Starting phenix.real_space_refine on Mon Aug 25 17:38:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8elj_28228/08_2025/8elj_28228.cif Found real_map, /net/cci-nas-00/data/ceres_data/8elj_28228/08_2025/8elj_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_28228/08_2025/8elj_28228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8elj_28228/08_2025/8elj_28228.map" model { file = "/net/cci-nas-00/data/ceres_data/8elj_28228/08_2025/8elj_28228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8elj_28228/08_2025/8elj_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 30 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 dihedrals: 30 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.23, per 1000 atoms: 0.21 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: 2.20 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.9 microseconds 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: 1.02 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: 7.17 Time building geometry restraints manager: 2.94 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: 17025 17.94 - 35.87: 1198 35.87 - 53.81: 198 53.81 - 71.74: 62 71.74 - 89.68: 39 Dihedral angle restraints: 18522 sinusoidal: 7827 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 18519 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: 0.07 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: 12.970 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.530 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 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 : 13.283 87.812 11544 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 aren 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 covalent geometry : bond 0.01028 (30129) covalent geometry : angle 1.78315 (40998) SS BOND : bond 0.02681 ( 42) SS BOND : angle 2.82716 ( 84) hydrogen bonds : bond 0.21027 ( 1165) hydrogen bonds : angle 7.98400 ( 3204) Misc. bond : bond 0.35514 ( 7) link_BETA1-4 : bond 0.02230 ( 12) link_BETA1-4 : angle 4.43261 ( 36) link_NAG-ASN : bond 0.01407 ( 39) link_NAG-ASN : angle 4.40258 ( 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 : 0.937 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: 0.1858 time to fit residues: 121.8413 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 : 0.720 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 41 HIS W 3 GLN W 43 GLN ** 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 = 0.3870 r_free = 0.3870 target = 0.083773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053605 restraints weight = 125614.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.055581 restraints weight = 57673.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.056819 restraints weight = 36159.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.057569 restraints weight = 26946.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.057977 restraints weight = 22457.260| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 30229 Z= 0.167 Angle : 0.764 26.044 41235 Z= 0.387 Chirality : 0.048 0.315 4785 Planarity : 0.012 0.456 5208 Dihedral : 6.212 114.683 5101 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.42 % Favored : 97.49 % Rotamer: Outliers : 1.66 % Allowed : 8.23 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 1.17 % 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 aren not related in a simple way. whole: -0.21 (0.13), residues: 3630 helix: 1.22 (0.20), residues: 684 sheet: 0.08 (0.14), residues: 1050 loop : -0.73 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG C 328 TYR 0.043 0.002 TYR U 102 PHE 0.031 0.002 PHE C 486 TRP 0.028 0.002 TRP S 104 HIS 0.012 0.001 HIS U 100 Details of bonding type rmsd covalent geometry : bond 0.00359 (30129) covalent geometry : angle 0.74982 (40998) SS BOND : bond 0.00208 ( 42) SS BOND : angle 1.29433 ( 84) hydrogen bonds : bond 0.06683 ( 1165) hydrogen bonds : angle 6.13210 ( 3204) Misc. bond : bond 0.00608 ( 7) link_BETA1-4 : bond 0.00855 ( 12) link_BETA1-4 : angle 1.91113 ( 36) link_NAG-ASN : bond 0.00531 ( 39) link_NAG-ASN : angle 2.54552 ( 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 252 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 199 time to evaluate : 1.093 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 117 LEU cc_start: 0.7488 (tp) cc_final: 0.7126 (mt) REVERT: A 505 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8424 (t80) REVERT: B 276 LEU cc_start: 0.9377 (tp) cc_final: 0.9169 (tp) REVERT: B 334 ASN cc_start: 0.6623 (OUTLIER) cc_final: 0.6423 (p0) REVERT: C 117 LEU cc_start: 0.7618 (tp) cc_final: 0.7165 (mt) REVERT: C 417 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8518 (mtpt) REVERT: C 505 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.8428 (t80) REVERT: C 900 MET cc_start: 0.8519 (mtp) cc_final: 0.8094 (mtm) REVERT: S 70 MET cc_start: 0.6333 (mpp) cc_final: 0.4677 (mmt) REVERT: T 38 TYR cc_start: 0.6420 (m-80) cc_final: 0.6009 (m-80) REVERT: U 101 THR cc_start: 0.7409 (OUTLIER) cc_final: 0.7190 (m) REVERT: V 38 TYR cc_start: 0.6535 (m-80) cc_final: 0.6316 (m-80) REVERT: W 101 THR cc_start: 0.7184 (OUTLIER) cc_final: 0.6936 (m) REVERT: X 38 TYR cc_start: 0.6482 (m-80) cc_final: 0.6137 (m-80) outliers start: 53 outliers final: 16 residues processed: 245 average time/residue: 0.1911 time to fit residues: 71.4056 Evaluate side-chains 142 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 178 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 169 optimal weight: 0.4980 chunk 175 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 235 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 207 HIS 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** T 33 ASN 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.081301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.051444 restraints weight = 124767.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.053267 restraints weight = 59130.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.054374 restraints weight = 37637.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 72)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.055090 restraints weight = 28500.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.055503 restraints weight = 23979.560| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 30229 Z= 0.167 Angle : 0.674 28.499 41235 Z= 0.340 Chirality : 0.046 0.228 4785 Planarity : 0.010 0.438 5208 Dihedral : 5.661 149.939 5094 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.14 % Favored : 96.83 % Rotamer: Outliers : 1.82 % Allowed : 8.92 % Favored : 89.26 % 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 aren not related in a simple way. whole: 0.05 (0.14), residues: 3630 helix: 1.88 (0.21), residues: 648 sheet: 0.18 (0.15), residues: 1044 loop : -0.67 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 328 TYR 0.041 0.002 TYR S 102 PHE 0.024 0.001 PHE B 486 TRP 0.046 0.002 TRP S 104 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00374 (30129) covalent geometry : angle 0.66390 (40998) SS BOND : bond 0.00185 ( 42) SS BOND : angle 1.10386 ( 84) hydrogen bonds : bond 0.05972 ( 1165) hydrogen bonds : angle 5.69840 ( 3204) Misc. bond : bond 0.00519 ( 7) link_BETA1-4 : bond 0.00619 ( 12) link_BETA1-4 : angle 1.66949 ( 36) link_NAG-ASN : bond 0.00409 ( 39) link_NAG-ASN : angle 1.96958 ( 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 196 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 138 time to evaluate : 1.093 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: A 117 LEU cc_start: 0.7787 (tp) cc_final: 0.7373 (mp) REVERT: A 239 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6420 (tp40) REVERT: A 505 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8515 (t80) REVERT: B 334 ASN cc_start: 0.6994 (OUTLIER) cc_final: 0.6774 (p0) REVERT: C 117 LEU cc_start: 0.7796 (tp) cc_final: 0.7323 (mp) REVERT: C 239 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6016 (tp40) REVERT: C 505 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.8508 (t80) REVERT: S 3 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8176 (tm-30) REVERT: S 70 MET cc_start: 0.6188 (mpp) cc_final: 0.4625 (mmt) REVERT: S 98 ARG cc_start: 0.6581 (tmm-80) cc_final: 0.6327 (tmm160) REVERT: V 56 ARG cc_start: 0.7939 (mpt180) cc_final: 0.7701 (mpt180) REVERT: V 63 ARG cc_start: 0.8342 (ptt180) cc_final: 0.7621 (ppt170) REVERT: X 63 ARG cc_start: 0.8245 (ptt90) cc_final: 0.7866 (ptt180) outliers start: 58 outliers final: 26 residues processed: 189 average time/residue: 0.2009 time to fit residues: 58.5326 Evaluate side-chains 141 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 239 GLN 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 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 334 ASN 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 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 C residue 1104 VAL Chi-restraints excluded: chain T residue 51 TYR 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: 7.9990 chunk 244 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 338 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1135 ASN B 239 GLN B1135 ASN C 901 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.077667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.047909 restraints weight = 127687.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.049465 restraints weight = 64260.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.050461 restraints weight = 42241.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.051071 restraints weight = 32421.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.051424 restraints weight = 27528.931| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 30229 Z= 0.318 Angle : 0.807 23.222 41235 Z= 0.410 Chirality : 0.049 0.268 4785 Planarity : 0.013 0.433 5208 Dihedral : 5.916 104.546 5094 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.30 % Favored : 95.67 % Rotamer: Outliers : 2.47 % Allowed : 10.02 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: -0.45 (0.13), residues: 3630 helix: 1.43 (0.20), residues: 663 sheet: -0.12 (0.15), residues: 1029 loop : -1.01 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG C 328 TYR 0.042 0.002 TYR U 102 PHE 0.026 0.002 PHE C 92 TRP 0.062 0.003 TRP S 104 HIS 0.011 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00744 (30129) covalent geometry : angle 0.79663 (40998) SS BOND : bond 0.00311 ( 42) SS BOND : angle 1.34467 ( 84) hydrogen bonds : bond 0.07195 ( 1165) hydrogen bonds : angle 6.07444 ( 3204) Misc. bond : bond 0.00188 ( 7) link_BETA1-4 : bond 0.00644 ( 12) link_BETA1-4 : angle 1.81258 ( 36) link_NAG-ASN : bond 0.00653 ( 39) link_NAG-ASN : angle 2.18498 ( 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 199 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 120 time to evaluate : 1.010 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: A 505 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8616 (t80) REVERT: C 380 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.8941 (m-80) REVERT: C 505 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.8629 (t80) REVERT: C 900 MET cc_start: 0.8782 (mtp) cc_final: 0.8378 (mtm) REVERT: S 70 MET cc_start: 0.6285 (mpp) cc_final: 0.4806 (mmt) REVERT: T 38 TYR cc_start: 0.6273 (m-80) cc_final: 0.6031 (m-80) REVERT: T 63 ARG cc_start: 0.7917 (ptt180) cc_final: 0.7565 (ptm160) REVERT: U 70 MET cc_start: 0.6117 (mmt) cc_final: 0.4859 (mmm) REVERT: W 70 MET cc_start: 0.6059 (mmt) cc_final: 0.5268 (mmm) outliers start: 79 outliers final: 51 residues processed: 194 average time/residue: 0.1906 time to fit residues: 57.5577 Evaluate side-chains 153 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 99 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 380 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL 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 529 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 334 ASN 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 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 B residue 915 VAL Chi-restraints excluded: chain B residue 951 VAL 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 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 560 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 51 TYR 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: 4.9990 chunk 143 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 296 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 247 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN C 901 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN S 100 HIS ** U 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.079313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.049851 restraints weight = 128193.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.051550 restraints weight = 61830.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.052632 restraints weight = 39678.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.053263 restraints weight = 30027.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.053703 restraints weight = 25349.128| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 30229 Z= 0.131 Angle : 0.613 24.652 41235 Z= 0.312 Chirality : 0.045 0.217 4785 Planarity : 0.011 0.446 5208 Dihedral : 5.137 97.615 5094 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.33 % Favored : 96.64 % Rotamer: Outliers : 1.97 % Allowed : 11.36 % Favored : 86.67 % 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 aren not related in a simple way. whole: -0.19 (0.13), residues: 3630 helix: 2.01 (0.21), residues: 663 sheet: 0.01 (0.15), residues: 1026 loop : -0.97 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 328 TYR 0.031 0.001 TYR W 102 PHE 0.014 0.001 PHE B 464 TRP 0.051 0.002 TRP S 104 HIS 0.003 0.000 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00279 (30129) covalent geometry : angle 0.60366 (40998) SS BOND : bond 0.00450 ( 42) SS BOND : angle 1.18715 ( 84) hydrogen bonds : bond 0.05638 ( 1165) hydrogen bonds : angle 5.43009 ( 3204) Misc. bond : bond 0.00607 ( 7) link_BETA1-4 : bond 0.00334 ( 12) link_BETA1-4 : angle 1.54154 ( 36) link_NAG-ASN : bond 0.00404 ( 39) link_NAG-ASN : angle 1.69842 ( 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 168 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 105 time to evaluate : 1.020 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 117 LEU cc_start: 0.7924 (tp) cc_final: 0.7635 (mp) REVERT: A 505 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8548 (t80) REVERT: B 117 LEU cc_start: 0.7847 (tp) cc_final: 0.7494 (mp) REVERT: B 403 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8081 (ttm-80) REVERT: C 117 LEU cc_start: 0.7974 (tp) cc_final: 0.7565 (mp) REVERT: C 403 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7975 (ttm-80) REVERT: C 505 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8343 (t80) REVERT: S 19 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7543 (tptp) REVERT: S 70 MET cc_start: 0.5961 (mpp) cc_final: 0.4670 (mmt) REVERT: W 70 MET cc_start: 0.6474 (mmt) cc_final: 0.6238 (mmt) REVERT: X 63 ARG cc_start: 0.7593 (ptt180) cc_final: 0.7207 (ptm160) outliers start: 63 outliers final: 30 residues processed: 163 average time/residue: 0.2030 time to fit residues: 50.7261 Evaluate side-chains 135 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 334 ASN 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 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 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 980 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 100 HIS Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain W residue 100 HIS Chi-restraints excluded: chain X residue 5 THR 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: 2.9990 chunk 302 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 254 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.079430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.049833 restraints weight = 126379.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.051517 restraints weight = 61614.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.052595 restraints weight = 39750.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053265 restraints weight = 30147.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.053628 restraints weight = 25367.660| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 30229 Z= 0.142 Angle : 0.606 22.150 41235 Z= 0.308 Chirality : 0.044 0.208 4785 Planarity : 0.011 0.452 5208 Dihedral : 5.066 96.033 5094 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 1.72 % Allowed : 11.80 % Favored : 86.48 % 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 aren not related in a simple way. whole: -0.13 (0.13), residues: 3630 helix: 2.13 (0.21), residues: 666 sheet: 0.01 (0.15), residues: 1050 loop : -0.95 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG S 72 TYR 0.027 0.001 TYR U 102 PHE 0.036 0.001 PHE B 486 TRP 0.043 0.002 TRP U 104 HIS 0.013 0.001 HIS S 100 Details of bonding type rmsd covalent geometry : bond 0.00322 (30129) covalent geometry : angle 0.59780 (40998) SS BOND : bond 0.00203 ( 42) SS BOND : angle 1.08223 ( 84) hydrogen bonds : bond 0.05349 ( 1165) hydrogen bonds : angle 5.30661 ( 3204) Misc. bond : bond 0.00708 ( 7) link_BETA1-4 : bond 0.00270 ( 12) link_BETA1-4 : angle 1.47129 ( 36) link_NAG-ASN : bond 0.00328 ( 39) link_NAG-ASN : angle 1.66554 ( 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 155 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 100 time to evaluate : 0.763 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 117 LEU cc_start: 0.7981 (tp) cc_final: 0.7670 (mp) REVERT: A 403 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7952 (ttm-80) REVERT: A 505 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8312 (t80) REVERT: B 117 LEU cc_start: 0.7932 (tp) cc_final: 0.7529 (mp) REVERT: B 403 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8013 (ttm-80) REVERT: B 532 ASN cc_start: 0.9023 (t0) cc_final: 0.8734 (t0) REVERT: C 117 LEU cc_start: 0.8012 (tp) cc_final: 0.7589 (mp) REVERT: C 403 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7934 (ttm-80) REVERT: C 505 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.8263 (t80) REVERT: S 19 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7473 (tptp) REVERT: S 70 MET cc_start: 0.5829 (mpp) cc_final: 0.4023 (mmt) REVERT: U 70 MET cc_start: 0.6969 (mmt) cc_final: 0.6396 (mmm) REVERT: X 63 ARG cc_start: 0.7633 (ptt180) cc_final: 0.7367 (ptm160) outliers start: 55 outliers final: 30 residues processed: 151 average time/residue: 0.1761 time to fit residues: 41.9525 Evaluate side-chains 134 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL 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 114 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 334 ASN 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 1027 THR 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 318 PHE 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 581 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 72 ARG 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: 5.9990 chunk 328 optimal weight: 0.7980 chunk 184 optimal weight: 0.6980 chunk 318 optimal weight: 30.0000 chunk 155 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 365 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 274 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 262 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.077999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.048550 restraints weight = 127075.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.050192 restraints weight = 63104.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.051232 restraints weight = 41140.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.051852 restraints weight = 31507.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.052202 restraints weight = 26744.646| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 30229 Z= 0.142 Angle : 0.588 19.375 41235 Z= 0.300 Chirality : 0.044 0.195 4785 Planarity : 0.011 0.452 5208 Dihedral : 4.864 89.101 5094 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.97 % Favored : 96.01 % Rotamer: Outliers : 1.60 % Allowed : 11.77 % Favored : 86.64 % 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 aren not related in a simple way. whole: -0.10 (0.14), residues: 3630 helix: 2.23 (0.21), residues: 666 sheet: -0.01 (0.15), residues: 1077 loop : -0.95 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG S 72 TYR 0.024 0.001 TYR U 102 PHE 0.033 0.001 PHE B 486 TRP 0.041 0.002 TRP W 104 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00327 (30129) covalent geometry : angle 0.57926 (40998) SS BOND : bond 0.00199 ( 42) SS BOND : angle 1.29233 ( 84) hydrogen bonds : bond 0.05151 ( 1165) hydrogen bonds : angle 5.20942 ( 3204) Misc. bond : bond 0.00480 ( 7) link_BETA1-4 : bond 0.00271 ( 12) link_BETA1-4 : angle 1.43747 ( 36) link_NAG-ASN : bond 0.00307 ( 39) link_NAG-ASN : angle 1.60584 ( 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 159 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 108 time to evaluate : 0.995 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: A 117 LEU cc_start: 0.8141 (tp) cc_final: 0.7744 (mp) REVERT: A 403 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8014 (ttm-80) REVERT: A 505 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.8314 (t80) REVERT: B 117 LEU cc_start: 0.8029 (tp) cc_final: 0.7597 (mp) REVERT: B 403 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8051 (ttm-80) REVERT: B 532 ASN cc_start: 0.8913 (t0) cc_final: 0.8661 (t0) REVERT: C 117 LEU cc_start: 0.8124 (tp) cc_final: 0.7689 (mp) REVERT: C 403 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7976 (ttm-80) REVERT: C 505 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.8323 (t80) REVERT: S 70 MET cc_start: 0.5919 (mpp) cc_final: 0.4779 (mmt) REVERT: T 63 ARG cc_start: 0.7773 (ptm160) cc_final: 0.7144 (ptm160) REVERT: U 70 MET cc_start: 0.6363 (mmt) cc_final: 0.5754 (mmm) REVERT: V 49 MET cc_start: 0.6005 (ptt) cc_final: 0.5755 (ptt) REVERT: W 48 MET cc_start: 0.6423 (tpt) cc_final: 0.5861 (mmm) REVERT: X 63 ARG cc_start: 0.7629 (ptt180) cc_final: 0.7379 (ptm160) outliers start: 51 outliers final: 32 residues processed: 158 average time/residue: 0.1837 time to fit residues: 46.1337 Evaluate side-chains 134 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 318 PHE 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 603 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 334 ASN 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 574 ASP Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 1094 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 318 PHE Chi-restraints excluded: chain C residue 336 CYS 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 581 THR 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 W residue 72 ARG 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: 5.9990 chunk 16 optimal weight: 4.9990 chunk 236 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 238 optimal weight: 10.0000 chunk 268 optimal weight: 0.5980 chunk 245 optimal weight: 0.9980 chunk 128 optimal weight: 0.5980 chunk 318 optimal weight: 30.0000 chunk 274 optimal weight: 3.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN C 901 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 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 = 0.3702 r_free = 0.3702 target = 0.076147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.046178 restraints weight = 125571.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.047757 restraints weight = 63654.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.048759 restraints weight = 42240.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.049393 restraints weight = 32599.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.049810 restraints weight = 27858.032| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 30229 Z= 0.194 Angle : 0.632 20.675 41235 Z= 0.322 Chirality : 0.045 0.206 4785 Planarity : 0.011 0.430 5208 Dihedral : 5.095 82.982 5094 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.50 % Allowed : 12.30 % Favored : 86.20 % 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 aren not related in a simple way. whole: -0.13 (0.14), residues: 3630 helix: 2.19 (0.21), residues: 663 sheet: -0.04 (0.15), residues: 1056 loop : -0.94 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG U 72 TYR 0.019 0.001 TYR B 266 PHE 0.029 0.001 PHE B 486 TRP 0.043 0.002 TRP W 104 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00452 (30129) covalent geometry : angle 0.62198 (40998) SS BOND : bond 0.00328 ( 42) SS BOND : angle 1.43692 ( 84) hydrogen bonds : bond 0.05579 ( 1165) hydrogen bonds : angle 5.31429 ( 3204) Misc. bond : bond 0.00551 ( 7) link_BETA1-4 : bond 0.00213 ( 12) link_BETA1-4 : angle 1.47455 ( 36) link_NAG-ASN : bond 0.00332 ( 39) link_NAG-ASN : angle 1.68538 ( 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: 48 poor density : 98 time to evaluate : 1.140 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: A 117 LEU cc_start: 0.8107 (tp) cc_final: 0.7719 (mp) REVERT: A 403 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8106 (ttm-80) REVERT: A 505 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8356 (t80) REVERT: B 117 LEU cc_start: 0.8179 (tp) cc_final: 0.7663 (mp) REVERT: B 403 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8049 (ttm-80) REVERT: B 532 ASN cc_start: 0.8917 (t0) cc_final: 0.8714 (t0) REVERT: C 117 LEU cc_start: 0.8186 (tp) cc_final: 0.7749 (mp) REVERT: C 403 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8026 (ttm-80) REVERT: C 505 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.8349 (t80) REVERT: S 70 MET cc_start: 0.6002 (mpp) cc_final: 0.5528 (mmm) REVERT: T 63 ARG cc_start: 0.7580 (ptm160) cc_final: 0.7277 (ptm160) REVERT: U 70 MET cc_start: 0.6602 (mmt) cc_final: 0.6052 (mmm) REVERT: W 48 MET cc_start: 0.6513 (tpt) cc_final: 0.5957 (mmm) REVERT: X 63 ARG cc_start: 0.7608 (ptt180) cc_final: 0.7342 (ptm160) outliers start: 48 outliers final: 37 residues processed: 144 average time/residue: 0.1825 time to fit residues: 42.6058 Evaluate side-chains 135 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 318 PHE 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 603 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 334 ASN 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 574 ASP Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 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 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 V residue 51 TYR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 72 ARG 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: 0.9990 chunk 132 optimal weight: 7.9990 chunk 308 optimal weight: 5.9990 chunk 317 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 359 optimal weight: 2.9990 chunk 279 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100 HIS T 81 GLN U 100 HIS W 100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.076179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.047029 restraints weight = 128128.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.048557 restraints weight = 66302.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.049510 restraints weight = 44122.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.050060 restraints weight = 34332.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.050526 restraints weight = 29460.911| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 30229 Z= 0.199 Angle : 0.629 21.646 41235 Z= 0.322 Chirality : 0.045 0.192 4785 Planarity : 0.010 0.415 5208 Dihedral : 5.131 74.068 5094 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.77 % Favored : 95.18 % Rotamer: Outliers : 1.50 % Allowed : 12.55 % Favored : 85.95 % 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 aren not related in a simple way. whole: -0.21 (0.14), residues: 3630 helix: 2.15 (0.21), residues: 663 sheet: -0.05 (0.15), residues: 1038 loop : -1.03 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG S 72 TYR 0.022 0.001 TYR X 34 PHE 0.031 0.001 PHE B 486 TRP 0.040 0.002 TRP W 104 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00464 (30129) covalent geometry : angle 0.61933 (40998) SS BOND : bond 0.00340 ( 42) SS BOND : angle 1.44819 ( 84) hydrogen bonds : bond 0.05659 ( 1165) hydrogen bonds : angle 5.35830 ( 3204) Misc. bond : bond 0.00564 ( 7) link_BETA1-4 : bond 0.00196 ( 12) link_BETA1-4 : angle 1.48043 ( 36) link_NAG-ASN : bond 0.00316 ( 39) link_NAG-ASN : angle 1.68008 ( 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 152 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 104 time to evaluate : 1.085 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: A 117 LEU cc_start: 0.8323 (tp) cc_final: 0.7928 (mp) REVERT: A 403 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8136 (ttm-80) REVERT: A 505 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8322 (t80) REVERT: B 117 LEU cc_start: 0.8269 (tp) cc_final: 0.7705 (mp) REVERT: B 403 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8047 (ttm-80) REVERT: B 912 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8746 (p) REVERT: C 117 LEU cc_start: 0.8245 (tp) cc_final: 0.7781 (mp) REVERT: C 403 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8000 (ttm-80) REVERT: C 505 TYR cc_start: 0.8976 (OUTLIER) cc_final: 0.8333 (t80) REVERT: S 70 MET cc_start: 0.6271 (mpp) cc_final: 0.5832 (mmm) REVERT: U 70 MET cc_start: 0.6818 (mmt) cc_final: 0.6083 (mmm) REVERT: W 48 MET cc_start: 0.6556 (tpt) cc_final: 0.5991 (mmm) REVERT: X 63 ARG cc_start: 0.7520 (ptt180) cc_final: 0.7250 (ptm160) outliers start: 48 outliers final: 31 residues processed: 151 average time/residue: 0.1760 time to fit residues: 43.2013 Evaluate side-chains 132 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 318 PHE 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 603 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 334 ASN 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 912 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 84 LEU 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 980 ILE Chi-restraints excluded: chain C residue 1094 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 363 optimal weight: 30.0000 chunk 249 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 312 optimal weight: 40.0000 chunk 23 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.074551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.044612 restraints weight = 127609.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.046178 restraints weight = 65528.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.047188 restraints weight = 43740.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.047803 restraints weight = 33942.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.048201 restraints weight = 28973.277| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 30229 Z= 0.246 Angle : 0.669 18.395 41235 Z= 0.343 Chirality : 0.046 0.195 4785 Planarity : 0.011 0.440 5208 Dihedral : 5.460 101.036 5094 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.44 % Allowed : 12.61 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -0.33 (0.13), residues: 3630 helix: 2.05 (0.20), residues: 660 sheet: -0.11 (0.15), residues: 1020 loop : -1.10 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG U 72 TYR 0.037 0.002 TYR C 904 PHE 0.029 0.002 PHE C 486 TRP 0.053 0.002 TRP W 104 HIS 0.012 0.001 HIS U 100 Details of bonding type rmsd covalent geometry : bond 0.00571 (30129) covalent geometry : angle 0.65893 (40998) SS BOND : bond 0.00340 ( 42) SS BOND : angle 1.52825 ( 84) hydrogen bonds : bond 0.06123 ( 1165) hydrogen bonds : angle 5.51530 ( 3204) Misc. bond : bond 0.00477 ( 7) link_BETA1-4 : bond 0.00233 ( 12) link_BETA1-4 : angle 1.50619 ( 36) link_NAG-ASN : bond 0.00371 ( 39) link_NAG-ASN : angle 1.77830 ( 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 141 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 95 time to evaluate : 1.025 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 403 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8086 (ttm-80) REVERT: A 505 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.8271 (t80) REVERT: B 403 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7971 (ttm-80) REVERT: C 403 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7932 (ttm-80) REVERT: C 505 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8247 (t80) REVERT: S 70 MET cc_start: 0.6393 (mpp) cc_final: 0.5935 (mmm) REVERT: U 70 MET cc_start: 0.6833 (mmt) cc_final: 0.5978 (mmm) REVERT: W 48 MET cc_start: 0.6631 (tpt) cc_final: 0.6079 (mmm) REVERT: X 63 ARG cc_start: 0.7496 (ptt180) cc_final: 0.7276 (ptm160) outliers start: 46 outliers final: 35 residues processed: 140 average time/residue: 0.1731 time to fit residues: 39.7478 Evaluate side-chains 132 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 128 ILE Chi-restraints excluded: chain A residue 318 PHE 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 603 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 385 THR 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 B residue 1027 THR Chi-restraints excluded: chain C residue 84 LEU 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 980 ILE Chi-restraints excluded: chain C residue 1094 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 53 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 2 optimal weight: 0.0570 chunk 201 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 355 optimal weight: 5.9990 chunk 299 optimal weight: 2.9990 chunk 351 optimal weight: 20.0000 chunk 324 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 901 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 HIS U 100 HIS X 41 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.075776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.046010 restraints weight = 127263.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.047625 restraints weight = 64488.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.048674 restraints weight = 42674.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.049304 restraints weight = 32851.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.049710 restraints weight = 27936.555| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 30229 Z= 0.135 Angle : 0.593 17.994 41235 Z= 0.305 Chirality : 0.044 0.174 4785 Planarity : 0.011 0.434 5208 Dihedral : 5.232 101.679 5094 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.24 % Favored : 95.73 % Rotamer: Outliers : 1.10 % Allowed : 13.08 % Favored : 85.82 % 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 aren not related in a simple way. whole: -0.15 (0.14), residues: 3630 helix: 2.36 (0.21), residues: 660 sheet: -0.04 (0.15), residues: 996 loop : -1.00 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG W 72 TYR 0.028 0.001 TYR C 904 PHE 0.025 0.001 PHE B 486 TRP 0.043 0.002 TRP W 104 HIS 0.007 0.001 HIS W 100 Details of bonding type rmsd covalent geometry : bond 0.00308 (30129) covalent geometry : angle 0.58460 (40998) SS BOND : bond 0.00277 ( 42) SS BOND : angle 1.28531 ( 84) hydrogen bonds : bond 0.05228 ( 1165) hydrogen bonds : angle 5.21819 ( 3204) Misc. bond : bond 0.00488 ( 7) link_BETA1-4 : bond 0.00343 ( 12) link_BETA1-4 : angle 1.41985 ( 36) link_NAG-ASN : bond 0.00317 ( 39) link_NAG-ASN : angle 1.60112 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6081.47 seconds wall clock time: 105 minutes 15.98 seconds (6315.98 seconds total)