Starting phenix.real_space_refine on Wed Jun 25 17:12:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8elj_28228/06_2025/8elj_28228.cif Found real_map, /net/cci-nas-00/data/ceres_data/8elj_28228/06_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_28228/06_2025/8elj_28228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8elj_28228/06_2025/8elj_28228.map" model { file = "/net/cci-nas-00/data/ceres_data/8elj_28228/06_2025/8elj_28228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8elj_28228/06_2025/8elj_28228.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 4.69s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 22.85, per 1000 atoms: 0.78 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: 12.59 Conformation dependent library (CDL) restraints added in 4.2 seconds 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6852 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 60 sheets defined 22.1% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.61 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: 33.83 Time building geometry restraints manager: 13.84 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: 0.18 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: 215.670 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: 0.050 Extract box with map and model: 1.150 Check model and map are aligned: 0.250 Set scattering table: 0.280 Process input model: 105.660 Find NCS groups from input model: 3.230 Set up NCS constraints: 0.920 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: 0.060 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 330.490 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.051 0.009 TRP S 50 HIS 0.019 0.005 HIS B1064 PHE 0.055 0.010 PHE A 888 TYR 0.067 0.009 TYR W 102 ARG 0.041 0.003 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.01407 ( 39) link_NAG-ASN : angle 4.40258 ( 117) link_BETA1-4 : bond 0.02230 ( 12) link_BETA1-4 : angle 4.43261 ( 36) hydrogen bonds : bond 0.21027 ( 1165) hydrogen bonds : angle 7.98400 ( 3204) SS BOND : bond 0.02681 ( 42) SS BOND : angle 2.82716 ( 84) covalent geometry : bond 0.01028 (30129) covalent geometry : angle 1.78315 (40998) Misc. bond : bond 0.35514 ( 7) *********************** 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 : 5.298 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 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: 0.9012 (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: 0.8276 (mt) REVERT: B 394 ASN cc_start: 0.9125 (m-40) cc_final: 0.8822 (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 242 LEU cc_start: 0.7612 (mt) cc_final: 0.7345 (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: 0.8903 (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: 0.7858 (mmm) REVERT: U 54 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8910 (mp) REVERT: U 82 GLU cc_start: 0.8545 (tt0) cc_final: 0.8266 (tp30) 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: 0.7782 (mmm) REVERT: V 63 ARG cc_start: 0.7734 (ptt90) cc_final: 0.7478 (ptt180) 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: 0.7711 (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: 0.6491 time to fit residues: 425.3778 Evaluate side-chains 186 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 182 time to evaluate : 4.103 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 5.9990 chunk 277 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 286 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 332 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 207 HIS A 474 GLN B 207 HIS B 321 GLN B 474 GLN C 66 HIS C 207 HIS C 360 ASN C 474 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 GLN ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 3 GLN ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 GLN ** U 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 3 GLN ** W 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 GLN ** W 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.084924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.054745 restraints weight = 127170.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.056640 restraints weight = 58951.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.057812 restraints weight = 36985.917| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 30229 Z= 0.178 Angle : 0.760 24.235 41235 Z= 0.387 Chirality : 0.048 0.272 4785 Planarity : 0.012 0.453 5208 Dihedral : 6.227 114.928 5099 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.40 % Favored : 97.52 % Rotamer: Outliers : 1.56 % Allowed : 8.51 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.13), residues: 3630 helix: 1.22 (0.20), residues: 684 sheet: 0.03 (0.14), residues: 1056 loop : -0.73 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP W 104 HIS 0.013 0.001 HIS U 100 PHE 0.029 0.002 PHE B 486 TYR 0.044 0.002 TYR U 102 ARG 0.029 0.001 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 39) link_NAG-ASN : angle 2.52307 ( 117) link_BETA1-4 : bond 0.00495 ( 12) link_BETA1-4 : angle 2.00781 ( 36) hydrogen bonds : bond 0.06802 ( 1165) hydrogen bonds : angle 6.14053 ( 3204) SS BOND : bond 0.01203 ( 42) SS BOND : angle 1.30359 ( 84) covalent geometry : bond 0.00388 (30129) covalent geometry : angle 0.74514 (40998) Misc. bond : bond 0.00463 ( 7) *********************** 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 251 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 201 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7544 (tp) cc_final: 0.7110 (mp) REVERT: A 417 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8476 (mtmt) REVERT: A 505 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8458 (t80) REVERT: B 276 LEU cc_start: 0.9390 (tp) cc_final: 0.9183 (tp) REVERT: C 117 LEU cc_start: 0.7671 (tp) cc_final: 0.7186 (mt) REVERT: C 417 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8517 (mtpt) REVERT: C 505 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8442 (t80) REVERT: C 900 MET cc_start: 0.8593 (mtp) cc_final: 0.8147 (mtm) REVERT: S 70 MET cc_start: 0.6378 (mpp) cc_final: 0.4871 (mmt) REVERT: T 38 TYR cc_start: 0.6471 (m-80) cc_final: 0.6005 (m-80) REVERT: T 63 ARG cc_start: 0.8143 (ptt180) cc_final: 0.7755 (ptt180) REVERT: T 85 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6532 (mt-10) REVERT: U 70 MET cc_start: 0.6537 (mtt) cc_final: 0.5022 (mmt) REVERT: U 101 THR cc_start: 0.7416 (OUTLIER) cc_final: 0.7189 (m) REVERT: V 38 TYR cc_start: 0.6566 (m-80) cc_final: 0.6316 (m-80) REVERT: V 85 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6712 (mt-10) REVERT: W 70 MET cc_start: 0.7407 (mtt) cc_final: 0.6654 (mtt) REVERT: W 101 THR cc_start: 0.7197 (OUTLIER) cc_final: 0.6911 (m) REVERT: X 38 TYR cc_start: 0.6517 (m-80) cc_final: 0.6223 (m-80) outliers start: 50 outliers final: 15 residues processed: 244 average time/residue: 0.5009 time to fit residues: 184.5821 Evaluate side-chains 151 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 3.190 ------------------------------------------------------------------------------- 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 417 LYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 1031 GLU 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 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 144 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 316 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 362 optimal weight: 30.0000 chunk 326 optimal weight: 9.9990 chunk 220 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 935 GLN B 388 ASN B1135 ASN C 388 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN ** S 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN ** 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 = 0.3738 r_free = 0.3738 target = 0.078091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.048195 restraints weight = 129957.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.049842 restraints weight = 63561.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.050846 restraints weight = 41173.990| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 30229 Z= 0.302 Angle : 0.824 27.284 41235 Z= 0.419 Chirality : 0.049 0.254 4785 Planarity : 0.010 0.382 5208 Dihedral : 6.321 154.209 5094 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.85 % Allowed : 8.70 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.13), residues: 3630 helix: 1.49 (0.21), residues: 639 sheet: -0.09 (0.15), residues: 1041 loop : -0.92 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP S 104 HIS 0.012 0.002 HIS A1064 PHE 0.037 0.002 PHE C 486 TYR 0.043 0.002 TYR S 102 ARG 0.039 0.001 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 39) link_NAG-ASN : angle 2.16519 ( 117) link_BETA1-4 : bond 0.00618 ( 12) link_BETA1-4 : angle 1.82935 ( 36) hydrogen bonds : bond 0.07447 ( 1165) hydrogen bonds : angle 6.07608 ( 3204) SS BOND : bond 0.00291 ( 42) SS BOND : angle 1.46591 ( 84) covalent geometry : bond 0.00702 (30129) covalent geometry : angle 0.81414 (40998) Misc. bond : bond 0.00843 ( 7) *********************** 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 231 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 140 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8990 (pp) REVERT: A 505 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.8638 (t80) REVERT: C 417 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8655 (mtpt) REVERT: C 505 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8610 (t80) REVERT: S 70 MET cc_start: 0.6506 (mpp) cc_final: 0.5697 (mmm) REVERT: T 63 ARG cc_start: 0.8154 (ptt180) cc_final: 0.7727 (ptt180) REVERT: T 85 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6701 (mt-10) REVERT: U 70 MET cc_start: 0.6897 (mtt) cc_final: 0.5234 (mtt) REVERT: V 63 ARG cc_start: 0.8169 (ptt180) cc_final: 0.7732 (ptm160) REVERT: W 48 MET cc_start: 0.7078 (mmm) cc_final: 0.6782 (mpp) REVERT: X 63 ARG cc_start: 0.8034 (ptt90) cc_final: 0.7402 (ptt180) outliers start: 91 outliers final: 50 residues processed: 224 average time/residue: 0.4711 time to fit residues: 162.3196 Evaluate side-chains 170 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 116 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU 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 620 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN 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 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 385 THR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 417 LYS 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 697 MET 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 T residue 5 THR Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain X residue 5 THR 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 106 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 335 optimal weight: 50.0000 chunk 183 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 chunk 328 optimal weight: 4.9990 chunk 285 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 ** 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 3 GLN ** W 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 = 0.3756 r_free = 0.3756 target = 0.078757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.049130 restraints weight = 128361.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.050804 restraints weight = 62114.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.051832 restraints weight = 40023.500| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 30229 Z= 0.187 Angle : 0.669 25.635 41235 Z= 0.337 Chirality : 0.046 0.218 4785 Planarity : 0.009 0.276 5208 Dihedral : 6.001 159.536 5094 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.94 % Allowed : 10.67 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 3630 helix: 1.80 (0.21), residues: 660 sheet: -0.08 (0.15), residues: 1056 loop : -0.96 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP S 104 HIS 0.005 0.001 HIS A1064 PHE 0.019 0.001 PHE A 486 TYR 0.037 0.001 TYR S 102 ARG 0.022 0.001 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 39) link_NAG-ASN : angle 1.84482 ( 117) link_BETA1-4 : bond 0.00334 ( 12) link_BETA1-4 : angle 1.57615 ( 36) hydrogen bonds : bond 0.05998 ( 1165) hydrogen bonds : angle 5.61542 ( 3204) SS BOND : bond 0.00231 ( 42) SS BOND : angle 1.14930 ( 84) covalent geometry : bond 0.00427 (30129) covalent geometry : angle 0.65951 (40998) Misc. bond : bond 0.00593 ( 7) *********************** 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 181 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 119 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.8512 (t80) REVERT: B 403 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7906 (ttm-80) REVERT: C 417 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8569 (mtpt) REVERT: C 505 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8490 (t80) REVERT: S 19 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7258 (tptp) REVERT: S 70 MET cc_start: 0.6112 (mpp) cc_final: 0.4725 (mmt) REVERT: S 82 GLU cc_start: 0.8117 (tt0) cc_final: 0.7858 (tm-30) REVERT: T 63 ARG cc_start: 0.8203 (ptt180) cc_final: 0.7773 (ptt180) REVERT: T 85 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6753 (mt-10) REVERT: U 70 MET cc_start: 0.6252 (mtt) cc_final: 0.4749 (mtt) REVERT: W 48 MET cc_start: 0.6790 (mmm) cc_final: 0.6492 (mpp) outliers start: 62 outliers final: 31 residues processed: 177 average time/residue: 0.4992 time to fit residues: 136.1323 Evaluate side-chains 140 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 114 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 980 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 72 ARG 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 299 optimal weight: 0.9990 chunk 171 optimal weight: 0.0060 chunk 174 optimal weight: 0.5980 chunk 337 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 chunk 312 optimal weight: 40.0000 chunk 61 optimal weight: 5.9990 chunk 139 optimal weight: 0.0970 chunk 3 optimal weight: 0.5980 chunk 69 optimal weight: 0.0670 chunk 44 optimal weight: 5.9990 overall best weight: 0.2732 ------------------------------------------------------------------------------- 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 ** 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** V 41 HIS W 100 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.080188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050798 restraints weight = 128027.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.052524 restraints weight = 61555.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.053628 restraints weight = 39371.695| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.150 30229 Z= 0.114 Angle : 0.601 22.860 41235 Z= 0.302 Chirality : 0.044 0.232 4785 Planarity : 0.007 0.209 5208 Dihedral : 5.625 172.648 5094 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.78 % Allowed : 11.46 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3630 helix: 2.15 (0.21), residues: 663 sheet: 0.13 (0.15), residues: 1047 loop : -0.89 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP U 104 HIS 0.002 0.000 HIS B1083 PHE 0.014 0.001 PHE B 486 TYR 0.034 0.001 TYR U 102 ARG 0.028 0.001 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 39) link_NAG-ASN : angle 1.65460 ( 117) link_BETA1-4 : bond 0.00441 ( 12) link_BETA1-4 : angle 1.43222 ( 36) hydrogen bonds : bond 0.04887 ( 1165) hydrogen bonds : angle 5.18366 ( 3204) SS BOND : bond 0.00192 ( 42) SS BOND : angle 1.02984 ( 84) covalent geometry : bond 0.00251 (30129) covalent geometry : angle 0.59307 (40998) Misc. bond : bond 0.00593 ( 7) *********************** 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 177 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 120 time to evaluate : 3.433 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: A 403 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8041 (ttm-80) REVERT: A 505 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.8367 (t80) REVERT: A 532 ASN cc_start: 0.9134 (t0) cc_final: 0.8920 (t0) REVERT: B 117 LEU cc_start: 0.7840 (tp) cc_final: 0.7496 (mp) REVERT: C 117 LEU cc_start: 0.7949 (tp) cc_final: 0.7561 (mp) REVERT: C 239 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7497 (tp40) REVERT: C 403 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.8031 (ttm-80) REVERT: C 505 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.8419 (t80) REVERT: S 19 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.6816 (tptp) REVERT: S 70 MET cc_start: 0.6197 (mpp) cc_final: 0.5453 (mmt) REVERT: T 85 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6825 (mt-10) REVERT: U 70 MET cc_start: 0.6061 (mtt) cc_final: 0.4776 (mtt) REVERT: W 1 GLU cc_start: 0.7515 (tp30) cc_final: 0.7315 (tm-30) REVERT: W 48 MET cc_start: 0.6531 (mmm) cc_final: 0.6195 (mpp) outliers start: 57 outliers final: 25 residues processed: 174 average time/residue: 0.5138 time to fit residues: 142.1087 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 : 3.237 ------------------------------------------------------------------------------- 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 533 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 334 ASN 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 C residue 114 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 334 ASN 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 S residue 19 LYS Chi-restraints excluded: chain S residue 100 HIS Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 100 HIS 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 285 optimal weight: 3.9990 chunk 232 optimal weight: 8.9990 chunk 282 optimal weight: 0.3980 chunk 235 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 299 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 347 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ** S 105 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 100 HIS W 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.079569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.050036 restraints weight = 127663.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.051735 restraints weight = 61833.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.052797 restraints weight = 39761.386| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 30229 Z= 0.133 Angle : 0.601 23.508 41235 Z= 0.301 Chirality : 0.044 0.198 4785 Planarity : 0.007 0.312 5208 Dihedral : 5.510 168.795 5094 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.66 % Allowed : 11.33 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3630 helix: 2.19 (0.21), residues: 666 sheet: 0.10 (0.15), residues: 1050 loop : -0.86 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP U 104 HIS 0.004 0.001 HIS B1064 PHE 0.010 0.001 PHE C 543 TYR 0.027 0.001 TYR U 102 ARG 0.030 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 39) link_NAG-ASN : angle 1.62633 ( 117) link_BETA1-4 : bond 0.00282 ( 12) link_BETA1-4 : angle 1.44078 ( 36) hydrogen bonds : bond 0.04945 ( 1165) hydrogen bonds : angle 5.15495 ( 3204) SS BOND : bond 0.00295 ( 42) SS BOND : angle 1.29087 ( 84) covalent geometry : bond 0.00304 (30129) covalent geometry : angle 0.59228 (40998) Misc. bond : bond 0.00510 ( 7) *********************** 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 177 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 3.208 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: A 117 LEU cc_start: 0.7929 (tp) cc_final: 0.7554 (mp) REVERT: A 403 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7991 (ttm-80) REVERT: A 505 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.8300 (t80) REVERT: B 117 LEU cc_start: 0.7965 (tp) cc_final: 0.7558 (mp) REVERT: B 532 ASN cc_start: 0.9041 (t0) cc_final: 0.8752 (t0) REVERT: C 117 LEU cc_start: 0.8050 (tp) cc_final: 0.7645 (mp) REVERT: C 403 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7949 (ttm-80) REVERT: C 505 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8310 (t80) REVERT: S 70 MET cc_start: 0.6463 (mpp) cc_final: 0.5930 (mmm) REVERT: S 100 HIS cc_start: 0.5264 (OUTLIER) cc_final: 0.4985 (t-90) REVERT: T 85 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6837 (mt-10) REVERT: U 3 GLN cc_start: 0.8223 (mm110) cc_final: 0.7933 (tp-100) REVERT: U 70 MET cc_start: 0.5970 (mtt) cc_final: 0.4221 (mmt) REVERT: V 49 MET cc_start: 0.6968 (ptt) cc_final: 0.6641 (ptt) REVERT: W 70 MET cc_start: 0.6249 (mmt) cc_final: 0.5748 (mmm) REVERT: W 98 ARG cc_start: 0.6450 (tmm-80) cc_final: 0.6089 (ttp80) REVERT: W 100 HIS cc_start: 0.5104 (OUTLIER) cc_final: 0.4879 (t-90) outliers start: 53 outliers final: 29 residues processed: 175 average time/residue: 0.4762 time to fit residues: 131.0590 Evaluate side-chains 144 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 3.179 ------------------------------------------------------------------------------- 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 533 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 114 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 380 TYR 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 114 THR Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 334 ASN 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 S residue 72 ARG Chi-restraints excluded: chain S residue 100 HIS Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 100 HIS 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 323 optimal weight: 30.0000 chunk 183 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 320 optimal weight: 10.0000 chunk 210 optimal weight: 0.0970 chunk 150 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 365 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.078595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.049388 restraints weight = 127023.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.051043 restraints weight = 61741.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.052111 restraints weight = 39730.966| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 : 0.004 0.072 30229 Z= 0.176 Angle : 0.615 20.994 41235 Z= 0.311 Chirality : 0.044 0.202 4785 Planarity : 0.007 0.256 5208 Dihedral : 5.586 166.715 5094 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.69 % Allowed : 11.39 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3630 helix: 2.18 (0.21), residues: 666 sheet: 0.03 (0.15), residues: 1059 loop : -0.92 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP U 104 HIS 0.017 0.001 HIS S 100 PHE 0.015 0.001 PHE C 186 TYR 0.014 0.001 TYR U 33 ARG 0.026 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 39) link_NAG-ASN : angle 1.64840 ( 117) link_BETA1-4 : bond 0.00211 ( 12) link_BETA1-4 : angle 1.48126 ( 36) hydrogen bonds : bond 0.05333 ( 1165) hydrogen bonds : angle 5.21506 ( 3204) SS BOND : bond 0.00500 ( 42) SS BOND : angle 1.33945 ( 84) covalent geometry : bond 0.00408 (30129) covalent geometry : angle 0.60564 (40998) Misc. bond : bond 0.00398 ( 7) *********************** 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 165 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 111 time to evaluate : 3.199 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: A 403 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8016 (ttm-80) REVERT: A 505 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8265 (t80) REVERT: B 117 LEU cc_start: 0.8069 (tp) cc_final: 0.7623 (mp) REVERT: B 403 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8111 (ttm-80) REVERT: B 532 ASN cc_start: 0.8985 (t0) cc_final: 0.8719 (t0) REVERT: C 403 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.8015 (ttm-80) REVERT: C 505 TYR cc_start: 0.8780 (OUTLIER) cc_final: 0.8281 (t80) REVERT: S 70 MET cc_start: 0.6279 (mpp) cc_final: 0.4705 (mmt) REVERT: U 3 GLN cc_start: 0.8300 (mm110) cc_final: 0.8098 (tp-100) REVERT: U 70 MET cc_start: 0.6079 (mtt) cc_final: 0.4667 (mtt) REVERT: V 49 MET cc_start: 0.6963 (ptt) cc_final: 0.6569 (ptt) REVERT: W 70 MET cc_start: 0.6502 (mmt) cc_final: 0.5699 (mmm) REVERT: W 98 ARG cc_start: 0.6567 (tmm-80) cc_final: 0.5749 (tmm-80) outliers start: 54 outliers final: 36 residues processed: 163 average time/residue: 0.4512 time to fit residues: 118.3040 Evaluate side-chains 146 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 3.589 ------------------------------------------------------------------------------- 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 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 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 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 334 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 51 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 98 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 292 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 chunk 214 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 281 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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** S 100 HIS ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3679 r_free = 0.3679 target = 0.075082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.044972 restraints weight = 127972.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.046561 restraints weight = 65171.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.047578 restraints weight = 43258.975| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.5439 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= 0.247 Angle : 0.679 19.439 41235 Z= 0.346 Chirality : 0.046 0.232 4785 Planarity : 0.007 0.184 5208 Dihedral : 6.025 164.886 5094 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.00 % Allowed : 11.14 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3630 helix: 1.94 (0.20), residues: 666 sheet: -0.01 (0.15), residues: 1053 loop : -1.05 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP S 104 HIS 0.012 0.001 HIS U 100 PHE 0.034 0.002 PHE B 486 TYR 0.017 0.002 TYR T 51 ARG 0.021 0.001 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 39) link_NAG-ASN : angle 1.80753 ( 117) link_BETA1-4 : bond 0.00241 ( 12) link_BETA1-4 : angle 1.56409 ( 36) hydrogen bonds : bond 0.06219 ( 1165) hydrogen bonds : angle 5.49796 ( 3204) SS BOND : bond 0.00513 ( 42) SS BOND : angle 1.47454 ( 84) covalent geometry : bond 0.00575 (30129) covalent geometry : angle 0.66898 (40998) Misc. bond : bond 0.00329 ( 7) *********************** 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 176 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 112 time to evaluate : 3.691 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: A 403 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8100 (ttm-80) REVERT: A 505 TYR cc_start: 0.8930 (OUTLIER) cc_final: 0.8290 (t80) REVERT: B 117 LEU cc_start: 0.8211 (tp) cc_final: 0.7631 (mp) REVERT: B 403 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8135 (ttm-80) REVERT: B 532 ASN cc_start: 0.8993 (t0) cc_final: 0.8753 (t0) REVERT: C 403 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8107 (ttm-80) REVERT: C 434 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8708 (tp) REVERT: C 505 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.8230 (t80) REVERT: S 70 MET cc_start: 0.6544 (mpp) cc_final: 0.5987 (mmm) REVERT: U 70 MET cc_start: 0.6325 (mtt) cc_final: 0.4858 (mtt) REVERT: W 70 MET cc_start: 0.6966 (mmt) cc_final: 0.5885 (mmm) outliers start: 64 outliers final: 39 residues processed: 173 average time/residue: 0.4590 time to fit residues: 127.2060 Evaluate side-chains 152 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 107 time to evaluate : 3.505 ------------------------------------------------------------------------------- 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 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 533 LEU 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 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 318 PHE Chi-restraints excluded: chain C residue 334 ASN 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 434 ILE 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 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 51 TYR Chi-restraints excluded: chain X residue 63 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 272 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 263 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 313 optimal weight: 30.0000 chunk 236 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 353 optimal weight: 6.9990 chunk 201 optimal weight: 0.4980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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** S 3 GLN S 100 HIS ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 GLN W 3 GLN ** 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 = 0.3713 r_free = 0.3713 target = 0.076627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.046810 restraints weight = 126380.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.048463 restraints weight = 63474.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.049536 restraints weight = 41793.491| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30229 Z= 0.119 Angle : 0.592 20.457 41235 Z= 0.301 Chirality : 0.044 0.182 4785 Planarity : 0.006 0.179 5208 Dihedral : 5.723 165.042 5094 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.22 % Allowed : 12.27 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3630 helix: 2.29 (0.21), residues: 666 sheet: 0.05 (0.15), residues: 1053 loop : -0.92 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP U 104 HIS 0.010 0.001 HIS W 100 PHE 0.030 0.001 PHE B 486 TYR 0.017 0.001 TYR C 904 ARG 0.023 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 39) link_NAG-ASN : angle 1.59644 ( 117) link_BETA1-4 : bond 0.00436 ( 12) link_BETA1-4 : angle 1.41192 ( 36) hydrogen bonds : bond 0.05143 ( 1165) hydrogen bonds : angle 5.12999 ( 3204) SS BOND : bond 0.00324 ( 42) SS BOND : angle 1.33305 ( 84) covalent geometry : bond 0.00262 (30129) covalent geometry : angle 0.58288 (40998) Misc. bond : bond 0.00358 ( 7) *********************** 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 153 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 3.383 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: A 403 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8153 (ttm-80) REVERT: A 505 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.8262 (t80) REVERT: B 117 LEU cc_start: 0.8209 (tp) cc_final: 0.7681 (mp) REVERT: B 532 ASN cc_start: 0.9004 (t0) cc_final: 0.8776 (t0) REVERT: C 403 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8155 (ttm-80) REVERT: C 434 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8739 (tp) REVERT: C 505 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.8204 (t80) REVERT: S 70 MET cc_start: 0.6393 (mpp) cc_final: 0.5992 (mmm) REVERT: U 70 MET cc_start: 0.6209 (mtt) cc_final: 0.4985 (mtt) REVERT: W 70 MET cc_start: 0.7054 (mmt) cc_final: 0.5972 (mmm) outliers start: 39 outliers final: 30 residues processed: 150 average time/residue: 0.4473 time to fit residues: 107.3653 Evaluate side-chains 142 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 3.147 ------------------------------------------------------------------------------- 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 533 LEU 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 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 1094 VAL 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 403 ARG Chi-restraints excluded: chain C residue 434 ILE 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 S residue 72 ARG Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 51 TYR Chi-restraints excluded: chain X residue 63 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 315 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 357 optimal weight: 40.0000 chunk 184 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 290 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 388 ASN C 901 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.074742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.044649 restraints weight = 128503.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.046235 restraints weight = 65718.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 77)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.047266 restraints weight = 43784.492| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 30229 Z= 0.257 Angle : 0.691 23.324 41235 Z= 0.348 Chirality : 0.046 0.252 4785 Planarity : 0.007 0.170 5208 Dihedral : 6.049 161.925 5094 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.35 % Allowed : 12.14 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3630 helix: 2.02 (0.20), residues: 663 sheet: -0.06 (0.15), residues: 1044 loop : -1.02 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP U 104 HIS 0.006 0.001 HIS A1064 PHE 0.031 0.002 PHE B 486 TYR 0.017 0.002 TYR C 904 ARG 0.027 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 39) link_NAG-ASN : angle 1.81546 ( 117) link_BETA1-4 : bond 0.00341 ( 12) link_BETA1-4 : angle 1.56776 ( 36) hydrogen bonds : bond 0.06096 ( 1165) hydrogen bonds : angle 5.45260 ( 3204) SS BOND : bond 0.00362 ( 42) SS BOND : angle 1.55612 ( 84) covalent geometry : bond 0.00599 (30129) covalent geometry : angle 0.68085 (40998) Misc. bond : bond 0.00334 ( 7) ********************** 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 154 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 3.266 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: A 403 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8083 (ttm-80) REVERT: A 505 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.8255 (t80) REVERT: B 403 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8157 (ttm-80) REVERT: B 900 MET cc_start: 0.8530 (ptp) cc_final: 0.8322 (mtp) REVERT: C 403 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8046 (ttm-80) REVERT: C 486 PHE cc_start: 0.6754 (OUTLIER) cc_final: 0.5932 (t80) REVERT: C 505 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8166 (t80) REVERT: S 70 MET cc_start: 0.6524 (mpp) cc_final: 0.6001 (mmm) REVERT: V 49 MET cc_start: 0.7053 (ptt) cc_final: 0.6782 (ptt) REVERT: W 70 MET cc_start: 0.6521 (mmt) cc_final: 0.5448 (mmm) outliers start: 43 outliers final: 32 residues processed: 149 average time/residue: 0.4553 time to fit residues: 112.7950 Evaluate side-chains 143 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 3.043 ------------------------------------------------------------------------------- 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 533 LEU 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 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 1094 VAL 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 403 ARG Chi-restraints excluded: chain C residue 486 PHE 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 S residue 72 ARG Chi-restraints excluded: chain T residue 51 TYR Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain V residue 51 TYR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 51 TYR Chi-restraints excluded: chain X residue 63 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 221 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 286 optimal weight: 0.9980 chunk 270 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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** ** U 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 35 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 = 0.3704 r_free = 0.3704 target = 0.076561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.047559 restraints weight = 127843.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.049162 restraints weight = 63524.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.050196 restraints weight = 41472.722| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30229 Z= 0.135 Angle : 0.601 19.972 41235 Z= 0.304 Chirality : 0.044 0.175 4785 Planarity : 0.006 0.162 5208 Dihedral : 5.805 160.141 5094 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.25 % Allowed : 12.39 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3630 helix: 2.30 (0.21), residues: 666 sheet: 0.03 (0.15), residues: 1050 loop : -0.95 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP U 104 HIS 0.004 0.001 HIS W 100 PHE 0.028 0.001 PHE B 486 TYR 0.012 0.001 TYR S 102 ARG 0.027 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 39) link_NAG-ASN : angle 1.59914 ( 117) link_BETA1-4 : bond 0.00336 ( 12) link_BETA1-4 : angle 1.43632 ( 36) hydrogen bonds : bond 0.05186 ( 1165) hydrogen bonds : angle 5.17421 ( 3204) SS BOND : bond 0.00414 ( 42) SS BOND : angle 1.30028 ( 84) covalent geometry : bond 0.00306 (30129) covalent geometry : angle 0.59175 (40998) Misc. bond : bond 0.00378 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12891.03 seconds wall clock time: 225 minutes 56.19 seconds (13556.19 seconds total)