Starting phenix.real_space_refine on Sat Aug 8 00:50:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ysk_73394/08_2026/9ysk_73394.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ysk_73394/08_2026/9ysk_73394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ysk_73394/08_2026/9ysk_73394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ysk_73394/08_2026/9ysk_73394.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ysk_73394/08_2026/9ysk_73394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ysk_73394/08_2026/9ysk_73394.map" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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 102 5.16 5 C 15352 2.51 5 N 3898 2.21 5 O 4658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24010 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 7916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7916 Classifications: {'peptide': 1009} Link IDs: {'PTRANS': 54, 'TRANS': 954} Chain breaks: 9 Chain: "B" Number of atoms: 7685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7685 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 52, 'TRANS': 928} Chain breaks: 11 Chain: "C" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7835 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 9 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.08, per 1000 atoms: 0.21 Number of scatterers: 24010 At special positions: 0 Unit cell: (129.792, 128.128, 184.704, 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 102 16.00 O 4658 8.00 N 3898 7.00 C 15352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 354 " " NAG A1306 " - " ASN A 282 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 354 " " NAG B1306 " - " ASN B 282 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 354 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C 282 " " NAG D 1 " - " ASN A 801 " " NAG E 1 " - " ASN A1134 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C 801 " Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 848.3 milliseconds 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5618 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 40 sheets defined 27.2% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.949A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 748 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 759 through 783 Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.610A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.910A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.643A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.548A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.036A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1148 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.757A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.515A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 626 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 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.646A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.931A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.534A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1148 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.945A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.381A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.661A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 3.987A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.212A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1148 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 7.880A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.598A 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: 6.261A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.801A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.075A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.919A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.373A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.941A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.537A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.537A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.435A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.668A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 29 removed outlier: 5.377A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.006A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.160A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.977A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 6.770A pdb=" N GLU B 516 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL B 395 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N SER B 514 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA B 397 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL B 512 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER B 399 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL B 510 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B 401 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYR B 508 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.002A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.399A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.399A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.513A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 787 through 790 removed outlier: 5.541A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 5.597A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.051A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.908A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.886A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.539A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.539A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.993A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.584A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.584A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.529A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1122 1033 hydrogen bonds defined for protein. 2856 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: 5.39 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7519 1.34 - 1.46: 6020 1.46 - 1.58: 10893 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 24560 Sorted by residual: bond pdb=" N GLU A 465 " pdb=" CA GLU A 465 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.25e-02 6.40e+03 6.54e+00 bond pdb=" N VAL A 534 " pdb=" CA VAL A 534 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.40e+00 bond pdb=" N ARG A 466 " pdb=" CA ARG A 466 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.21e-02 6.83e+03 6.25e+00 bond pdb=" N THR A 430 " pdb=" CA THR A 430 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.17e-02 7.31e+03 4.90e+00 bond pdb=" N ASP A 467 " pdb=" CA ASP A 467 " ideal model delta sigma weight residual 1.461 1.489 -0.027 1.38e-02 5.25e+03 3.94e+00 ... (remaining 24555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 33273 2.98 - 5.96: 132 5.96 - 8.94: 6 8.94 - 11.92: 3 11.92 - 14.89: 3 Bond angle restraints: 33417 Sorted by residual: angle pdb=" CB LYS A 529 " pdb=" CG LYS A 529 " pdb=" CD LYS A 529 " ideal model delta sigma weight residual 111.30 121.53 -10.23 2.30e+00 1.89e-01 1.98e+01 angle pdb=" CA LEU C 118 " pdb=" CB LEU C 118 " pdb=" CG LEU C 118 " ideal model delta sigma weight residual 116.30 131.19 -14.89 3.50e+00 8.16e-02 1.81e+01 angle pdb=" CB MET B 177 " pdb=" CG MET B 177 " pdb=" SD MET B 177 " ideal model delta sigma weight residual 112.70 124.90 -12.20 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CA LEU B 118 " pdb=" CB LEU B 118 " pdb=" CG LEU B 118 " ideal model delta sigma weight residual 116.30 130.11 -13.81 3.50e+00 8.16e-02 1.56e+01 angle pdb=" CA GLN C1142 " pdb=" CB GLN C1142 " pdb=" CG GLN C1142 " ideal model delta sigma weight residual 114.10 121.40 -7.30 2.00e+00 2.50e-01 1.33e+01 ... (remaining 33412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 13471 17.72 - 35.44: 1258 35.44 - 53.16: 306 53.16 - 70.88: 84 70.88 - 88.60: 24 Dihedral angle restraints: 15143 sinusoidal: 6433 harmonic: 8710 Sorted by residual: dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -36.90 -49.10 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 -44.62 -41.38 1 1.00e+01 1.00e-02 2.40e+01 dihedral pdb=" CA LEU A 117 " pdb=" C LEU A 117 " pdb=" N LEU A 118 " pdb=" CA LEU A 118 " ideal model delta harmonic sigma weight residual -180.00 -155.65 -24.35 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 15140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3105 0.048 - 0.096: 593 0.096 - 0.144: 221 0.144 - 0.192: 5 0.192 - 0.240: 4 Chirality restraints: 3928 Sorted by residual: chirality pdb=" CG LEU A 229 " pdb=" CB LEU A 229 " pdb=" CD1 LEU A 229 " pdb=" CD2 LEU A 229 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C2 NAG B1306 " pdb=" C1 NAG B1306 " pdb=" C3 NAG B1306 " pdb=" N2 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.49 -2.27 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA VAL A 534 " pdb=" N VAL A 534 " pdb=" C VAL A 534 " pdb=" CB VAL A 534 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 3925 not shown) Planarity restraints: 4269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 466 " 0.220 9.50e-02 1.11e+02 9.86e-02 5.96e+00 pdb=" NE ARG A 466 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 466 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 466 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 466 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 86 " -0.009 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C PHE A 86 " 0.034 2.00e-02 2.50e+03 pdb=" O PHE A 86 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A 87 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 983 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.63e+00 pdb=" C ARG A 983 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG A 983 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU A 984 " 0.011 2.00e-02 2.50e+03 ... (remaining 4266 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2766 2.75 - 3.29: 22801 3.29 - 3.83: 40697 3.83 - 4.36: 47737 4.36 - 4.90: 83264 Nonbonded interactions: 197265 Sorted by model distance: nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR A 200 " pdb=" OD1 ASN B 394 " model vdw 2.242 3.040 nonbonded pdb=" OE1 GLN A 321 " pdb=" OG1 THR A 630 " model vdw 2.265 3.040 nonbonded pdb=" O SER A 637 " pdb=" OG SER A 637 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.289 3.040 ... (remaining 197260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 29 or resid 32 through 136 or resid 155 through \ 176 or resid 188 through 243 or resid 265 through 443 or resid 453 through 469 \ or resid 491 through 517 or resid 523 through 827 or resid 856 through 1148 or r \ esid 1301 through 1306)) selection = (chain 'B' and (resid 25 through 65 or resid 82 through 176 or resid 188 through \ 210 or resid 217 through 827 or resid 856 through 1306)) selection = (chain 'C' and (resid 26 through 30 or resid 32 through 65 or resid 82 through 1 \ 36 or resid 155 through 176 or resid 188 through 210 or resid 217 through 243 or \ resid 265 through 443 or resid 453 through 469 or resid 491 through 517 or resi \ d 523 through 1148 or resid 1302 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.890 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 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 : 0.003 0.045 24636 Z= 0.123 Angle : 0.525 14.894 33610 Z= 0.270 Chirality : 0.043 0.240 3928 Planarity : 0.003 0.099 4239 Dihedral : 14.900 88.596 9420 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.76 % Allowed : 18.31 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.15), residues: 2925 helix: 2.84 (0.19), residues: 722 sheet: -0.24 (0.19), residues: 639 loop : -0.94 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 983 TYR 0.021 0.001 TYR B 904 PHE 0.033 0.001 PHE B 127 TRP 0.010 0.001 TRP C 633 HIS 0.001 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (24560) covalent geometry : angle 0.51744 / 0.27 (33417) SS BOND : bond 0.00119 / 0.08 ( 35) SS BOND : angle 0.47536 / 0.29 ( 70) hydrogen bonds : bond 0.10697 / 6.60 ( 991) hydrogen bonds : angle 6.34809 / 4.46 ( 2856) link_BETA1-4 : bond 0.00271 / 0.16 ( 11) link_BETA1-4 : angle 0.96522 / 0.59 ( 33) link_NAG-ASN : bond 0.00328 / 0.24 ( 30) link_NAG-ASN : angle 1.74005 / 1.13 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.862 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: A 99 ASN cc_start: 0.9163 (m-40) cc_final: 0.8813 (t0) REVERT: A 173 GLN cc_start: 0.9032 (mt0) cc_final: 0.8772 (tm130) REVERT: A 269 TYR cc_start: 0.8466 (m-80) cc_final: 0.8037 (m-80) REVERT: A 347 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7636 (t80) REVERT: A 516 GLU cc_start: 0.8312 (tp30) cc_final: 0.7998 (tm-30) REVERT: A 568 ASP cc_start: 0.8508 (t0) cc_final: 0.8205 (t0) REVERT: A 740 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8687 (ttp) REVERT: A 814 LYS cc_start: 0.9049 (mtmt) cc_final: 0.8751 (mmtm) REVERT: A 985 ASP cc_start: 0.8331 (m-30) cc_final: 0.8081 (p0) REVERT: A 994 ASP cc_start: 0.8762 (t70) cc_final: 0.8528 (t70) REVERT: A 1092 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8394 (pt0) REVERT: B 127 PHE cc_start: 0.8262 (t80) cc_final: 0.8035 (t80) REVERT: B 353 TRP cc_start: 0.7401 (p-90) cc_final: 0.7098 (p-90) REVERT: B 509 ARG cc_start: 0.7944 (mtt180) cc_final: 0.7394 (mmm-85) REVERT: B 568 ASP cc_start: 0.8782 (t0) cc_final: 0.8479 (t0) REVERT: B 1005 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8599 (mt0) REVERT: C 32 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7261 (t80) REVERT: C 127 PHE cc_start: 0.7334 (m-80) cc_final: 0.7111 (m-80) REVERT: C 173 GLN cc_start: 0.9015 (mp10) cc_final: 0.8677 (tm130) REVERT: C 239 GLN cc_start: 0.8924 (pt0) cc_final: 0.8421 (pt0) REVERT: C 347 PHE cc_start: 0.7111 (p90) cc_final: 0.6895 (p90) REVERT: C 421 TYR cc_start: 0.8855 (m-80) cc_final: 0.8161 (m-80) REVERT: C 571 ASP cc_start: 0.9056 (m-30) cc_final: 0.8571 (t0) REVERT: C 586 ASP cc_start: 0.8224 (m-30) cc_final: 0.8016 (m-30) REVERT: C 988 GLU cc_start: 0.8573 (pm20) cc_final: 0.8199 (pm20) outliers start: 20 outliers final: 15 residues processed: 211 average time/residue: 0.5125 time to fit residues: 127.9873 Evaluate side-chains 175 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN A 751 ASN A1002 GLN B 239 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.092529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.056609 restraints weight = 52185.804| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.82 r_work: 0.2674 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24636 Z= 0.166 Angle : 0.519 10.093 33610 Z= 0.268 Chirality : 0.043 0.233 3928 Planarity : 0.003 0.042 4239 Dihedral : 5.016 74.180 4081 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.73 % Allowed : 16.91 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 2925 helix: 2.78 (0.19), residues: 723 sheet: -0.09 (0.19), residues: 641 loop : -0.96 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 34 TYR 0.020 0.001 TYR A1067 PHE 0.019 0.001 PHE A 168 TRP 0.009 0.001 TRP C 633 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (24560) covalent geometry : angle 0.50978 / 0.27 (33417) SS BOND : bond 0.00194 / 0.13 ( 35) SS BOND : angle 0.68119 / 0.43 ( 70) hydrogen bonds : bond 0.04226 / 2.68 ( 991) hydrogen bonds : angle 5.34604 / 3.73 ( 2856) link_BETA1-4 : bond 0.00307 / 0.20 ( 11) link_BETA1-4 : angle 1.05528 / 0.64 ( 33) link_NAG-ASN : bond 0.00294 / 0.21 ( 30) link_NAG-ASN : angle 1.86619 / 1.22 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 160 time to evaluate : 0.827 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: A 99 ASN cc_start: 0.9044 (m-40) cc_final: 0.8836 (t0) REVERT: A 118 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8616 (tm) REVERT: A 173 GLN cc_start: 0.9000 (mt0) cc_final: 0.8757 (tm130) REVERT: A 269 TYR cc_start: 0.8836 (m-80) cc_final: 0.8216 (m-80) REVERT: A 347 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7730 (t80) REVERT: A 490 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7766 (p90) REVERT: A 516 GLU cc_start: 0.8317 (tp30) cc_final: 0.8044 (tm-30) REVERT: A 568 ASP cc_start: 0.8681 (t0) cc_final: 0.8336 (t0) REVERT: A 636 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.8210 (t80) REVERT: A 780 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8996 (mm-30) REVERT: A 814 LYS cc_start: 0.9078 (mtmt) cc_final: 0.8824 (mmtm) REVERT: A 994 ASP cc_start: 0.8891 (t70) cc_final: 0.8640 (t70) REVERT: B 99 ASN cc_start: 0.9087 (m-40) cc_final: 0.8521 (p0) REVERT: B 127 PHE cc_start: 0.8364 (t80) cc_final: 0.8131 (t80) REVERT: B 160 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.6480 (m-80) REVERT: B 314 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8591 (tm-30) REVERT: B 353 TRP cc_start: 0.7238 (p-90) cc_final: 0.7000 (p-90) REVERT: B 509 ARG cc_start: 0.8006 (mtt180) cc_final: 0.7409 (mmm-85) REVERT: B 988 GLU cc_start: 0.9172 (mp0) cc_final: 0.8568 (pm20) REVERT: B 1005 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8739 (mt0) REVERT: C 32 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7220 (t80) REVERT: C 127 PHE cc_start: 0.7640 (m-80) cc_final: 0.7158 (m-80) REVERT: C 173 GLN cc_start: 0.9051 (mp10) cc_final: 0.8789 (tm130) REVERT: C 239 GLN cc_start: 0.8949 (pt0) cc_final: 0.8468 (pt0) REVERT: C 324 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: C 421 TYR cc_start: 0.8870 (m-80) cc_final: 0.8008 (m-80) REVERT: C 516 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6525 (tm-30) REVERT: C 571 ASP cc_start: 0.9113 (OUTLIER) cc_final: 0.8816 (t0) outliers start: 72 outliers final: 28 residues processed: 216 average time/residue: 0.4555 time to fit residues: 119.2454 Evaluate side-chains 185 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 79 optimal weight: 0.6980 chunk 177 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 59 optimal weight: 0.0000 chunk 190 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN B 239 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B1010 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.093474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.057880 restraints weight = 52341.319| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.82 r_work: 0.2748 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24636 Z= 0.103 Angle : 0.481 11.122 33610 Z= 0.246 Chirality : 0.042 0.231 3928 Planarity : 0.003 0.042 4239 Dihedral : 4.537 55.860 4061 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.43 % Allowed : 17.70 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.15), residues: 2925 helix: 2.88 (0.19), residues: 714 sheet: -0.06 (0.19), residues: 631 loop : -0.93 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.018 0.001 TYR A1067 PHE 0.020 0.001 PHE B 168 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.000 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (24560) covalent geometry : angle 0.47127 / 0.24 (33417) SS BOND : bond 0.00137 / 0.09 ( 35) SS BOND : angle 0.60878 / 0.39 ( 70) hydrogen bonds : bond 0.03679 / 2.34 ( 991) hydrogen bonds : angle 5.10369 / 3.55 ( 2856) link_BETA1-4 : bond 0.00338 / 0.20 ( 11) link_BETA1-4 : angle 0.94740 / 0.58 ( 33) link_NAG-ASN : bond 0.00313 / 0.23 ( 30) link_NAG-ASN : angle 1.77906 / 1.17 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 166 time to evaluate : 0.975 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: A 118 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8689 (tm) REVERT: A 173 GLN cc_start: 0.8980 (mt0) cc_final: 0.8733 (tm130) REVERT: A 269 TYR cc_start: 0.8795 (m-80) cc_final: 0.8209 (m-80) REVERT: A 490 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7754 (p90) REVERT: A 516 GLU cc_start: 0.8280 (tp30) cc_final: 0.8039 (tm-30) REVERT: A 568 ASP cc_start: 0.8718 (t0) cc_final: 0.8399 (t0) REVERT: A 636 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.8206 (t80) REVERT: A 780 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8859 (mt-10) REVERT: A 814 LYS cc_start: 0.9041 (mtmt) cc_final: 0.8798 (mmtm) REVERT: A 994 ASP cc_start: 0.8844 (t70) cc_final: 0.8597 (t70) REVERT: B 81 ASN cc_start: 0.7510 (OUTLIER) cc_final: 0.7130 (t0) REVERT: B 99 ASN cc_start: 0.9043 (m-40) cc_final: 0.8507 (p0) REVERT: B 160 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.6491 (m-80) REVERT: B 314 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8568 (tm-30) REVERT: B 350 VAL cc_start: 0.7265 (OUTLIER) cc_final: 0.7003 (t) REVERT: B 509 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7366 (mmm-85) REVERT: B 988 GLU cc_start: 0.9200 (mp0) cc_final: 0.8558 (pm20) REVERT: B 1005 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8706 (mt0) REVERT: C 115 GLN cc_start: 0.8784 (mp10) cc_final: 0.8426 (mm-40) REVERT: C 127 PHE cc_start: 0.7692 (m-80) cc_final: 0.7134 (m-80) REVERT: C 173 GLN cc_start: 0.9049 (mp10) cc_final: 0.8789 (tm130) REVERT: C 239 GLN cc_start: 0.8911 (pt0) cc_final: 0.8424 (pt0) REVERT: C 324 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8402 (pm20) REVERT: C 369 TYR cc_start: 0.9006 (m-80) cc_final: 0.8770 (m-80) REVERT: C 421 TYR cc_start: 0.8904 (m-80) cc_final: 0.8049 (m-80) REVERT: C 529 LYS cc_start: 0.9229 (mtpp) cc_final: 0.8970 (tppp) REVERT: C 571 ASP cc_start: 0.9108 (m-30) cc_final: 0.8812 (t0) outliers start: 64 outliers final: 21 residues processed: 213 average time/residue: 0.4915 time to fit residues: 126.8363 Evaluate side-chains 175 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 214 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 293 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 chunk 191 optimal weight: 0.0070 chunk 122 optimal weight: 0.3980 chunk 230 optimal weight: 9.9990 chunk 265 optimal weight: 3.9990 chunk 9 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 978 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1010 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.057926 restraints weight = 52129.739| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.80 r_work: 0.2725 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24636 Z= 0.121 Angle : 0.492 11.813 33610 Z= 0.250 Chirality : 0.042 0.229 3928 Planarity : 0.003 0.045 4239 Dihedral : 4.195 55.654 4049 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.46 % Allowed : 17.82 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 2925 helix: 2.85 (0.19), residues: 716 sheet: -0.09 (0.19), residues: 652 loop : -0.92 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 34 TYR 0.019 0.001 TYR A1067 PHE 0.029 0.001 PHE C 168 TRP 0.008 0.001 TRP A 452 HIS 0.002 0.000 HIS C 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (24560) covalent geometry : angle 0.48293 / 0.25 (33417) SS BOND : bond 0.00151 / 0.10 ( 35) SS BOND : angle 0.60613 / 0.39 ( 70) hydrogen bonds : bond 0.03712 / 2.36 ( 991) hydrogen bonds : angle 5.02285 / 3.49 ( 2856) link_BETA1-4 : bond 0.00275 / 0.17 ( 11) link_BETA1-4 : angle 1.00391 / 0.61 ( 33) link_NAG-ASN : bond 0.00284 / 0.21 ( 30) link_NAG-ASN : angle 1.78057 / 1.17 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 157 time to evaluate : 0.974 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: A 99 ASN cc_start: 0.9244 (m110) cc_final: 0.8905 (t0) REVERT: A 118 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8633 (tm) REVERT: A 173 GLN cc_start: 0.8963 (mt0) cc_final: 0.8716 (tm130) REVERT: A 269 TYR cc_start: 0.8825 (m-80) cc_final: 0.8236 (m-80) REVERT: A 347 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.7731 (t80) REVERT: A 490 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7789 (p90) REVERT: A 492 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.5352 (pp) REVERT: A 516 GLU cc_start: 0.8309 (tp30) cc_final: 0.8055 (tm-30) REVERT: A 568 ASP cc_start: 0.8789 (t0) cc_final: 0.8474 (t0) REVERT: A 636 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8195 (t80) REVERT: A 748 GLU cc_start: 0.8991 (mp0) cc_final: 0.8517 (mp0) REVERT: A 780 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8943 (mt-10) REVERT: A 814 LYS cc_start: 0.9050 (mtmt) cc_final: 0.8824 (mmtm) REVERT: A 994 ASP cc_start: 0.8883 (t70) cc_final: 0.8628 (t70) REVERT: B 81 ASN cc_start: 0.7601 (OUTLIER) cc_final: 0.7359 (t0) REVERT: B 99 ASN cc_start: 0.9040 (m-40) cc_final: 0.8509 (p0) REVERT: B 160 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.6511 (m-80) REVERT: B 314 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8623 (tm-30) REVERT: B 509 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7384 (mmm-85) REVERT: B 516 GLU cc_start: 0.8340 (tp30) cc_final: 0.8013 (tp30) REVERT: B 1005 GLN cc_start: 0.9111 (mm-40) cc_final: 0.8764 (mt0) REVERT: C 32 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7266 (t80) REVERT: C 115 GLN cc_start: 0.8835 (mp10) cc_final: 0.8453 (mm-40) REVERT: C 127 PHE cc_start: 0.7670 (m-80) cc_final: 0.7101 (m-80) REVERT: C 173 GLN cc_start: 0.9068 (mp10) cc_final: 0.8809 (tm130) REVERT: C 191 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8811 (mt-10) REVERT: C 239 GLN cc_start: 0.8954 (pt0) cc_final: 0.8505 (pt0) REVERT: C 324 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8328 (pm20) REVERT: C 369 TYR cc_start: 0.8983 (m-80) cc_final: 0.8773 (m-80) REVERT: C 421 TYR cc_start: 0.8928 (m-80) cc_final: 0.7997 (m-80) REVERT: C 529 LYS cc_start: 0.9237 (mtpp) cc_final: 0.8983 (tppp) REVERT: C 571 ASP cc_start: 0.9093 (m-30) cc_final: 0.8815 (t0) outliers start: 65 outliers final: 25 residues processed: 207 average time/residue: 0.4999 time to fit residues: 124.9043 Evaluate side-chains 190 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 10 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 289 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 175 optimal weight: 0.4980 chunk 226 optimal weight: 0.9990 chunk 249 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1010 GLN C 422 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.091639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.055954 restraints weight = 52261.008| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.78 r_work: 0.2676 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24636 Z= 0.223 Angle : 0.535 12.157 33610 Z= 0.272 Chirality : 0.044 0.224 3928 Planarity : 0.003 0.046 4239 Dihedral : 4.466 55.106 4049 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.92 % Allowed : 17.29 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 2925 helix: 2.73 (0.19), residues: 713 sheet: -0.13 (0.19), residues: 652 loop : -0.96 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.018 0.001 TYR A1067 PHE 0.018 0.001 PHE C 168 TRP 0.009 0.001 TRP C 633 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (24560) covalent geometry : angle 0.52545 / 0.27 (33417) SS BOND : bond 0.00260 / 0.16 ( 35) SS BOND : angle 0.75567 / 0.48 ( 70) hydrogen bonds : bond 0.04422 / 2.81 ( 991) hydrogen bonds : angle 5.18960 / 3.61 ( 2856) link_BETA1-4 : bond 0.00159 / 0.08 ( 11) link_BETA1-4 : angle 1.10430 / 0.68 ( 33) link_NAG-ASN : bond 0.00329 / 0.22 ( 30) link_NAG-ASN : angle 1.89530 / 1.25 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 159 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.9262 (m110) cc_final: 0.8863 (t0) REVERT: A 118 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8680 (tm) REVERT: A 173 GLN cc_start: 0.8932 (mt0) cc_final: 0.8687 (tm130) REVERT: A 269 TYR cc_start: 0.8897 (m-80) cc_final: 0.8665 (m-80) REVERT: A 347 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7679 (t80) REVERT: A 490 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.7833 (p90) REVERT: A 516 GLU cc_start: 0.8186 (tp30) cc_final: 0.7985 (tm-30) REVERT: A 568 ASP cc_start: 0.8825 (t0) cc_final: 0.8526 (t0) REVERT: A 636 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.8257 (t80) REVERT: A 743 CYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7375 (m) REVERT: A 748 GLU cc_start: 0.9029 (mp0) cc_final: 0.8518 (mp0) REVERT: A 780 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8978 (mt-10) REVERT: A 814 LYS cc_start: 0.9066 (mtmt) cc_final: 0.8847 (mmtm) REVERT: A 994 ASP cc_start: 0.8946 (t70) cc_final: 0.8681 (t70) REVERT: B 99 ASN cc_start: 0.9088 (m-40) cc_final: 0.8581 (p0) REVERT: B 160 TYR cc_start: 0.6837 (OUTLIER) cc_final: 0.6337 (m-80) REVERT: B 314 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8636 (tm-30) REVERT: B 378 LYS cc_start: 0.8413 (ttpp) cc_final: 0.8192 (tmmt) REVERT: B 509 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7366 (mmm-85) REVERT: B 516 GLU cc_start: 0.8365 (tp30) cc_final: 0.8012 (tp30) REVERT: B 602 THR cc_start: 0.9331 (OUTLIER) cc_final: 0.9008 (p) REVERT: B 988 GLU cc_start: 0.9154 (mp0) cc_final: 0.8647 (pm20) REVERT: B 990 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8211 (mm-30) REVERT: B 1005 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8739 (mt0) REVERT: C 115 GLN cc_start: 0.8854 (mp10) cc_final: 0.8386 (mm-40) REVERT: C 127 PHE cc_start: 0.7794 (m-80) cc_final: 0.7223 (m-80) REVERT: C 173 GLN cc_start: 0.9096 (mp10) cc_final: 0.8875 (tm130) REVERT: C 191 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8861 (mt-10) REVERT: C 239 GLN cc_start: 0.9014 (pt0) cc_final: 0.8550 (pt0) REVERT: C 421 TYR cc_start: 0.8903 (m-80) cc_final: 0.7981 (m-80) REVERT: C 529 LYS cc_start: 0.9249 (mtpp) cc_final: 0.9000 (tppp) REVERT: C 571 ASP cc_start: 0.9089 (m-30) cc_final: 0.8831 (t0) outliers start: 77 outliers final: 40 residues processed: 219 average time/residue: 0.4887 time to fit residues: 129.8463 Evaluate side-chains 196 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 255 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 280 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1010 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.091971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.056306 restraints weight = 52393.949| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.79 r_work: 0.2686 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24636 Z= 0.171 Angle : 0.527 13.036 33610 Z= 0.266 Chirality : 0.043 0.224 3928 Planarity : 0.003 0.048 4239 Dihedral : 4.472 55.384 4049 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.65 % Allowed : 17.97 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.15), residues: 2925 helix: 2.80 (0.19), residues: 707 sheet: -0.12 (0.19), residues: 649 loop : -0.95 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.018 0.001 TYR A1067 PHE 0.025 0.001 PHE B 127 TRP 0.009 0.001 TRP C 633 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (24560) covalent geometry : angle 0.51783 / 0.26 (33417) SS BOND : bond 0.00210 / 0.14 ( 35) SS BOND : angle 0.70978 / 0.45 ( 70) hydrogen bonds : bond 0.04123 / 2.62 ( 991) hydrogen bonds : angle 5.13544 / 3.57 ( 2856) link_BETA1-4 : bond 0.00185 / 0.11 ( 11) link_BETA1-4 : angle 1.00352 / 0.62 ( 33) link_NAG-ASN : bond 0.00322 / 0.23 ( 30) link_NAG-ASN : angle 1.86372 / 1.23 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 150 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.9262 (m110) cc_final: 0.8871 (t0) REVERT: A 118 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8735 (tm) REVERT: A 173 GLN cc_start: 0.8958 (mt0) cc_final: 0.8665 (tm130) REVERT: A 269 TYR cc_start: 0.8890 (m-80) cc_final: 0.8638 (m-80) REVERT: A 333 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8805 (t) REVERT: A 347 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7678 (t80) REVERT: A 490 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.7836 (p90) REVERT: A 516 GLU cc_start: 0.8157 (tp30) cc_final: 0.7951 (tm-30) REVERT: A 568 ASP cc_start: 0.8831 (t0) cc_final: 0.8533 (t0) REVERT: A 743 CYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7414 (m) REVERT: A 748 GLU cc_start: 0.9026 (mp0) cc_final: 0.8588 (mp0) REVERT: A 780 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8933 (mt-10) REVERT: A 814 LYS cc_start: 0.9069 (mtmt) cc_final: 0.8840 (mmtm) REVERT: A 994 ASP cc_start: 0.8959 (t70) cc_final: 0.8697 (t70) REVERT: B 160 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.6387 (m-80) REVERT: B 314 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8631 (tm-30) REVERT: B 378 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8252 (tmmt) REVERT: B 492 LEU cc_start: 0.9086 (pp) cc_final: 0.8708 (tt) REVERT: B 509 ARG cc_start: 0.7957 (mtt180) cc_final: 0.7357 (mmm-85) REVERT: B 516 GLU cc_start: 0.8374 (tp30) cc_final: 0.8053 (tp30) REVERT: B 602 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9006 (p) REVERT: B 988 GLU cc_start: 0.9164 (mp0) cc_final: 0.8646 (pm20) REVERT: B 990 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8209 (mm-30) REVERT: B 1005 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8742 (mt0) REVERT: C 32 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7287 (t80) REVERT: C 115 GLN cc_start: 0.8871 (mp10) cc_final: 0.8445 (mm-40) REVERT: C 127 PHE cc_start: 0.7776 (m-80) cc_final: 0.7195 (m-80) REVERT: C 161 SER cc_start: 0.5778 (OUTLIER) cc_final: 0.5524 (p) REVERT: C 173 GLN cc_start: 0.9099 (mp10) cc_final: 0.8884 (tm130) REVERT: C 239 GLN cc_start: 0.9035 (pt0) cc_final: 0.8549 (pt0) REVERT: C 421 TYR cc_start: 0.8930 (m-80) cc_final: 0.8001 (m-80) REVERT: C 529 LYS cc_start: 0.9242 (mtpp) cc_final: 0.9001 (tppp) REVERT: C 571 ASP cc_start: 0.9087 (m-30) cc_final: 0.8823 (t0) outliers start: 70 outliers final: 37 residues processed: 209 average time/residue: 0.4897 time to fit residues: 124.3152 Evaluate side-chains 190 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 937 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 105 optimal weight: 3.9990 chunk 270 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 chunk 233 optimal weight: 0.0470 chunk 272 optimal weight: 3.9990 chunk 266 optimal weight: 0.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1010 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.093059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.057575 restraints weight = 52159.406| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.79 r_work: 0.2724 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24636 Z= 0.111 Angle : 0.510 14.406 33610 Z= 0.257 Chirality : 0.043 0.227 3928 Planarity : 0.003 0.049 4239 Dihedral : 4.322 55.712 4049 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.08 % Allowed : 18.65 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 2925 helix: 2.98 (0.19), residues: 701 sheet: -0.09 (0.19), residues: 641 loop : -0.89 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.018 0.001 TYR A1067 PHE 0.017 0.001 PHE C 168 TRP 0.010 0.001 TRP C 633 HIS 0.002 0.000 HIS C 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (24560) covalent geometry : angle 0.50102 / 0.26 (33417) SS BOND : bond 0.00150 / 0.10 ( 35) SS BOND : angle 0.65161 / 0.41 ( 70) hydrogen bonds : bond 0.03662 / 2.32 ( 991) hydrogen bonds : angle 4.97047 / 3.44 ( 2856) link_BETA1-4 : bond 0.00313 / 0.18 ( 11) link_BETA1-4 : angle 0.95196 / 0.58 ( 33) link_NAG-ASN : bond 0.00321 / 0.24 ( 30) link_NAG-ASN : angle 1.80114 / 1.19 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 155 time to evaluate : 0.985 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: A 99 ASN cc_start: 0.9246 (m110) cc_final: 0.8859 (t0) REVERT: A 118 LEU cc_start: 0.8991 (mt) cc_final: 0.8696 (tm) REVERT: A 173 GLN cc_start: 0.9023 (mt0) cc_final: 0.8699 (tm130) REVERT: A 269 TYR cc_start: 0.8863 (m-80) cc_final: 0.8604 (m-80) REVERT: A 333 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8801 (t) REVERT: A 347 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7649 (t80) REVERT: A 490 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7779 (p90) REVERT: A 636 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.8231 (t80) REVERT: A 748 GLU cc_start: 0.8989 (mp0) cc_final: 0.8515 (mp0) REVERT: A 780 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8864 (mt-10) REVERT: A 814 LYS cc_start: 0.9053 (mtmt) cc_final: 0.8822 (mmtm) REVERT: A 994 ASP cc_start: 0.8959 (t70) cc_final: 0.8701 (t70) REVERT: B 160 TYR cc_start: 0.6825 (OUTLIER) cc_final: 0.6462 (m-80) REVERT: B 314 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8619 (tm-30) REVERT: B 492 LEU cc_start: 0.9100 (pp) cc_final: 0.8727 (tt) REVERT: B 509 ARG cc_start: 0.7970 (mtt180) cc_final: 0.7380 (mmm-85) REVERT: B 516 GLU cc_start: 0.8382 (tp30) cc_final: 0.8085 (tp30) REVERT: B 988 GLU cc_start: 0.9189 (mp0) cc_final: 0.8666 (pm20) REVERT: B 990 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8148 (mm-30) REVERT: B 1005 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8758 (mt0) REVERT: C 115 GLN cc_start: 0.8885 (mp10) cc_final: 0.8446 (mm-40) REVERT: C 127 PHE cc_start: 0.7726 (m-80) cc_final: 0.7203 (m-80) REVERT: C 191 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8783 (mt-10) REVERT: C 239 GLN cc_start: 0.8985 (pt0) cc_final: 0.8513 (pt0) REVERT: C 324 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8308 (pm20) REVERT: C 421 TYR cc_start: 0.8935 (m-80) cc_final: 0.7990 (m-80) REVERT: C 503 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.8084 (p) REVERT: C 529 LYS cc_start: 0.9241 (mtpp) cc_final: 0.8992 (tppp) REVERT: C 571 ASP cc_start: 0.9081 (m-30) cc_final: 0.8811 (t0) outliers start: 55 outliers final: 28 residues processed: 200 average time/residue: 0.5190 time to fit residues: 124.7846 Evaluate side-chains 183 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 219 optimal weight: 2.9990 chunk 242 optimal weight: 6.9990 chunk 110 optimal weight: 0.0170 chunk 118 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 232 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 222 optimal weight: 0.7980 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1010 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.093074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.057590 restraints weight = 51908.574| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.79 r_work: 0.2722 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24636 Z= 0.126 Angle : 0.517 14.881 33610 Z= 0.260 Chirality : 0.043 0.227 3928 Planarity : 0.003 0.046 4239 Dihedral : 4.259 55.554 4048 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.16 % Allowed : 18.69 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 2925 helix: 2.94 (0.19), residues: 708 sheet: -0.09 (0.19), residues: 637 loop : -0.89 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.019 0.001 TYR B 904 PHE 0.028 0.001 PHE B 127 TRP 0.009 0.001 TRP C 633 HIS 0.002 0.000 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (24560) covalent geometry : angle 0.50831 / 0.26 (33417) SS BOND : bond 0.00154 / 0.10 ( 35) SS BOND : angle 0.63446 / 0.40 ( 70) hydrogen bonds : bond 0.03739 / 2.37 ( 991) hydrogen bonds : angle 4.93991 / 3.43 ( 2856) link_BETA1-4 : bond 0.00282 / 0.17 ( 11) link_BETA1-4 : angle 0.98224 / 0.60 ( 33) link_NAG-ASN : bond 0.00299 / 0.22 ( 30) link_NAG-ASN : angle 1.79014 / 1.18 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 152 time to evaluate : 0.949 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: A 99 ASN cc_start: 0.9233 (m110) cc_final: 0.8855 (t0) REVERT: A 118 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8714 (tm) REVERT: A 173 GLN cc_start: 0.9032 (mt0) cc_final: 0.8691 (tm130) REVERT: A 269 TYR cc_start: 0.8875 (m-80) cc_final: 0.8607 (m-80) REVERT: A 333 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8776 (t) REVERT: A 347 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7651 (t80) REVERT: A 490 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7774 (p90) REVERT: A 568 ASP cc_start: 0.8575 (t0) cc_final: 0.8346 (t0) REVERT: A 743 CYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7406 (m) REVERT: A 748 GLU cc_start: 0.8990 (mp0) cc_final: 0.8525 (mp0) REVERT: A 780 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8850 (mt-10) REVERT: A 814 LYS cc_start: 0.9037 (mtmt) cc_final: 0.8818 (mmtm) REVERT: A 994 ASP cc_start: 0.8969 (t70) cc_final: 0.8712 (t70) REVERT: B 160 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.6559 (m-80) REVERT: B 314 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8626 (tm-30) REVERT: B 509 ARG cc_start: 0.7948 (mtt180) cc_final: 0.7306 (mmm-85) REVERT: B 516 GLU cc_start: 0.8372 (tp30) cc_final: 0.8058 (tp30) REVERT: B 988 GLU cc_start: 0.9188 (mp0) cc_final: 0.8604 (pm20) REVERT: B 990 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8150 (mm-30) REVERT: B 1005 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8761 (mt0) REVERT: C 115 GLN cc_start: 0.8906 (mp10) cc_final: 0.8443 (mm-40) REVERT: C 127 PHE cc_start: 0.7704 (m-80) cc_final: 0.7179 (m-80) REVERT: C 161 SER cc_start: 0.5786 (OUTLIER) cc_final: 0.5540 (p) REVERT: C 191 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8783 (mt-10) REVERT: C 239 GLN cc_start: 0.8996 (pt0) cc_final: 0.8523 (pt0) REVERT: C 324 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8303 (pm20) REVERT: C 347 PHE cc_start: 0.7158 (p90) cc_final: 0.6957 (p90) REVERT: C 378 LYS cc_start: 0.8485 (ptmm) cc_final: 0.8244 (tmmm) REVERT: C 421 TYR cc_start: 0.8941 (m-80) cc_final: 0.7996 (m-80) REVERT: C 503 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8111 (p) REVERT: C 529 LYS cc_start: 0.9244 (mtpp) cc_final: 0.8988 (tppp) REVERT: C 571 ASP cc_start: 0.9075 (m-30) cc_final: 0.8821 (t0) outliers start: 57 outliers final: 32 residues processed: 196 average time/residue: 0.5163 time to fit residues: 121.7282 Evaluate side-chains 191 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 234 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 72 optimal weight: 0.0040 chunk 104 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 258 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1010 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.092690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.057138 restraints weight = 52261.914| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.80 r_work: 0.2702 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24636 Z= 0.158 Angle : 0.535 15.337 33610 Z= 0.269 Chirality : 0.043 0.226 3928 Planarity : 0.003 0.045 4239 Dihedral : 4.325 55.405 4048 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.24 % Allowed : 18.57 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 2925 helix: 2.90 (0.19), residues: 707 sheet: -0.09 (0.19), residues: 642 loop : -0.92 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.024 0.001 TYR B 904 PHE 0.015 0.001 PHE B 898 TRP 0.009 0.001 TRP C 452 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (24560) covalent geometry : angle 0.52641 / 0.27 (33417) SS BOND : bond 0.00193 / 0.12 ( 35) SS BOND : angle 0.67034 / 0.43 ( 70) hydrogen bonds : bond 0.03946 / 2.50 ( 991) hydrogen bonds : angle 4.99103 / 3.47 ( 2856) link_BETA1-4 : bond 0.00212 / 0.13 ( 11) link_BETA1-4 : angle 0.99343 / 0.61 ( 33) link_NAG-ASN : bond 0.00298 / 0.21 ( 30) link_NAG-ASN : angle 1.81794 / 1.20 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 155 time to evaluate : 0.967 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: A 99 ASN cc_start: 0.9229 (m110) cc_final: 0.8838 (t0) REVERT: A 118 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8769 (tm) REVERT: A 127 PHE cc_start: 0.8350 (t80) cc_final: 0.8072 (t80) REVERT: A 269 TYR cc_start: 0.8896 (m-80) cc_final: 0.8639 (m-80) REVERT: A 333 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8808 (t) REVERT: A 347 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.7634 (t80) REVERT: A 490 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7831 (p90) REVERT: A 636 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8211 (t80) REVERT: A 743 CYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7385 (m) REVERT: A 748 GLU cc_start: 0.8992 (mp0) cc_final: 0.8516 (mp0) REVERT: A 780 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8938 (mt-10) REVERT: A 814 LYS cc_start: 0.9054 (mtmt) cc_final: 0.8780 (mmpt) REVERT: A 994 ASP cc_start: 0.8958 (t70) cc_final: 0.8703 (t70) REVERT: B 160 TYR cc_start: 0.6909 (OUTLIER) cc_final: 0.6483 (m-80) REVERT: B 314 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8633 (tm-30) REVERT: B 492 LEU cc_start: 0.9085 (pp) cc_final: 0.8807 (tt) REVERT: B 509 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7290 (mmm-85) REVERT: B 516 GLU cc_start: 0.8391 (tp30) cc_final: 0.8081 (tp30) REVERT: B 988 GLU cc_start: 0.9188 (mp0) cc_final: 0.8657 (pm20) REVERT: B 990 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8158 (mm-30) REVERT: B 1005 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8761 (mt0) REVERT: C 115 GLN cc_start: 0.8941 (mp10) cc_final: 0.8492 (mm-40) REVERT: C 127 PHE cc_start: 0.7708 (m-80) cc_final: 0.7230 (m-80) REVERT: C 161 SER cc_start: 0.5766 (OUTLIER) cc_final: 0.5523 (p) REVERT: C 191 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8766 (mt-10) REVERT: C 239 GLN cc_start: 0.9009 (pt0) cc_final: 0.8528 (pt0) REVERT: C 347 PHE cc_start: 0.7124 (p90) cc_final: 0.6898 (p90) REVERT: C 421 TYR cc_start: 0.8945 (m-80) cc_final: 0.8004 (m-80) REVERT: C 529 LYS cc_start: 0.9247 (mtpp) cc_final: 0.8996 (tppp) REVERT: C 571 ASP cc_start: 0.9075 (m-30) cc_final: 0.8826 (t0) outliers start: 59 outliers final: 37 residues processed: 201 average time/residue: 0.5033 time to fit residues: 122.4315 Evaluate side-chains 190 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 0 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 36 optimal weight: 8.9990 chunk 265 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1002 GLN B1010 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.092088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.056442 restraints weight = 52434.694| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.80 r_work: 0.2691 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24636 Z= 0.179 Angle : 0.554 15.698 33610 Z= 0.280 Chirality : 0.044 0.225 3928 Planarity : 0.003 0.044 4239 Dihedral : 4.416 55.360 4048 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.86 % Allowed : 19.14 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 2925 helix: 2.87 (0.19), residues: 706 sheet: -0.12 (0.19), residues: 640 loop : -0.91 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.032 0.001 TYR B 904 PHE 0.033 0.001 PHE B 168 TRP 0.009 0.001 TRP C 452 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (24560) covalent geometry : angle 0.54586 / 0.28 (33417) SS BOND : bond 0.00212 / 0.14 ( 35) SS BOND : angle 0.68524 / 0.43 ( 70) hydrogen bonds : bond 0.04074 / 2.58 ( 991) hydrogen bonds : angle 5.03987 / 3.51 ( 2856) link_BETA1-4 : bond 0.00158 / 0.11 ( 11) link_BETA1-4 : angle 0.98272 / 0.60 ( 33) link_NAG-ASN : bond 0.00310 / 0.22 ( 30) link_NAG-ASN : angle 1.85016 / 1.22 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 149 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.9230 (m110) cc_final: 0.8832 (t0) REVERT: A 118 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8735 (tm) REVERT: A 269 TYR cc_start: 0.8911 (m-80) cc_final: 0.8629 (m-80) REVERT: A 333 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8823 (t) REVERT: A 347 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7622 (t80) REVERT: A 490 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7817 (p90) REVERT: A 636 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.8252 (t80) REVERT: A 743 CYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7401 (m) REVERT: A 748 GLU cc_start: 0.9016 (mp0) cc_final: 0.8531 (mp0) REVERT: A 780 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8959 (mt-10) REVERT: A 814 LYS cc_start: 0.9063 (mtmt) cc_final: 0.8840 (mmtm) REVERT: A 994 ASP cc_start: 0.8966 (t70) cc_final: 0.8711 (t70) REVERT: B 160 TYR cc_start: 0.6950 (OUTLIER) cc_final: 0.6450 (m-80) REVERT: B 314 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8641 (tm-30) REVERT: B 492 LEU cc_start: 0.9141 (pp) cc_final: 0.8805 (tt) REVERT: B 509 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7315 (mmm-85) REVERT: B 516 GLU cc_start: 0.8377 (tp30) cc_final: 0.8084 (tp30) REVERT: B 988 GLU cc_start: 0.9183 (mp0) cc_final: 0.8651 (pm20) REVERT: B 990 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8214 (mm-30) REVERT: B 1005 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8745 (mt0) REVERT: C 115 GLN cc_start: 0.8938 (mp10) cc_final: 0.8484 (mm-40) REVERT: C 127 PHE cc_start: 0.7774 (m-80) cc_final: 0.7244 (m-80) REVERT: C 161 SER cc_start: 0.5924 (OUTLIER) cc_final: 0.5673 (p) REVERT: C 191 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8786 (mt-10) REVERT: C 239 GLN cc_start: 0.9040 (pt0) cc_final: 0.8597 (pt0) REVERT: C 321 GLN cc_start: 0.9275 (mm110) cc_final: 0.9035 (mm-40) REVERT: C 347 PHE cc_start: 0.7097 (p90) cc_final: 0.6860 (p90) REVERT: C 421 TYR cc_start: 0.8946 (m-80) cc_final: 0.8008 (m-80) REVERT: C 529 LYS cc_start: 0.9245 (mtpp) cc_final: 0.9001 (tppp) REVERT: C 571 ASP cc_start: 0.9074 (m-30) cc_final: 0.8826 (t0) outliers start: 49 outliers final: 38 residues processed: 189 average time/residue: 0.4379 time to fit residues: 99.6049 Evaluate side-chains 191 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 136 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 281 optimal weight: 0.7980 chunk 240 optimal weight: 7.9990 chunk 284 optimal weight: 0.7980 chunk 209 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 282 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 206 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1010 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.093457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.058158 restraints weight = 52090.601| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.78 r_work: 0.2726 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24636 Z= 0.116 Angle : 0.538 16.070 33610 Z= 0.271 Chirality : 0.043 0.226 3928 Planarity : 0.003 0.040 4239 Dihedral : 4.325 57.001 4048 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.86 % Allowed : 19.11 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.15), residues: 2925 helix: 2.93 (0.19), residues: 707 sheet: -0.14 (0.19), residues: 642 loop : -0.89 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.029 0.001 TYR B 904 PHE 0.034 0.001 PHE A 127 TRP 0.010 0.001 TRP C 633 HIS 0.002 0.000 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (24560) covalent geometry : angle 0.52954 / 0.27 (33417) SS BOND : bond 0.00156 / 0.11 ( 35) SS BOND : angle 0.66399 / 0.42 ( 70) hydrogen bonds : bond 0.03660 / 2.32 ( 991) hydrogen bonds : angle 4.92007 / 3.42 ( 2856) link_BETA1-4 : bond 0.00318 / 0.19 ( 11) link_BETA1-4 : angle 0.93769 / 0.57 ( 33) link_NAG-ASN : bond 0.00318 / 0.23 ( 30) link_NAG-ASN : angle 1.79738 / 1.19 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9949.52 seconds wall clock time: 170 minutes 15.43 seconds (10215.43 seconds total)