm-80) REVERT: C 505 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8270 (t80) REVERT: S 70 MET cc_start: 0.6059 (mpp) cc_final: 0.5038 (mmt) REVERT: T 63 ARG cc_start: 0.7698 (ptm160) cc_final: 0.7352 (ptm160) REVERT: U 70 MET cc_start: 0.7292 (mmt) cc_final: 0.5740 (mmt) REVERT: X 63 ARG cc_start: 0.8045 (ptt180) cc_final: 0.7831 (ptt180) outliers start: 40 outliers final: 24 residues processed: 150 average time/residue: 0.2109 time to fit residues: 49.9074 Evaluate side-chains 130 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 236 optimal weight: 0.0010 chunk 100 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 238 optimal weight: 20.0000 chunk 268 optimal weight: 0.4980 chunk 245 optimal weight: 3.9990 chunk 128 optimal weight: 0.0270 chunk 318 optimal weight: 5.9990 chunk 274 optimal weight: 4.9990 overall best weight: 0.5048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1106 GLN S 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.080989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.051671 restraints weight = 126127.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.053419 restraints weight = 60722.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.054509 restraints weight = 38746.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.055223 restraints weight = 29207.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.055628 restraints weight = 24405.728| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 30229 Z= 0.102 Angle : 0.550 20.288 41235 Z= 0.282 Chirality : 0.043 0.179 4785 Planarity : 0.008 0.422 5208 Dihedral : 5.662 166.163 3960 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.94 % Allowed : 11.99 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.15 (0.14), residues: 3630 helix: 2.27 (0.21), residues: 690 sheet: 0.16 (0.15), residues: 1068 loop : -0.75 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG U 72 TYR 0.013 0.001 TYR U 33 PHE 0.024 0.001 PHE B 486 TRP 0.041 0.002 TRP S 104 HIS 0.002 0.000 HIS U 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (30129) covalent geometry : angle 0.54272 / 0.28 (40998) SS BOND : bond 0.00339 / 0.19 ( 42) SS BOND : angle 1.17541 / 0.68 ( 84) hydrogen bonds : bond 0.04360 / 2.71 ( 1165) hydrogen bonds : angle 4.93221 / 3.38 ( 3204) Misc. bond : bond 0.00319 / 0.22 ( 7) link_BETA1-4 : bond 0.00333 / 0.19 ( 12) link_BETA1-4 : angle 1.24968 / 0.84 ( 36) link_NAG-ASN : bond 0.00306 / 0.18 ( 39) link_NAG-ASN : angle 1.41925 / 0.99 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 1.153 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 117 LEU cc_start: 0.7842 (tp) cc_final: 0.7546 (mp) REVERT: A 505 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.8506 (t80) REVERT: A 603 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7918 (t0) REVERT: B 117 LEU cc_start: 0.7815 (tp) cc_final: 0.7510 (mp) REVERT: B 603 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7683 (t0) REVERT: C 239 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7608 (tp40) REVERT: C 403 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.8023 (ttm-80) REVERT: C 505 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.8389 (t80) REVERT: S 70 MET cc_start: 0.5993 (mpp) cc_final: 0.5588 (mmt) REVERT: T 63 ARG cc_start: 0.7766 (ptm160) cc_final: 0.7047 (ptm160) REVERT: U 3 GLN cc_start: 0.8133 (mm110) cc_final: 0.7722 (tp-100) REVERT: U 70 MET cc_start: 0.7294 (mmt) cc_final: 0.6652 (mmm) REVERT: U 81 MET cc_start: 0.6632 (tpt) cc_final: 0.6282 (tpp) REVERT: X 63 ARG cc_start: 0.7968 (ptt180) cc_final: 0.7733 (ptt180) outliers start: 30 outliers final: 19 residues processed: 145 average time/residue: 0.2108 time to fit residues: 48.1585 Evaluate side-chains 133 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 303 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 317 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 359 optimal weight: 5.9990 chunk 279 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 901 GLN U 100 HIS ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.077435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.047689 restraints weight = 128027.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.049302 restraints weight = 64445.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.050341 restraints weight = 42318.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.050972 restraints weight = 32470.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.051389 restraints weight = 27519.267| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30229 Z= 0.204 Angle : 0.637 23.288 41235 Z= 0.324 Chirality : 0.046 0.470 4785 Planarity : 0.008 0.366 5208 Dihedral : 5.884 166.879 3960 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.19 % Allowed : 12.05 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3630 helix: 2.15 (0.21), residues: 669 sheet: 0.07 (0.15), residues: 1053 loop : -0.76 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG U 72 TYR 0.020 0.001 TYR U 102 PHE 0.034 0.002 PHE B 543 TRP 0.046 0.002 TRP S 104 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (30129) covalent geometry : angle 0.62839 / 0.32 (40998) SS BOND : bond 0.00363 / 0.24 ( 42) SS BOND : angle 1.44865 / 0.84 ( 84) hydrogen bonds : bond 0.05508 / 3.48 ( 1165) hydrogen bonds : angle 5.17428 / 3.56 ( 3204) Misc. bond : bond 0.00384 / 0.25 ( 7) link_BETA1-4 : bond 0.00386 / 0.23 ( 12) link_BETA1-4 : angle 1.43446 / 0.93 ( 36) link_NAG-ASN : bond 0.00332 / 0.21 ( 39) link_NAG-ASN : angle 1.58791 / 1.10 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 117 LEU cc_start: 0.8094 (tp) cc_final: 0.7718 (mp) REVERT: A 505 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.8519 (t80) REVERT: B 117 LEU cc_start: 0.8178 (tp) cc_final: 0.7701 (mp) REVERT: B 403 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8221 (ttm-80) REVERT: C 403 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8022 (ttm-80) REVERT: C 505 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.8354 (t80) REVERT: S 70 MET cc_start: 0.6032 (mpp) cc_final: 0.5553 (mmt) REVERT: U 70 MET cc_start: 0.7215 (mmt) cc_final: 0.6790 (mmm) REVERT: U 81 MET cc_start: 0.6938 (tpt) cc_final: 0.6674 (tpp) outliers start: 38 outliers final: 30 residues processed: 141 average time/residue: 0.1953 time to fit residues: 44.3735 Evaluate side-chains 135 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 363 optimal weight: 20.0000 chunk 249 optimal weight: 3.9990 chunk 186 optimal weight: 0.5980 chunk 235 optimal weight: 5.9990 chunk 236 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 226 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 312 optimal weight: 30.0000 chunk 23 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 GLN C 901 GLN T 81 GLN ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.075323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.045271 restraints weight = 126245.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.046868 restraints weight = 64081.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.047873 restraints weight = 42417.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.048534 restraints weight = 32768.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.048882 restraints weight = 27878.867| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 30229 Z= 0.232 Angle : 0.671 25.813 41235 Z= 0.343 Chirality : 0.046 0.360 4785 Planarity : 0.007 0.280 5208 Dihedral : 6.051 165.896 3960 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.04 % Favored : 94.93 % Rotamer: Outliers : 1.16 % Allowed : 12.18 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.23 (0.14), residues: 3630 helix: 1.90 (0.21), residues: 663 sheet: -0.08 (0.15), residues: 1053 loop : -0.93 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG B 328 TYR 0.030 0.002 TYR C 904 PHE 0.023 0.002 PHE C 486 TRP 0.051 0.002 TRP S 104 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (30129) covalent geometry : angle 0.66231 / 0.34 (40998) SS BOND : bond 0.00345 / 0.22 ( 42) SS BOND : angle 1.46264 / 0.86 ( 84) hydrogen bonds : bond 0.06110 / 3.88 ( 1165) hydrogen bonds : angle 5.43116 / 3.76 ( 3204) Misc. bond : bond 0.00483 / 0.28 ( 7) link_BETA1-4 : bond 0.00267 / 0.17 ( 12) link_BETA1-4 : angle 1.40782 / 0.91 ( 36) link_NAG-ASN : bond 0.00344 / 0.22 ( 39) link_NAG-ASN : angle 1.70876 / 1.18 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 1.111 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: symmetry clash revert: symmetry clash REVERT: A 505 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.8311 (t80) REVERT: B 117 LEU cc_start: 0.8207 (tp) cc_final: 0.7640 (mp) REVERT: B 403 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8184 (ttm-80) REVERT: B 532 ASN cc_start: 0.9081 (t0) cc_final: 0.8852 (t0) REVERT: C 403 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8005 (ttm-80) REVERT: C 505 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.8321 (t80) REVERT: S 70 MET cc_start: 0.6273 (mpp) cc_final: 0.5306 (mmt) REVERT: U 70 MET cc_start: 0.7267 (mmt) cc_final: 0.6980 (mmm) REVERT: W 48 MET cc_start: 0.7253 (mtt) cc_final: 0.6587 (mpp) outliers start: 37 outliers final: 26 residues processed: 152 average time/residue: 0.2057 time to fit residues: 50.5982 Evaluate side-chains 131 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 53 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 201 optimal weight: 0.7980 chunk 249 optimal weight: 1.9990 chunk 355 optimal weight: 30.0000 chunk 299 optimal weight: 0.4980 chunk 351 optimal weight: 7.9990 chunk 324 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 GLN U 105 ASN ** W 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.077255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.048001 restraints weight = 127877.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.049622 restraints weight = 63603.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.050648 restraints weight = 41539.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.051337 restraints weight = 31822.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.051725 restraints weight = 26788.651| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30229 Z= 0.122 Angle : 0.587 18.495 41235 Z= 0.301 Chirality : 0.044 0.177 4785 Planarity : 0.007 0.249 5208 Dihedral : 5.811 167.646 3960 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 1.00 % Allowed : 12.55 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.14), residues: 3630 helix: 2.24 (0.21), residues: 663 sheet: 0.09 (0.15), residues: 1038 loop : -0.84 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG U 72 TYR 0.018 0.001 TYR C 904 PHE 0.020 0.001 PHE B 543 TRP 0.046 0.002 TRP S 104 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (30129) covalent geometry : angle 0.57923 / 0.30 (40998) SS BOND : bond 0.00272 / 0.16 ( 42) SS BOND : angle 1.24331 / 0.73 ( 84) hydrogen bonds : bond 0.05115 / 3.19 ( 1165) hydrogen bonds : angle 5.08918 / 3.52 ( 3204) Misc. bond : bond 0.00381 / 0.23 ( 7) link_BETA1-4 : bond 0.00282 / 0.16 ( 12) link_BETA1-4 : angle 1.33657 / 0.89 ( 36) link_NAG-ASN : bond 0.00305 / 0.17 ( 39) link_NAG-ASN : angle 1.50673 / 1.06 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6568.30 seconds wall clock time: 113 minutes 39.94 seconds (6819.94 seconds total)