Starting phenix.real_space_refine on Sun Jul 5 20:11:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ukl_26583/07_2026/7ukl_26583.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukl_26583/07_2026/7ukl_26583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ukl_26583/07_2026/7ukl_26583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukl_26583/07_2026/7ukl_26583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ukl_26583/07_2026/7ukl_26583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukl_26583/07_2026/7ukl_26583.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ukl_26583/07_2026/7ukl_26583.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ukl_26583/07_2026/7ukl_26583.cif" } resolution = 3.09 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 19197 2.51 5 N 4965 2.21 5 O 5940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30234 Number of models: 1 Model: "" Number of chains: 12 Chain: "Y" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "B" Number of atoms: 8004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8004 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 51, 'TRANS': 973} Chain breaks: 7 Chain: "X" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1030 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "C" Number of atoms: 8004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8004 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 51, 'TRANS': 973} Chain breaks: 7 Chain: "A" Number of atoms: 8004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8004 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 51, 'TRANS': 973} Chain breaks: 7 Chain: "H" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1030 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "M" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1030 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "N" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen chiralities: 16 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen chiralities: 16 Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 6.57, per 1000 atoms: 0.22 Number of scatterers: 30234 At special positions: 0 Unit cell: (177.62, 172.64, 171.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 5940 8.00 N 4965 7.00 C 19197 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 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 X 22 " - pdb=" SG CYS X 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.09 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.01 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 H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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 NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A 717 " " NAG A1311 " - " ASN A 801 " " NAG A1312 " - " ASN A 122 " " NAG A1313 " - " ASN A 61 " " NAG A1314 " - " ASN A 234 " " NAG A1315 " - " ASN A 165 " " NAG A1316 " - " ASN A 343 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B1134 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B 717 " " NAG B1308 " - " ASN B 801 " " NAG B1309 " - " ASN B 61 " " NAG B1310 " - " ASN B 234 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B 603 " " NAG B1313 " - " ASN B 616 " " NAG B1314 " - " ASN B 343 " " NAG B1315 " - " ASN B 331 " " NAG B1316 " - " ASN B 122 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 122 " " NAG C1312 " - " ASN C 61 " " NAG C1313 " - " ASN C 234 " " NAG C1314 " - " ASN C 165 " " NAG C1315 " - " ASN C 603 " " NAG C1316 " - " ASN C 343 " Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.5 seconds 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7044 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 57 sheets defined 22.8% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'Y' and resid 27 through 31 Processing helix chain 'Y' and resid 79 through 83 removed outlier: 4.129A pdb=" N GLU Y 83 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.599A pdb=" N GLN B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 200 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.791A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.794A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.635A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.521A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.589A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.821A pdb=" N VAL B 622 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.797A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.517A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.547A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.507A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.523A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.703A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.662A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.947A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 32 Processing helix chain 'X' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.963A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 183 removed outlier: 3.786A pdb=" N LYS C 182 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.666A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.639A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.611A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 623 removed outlier: 3.548A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Proline residue: C 621 - end of helix Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.519A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.675A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.549A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.701A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.548A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.756A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.012A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.916A pdb=" N GLN A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.647A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.709A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.604A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.605A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.653A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.351A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'N' and resid 92 through 95A removed outlier: 3.513A pdb=" N THR N 95 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Y' and resid 9 through 13 removed outlier: 6.609A pdb=" N VAL Y 11 " --> pdb=" O THR Y 105 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA Y 84 " --> pdb=" O VAL Y 104 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP Y 35 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Y' and resid 19 through 24 Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 31 removed outlier: 5.419A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.149A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.873A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.683A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.373A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 356 through 358 removed outlier: 5.211A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.534A pdb=" N PHE B 392 " --> pdb=" O VAL B 524 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'B' and resid 538 through 543 removed outlier: 4.046A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.154A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AB6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.987A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.987A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.409A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 787 through 789 removed outlier: 5.711A pdb=" N ILE B 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'X' and resid 3 through 7 Processing sheet with id=AC3, first strand: chain 'X' and resid 10 through 12 removed outlier: 6.806A pdb=" N MET X 34 " --> pdb=" O ILE X 50 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE X 50 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.457A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.548A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.159A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.995A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.740A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.233A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.605A pdb=" N PHE C 392 " --> pdb=" O VAL C 524 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.523A pdb=" N VAL C 395 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N SER C 514 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA C 397 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL C 512 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER C 399 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 510 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL C 401 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR C 508 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'C' and resid 538 through 543 removed outlier: 4.918A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.242A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 701 through 703 Processing sheet with id=AD7, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.002A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.002A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.398A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.638A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.031A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.992A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AE5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.934A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.141A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.505A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AE9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.110A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.479A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AF6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.518A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.811A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.538A pdb=" N THR M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.923A pdb=" N MET M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.510A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP N 35 " --> pdb=" O VAL N 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 19 through 24 1189 hydrogen bonds defined for protein. 3108 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: 8.71 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4930 1.32 - 1.45: 8818 1.45 - 1.58: 16996 1.58 - 1.71: 0 1.71 - 1.83: 168 Bond restraints: 30912 Sorted by residual: bond pdb=" N CYS A 738 " pdb=" CA CYS A 738 " ideal model delta sigma weight residual 1.459 1.383 0.076 1.21e-02 6.83e+03 3.98e+01 bond pdb=" CA CYS A 738 " pdb=" C CYS A 738 " ideal model delta sigma weight residual 1.523 1.467 0.057 1.30e-02 5.92e+03 1.91e+01 bond pdb=" N VAL C1128 " pdb=" CA VAL C1128 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.06e-02 8.90e+03 1.83e+01 bond pdb=" C SER B 735 " pdb=" O SER B 735 " ideal model delta sigma weight residual 1.234 1.188 0.046 1.11e-02 8.12e+03 1.74e+01 bond pdb=" CA SER A 530 " pdb=" CB SER A 530 " ideal model delta sigma weight residual 1.528 1.477 0.052 1.35e-02 5.49e+03 1.46e+01 ... (remaining 30907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 40486 2.17 - 4.35: 1372 4.35 - 6.52: 184 6.52 - 8.69: 12 8.69 - 10.87: 3 Bond angle restraints: 42057 Sorted by residual: angle pdb=" N THR C 747 " pdb=" CA THR C 747 " pdb=" C THR C 747 " ideal model delta sigma weight residual 112.54 101.67 10.87 1.22e+00 6.72e-01 7.93e+01 angle pdb=" N VAL B 126 " pdb=" CA VAL B 126 " pdb=" C VAL B 126 " ideal model delta sigma weight residual 110.05 100.50 9.55 1.09e+00 8.42e-01 7.68e+01 angle pdb=" N PHE C 342 " pdb=" CA PHE C 342 " pdb=" C PHE C 342 " ideal model delta sigma weight residual 111.82 121.48 -9.66 1.16e+00 7.43e-01 6.94e+01 angle pdb=" N THR C 602 " pdb=" CA THR C 602 " pdb=" C THR C 602 " ideal model delta sigma weight residual 111.75 103.22 8.53 1.28e+00 6.10e-01 4.44e+01 angle pdb=" CA VAL A 395 " pdb=" C VAL A 395 " pdb=" O VAL A 395 " ideal model delta sigma weight residual 121.59 115.77 5.82 1.03e+00 9.43e-01 3.19e+01 ... (remaining 42052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 16549 17.58 - 35.16: 1103 35.16 - 52.74: 221 52.74 - 70.32: 59 70.32 - 87.90: 29 Dihedral angle restraints: 17961 sinusoidal: 6960 harmonic: 11001 Sorted by residual: 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 -31.31 -54.69 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -34.95 -51.05 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CA CYS A 617 " pdb=" C CYS A 617 " pdb=" N THR A 618 " pdb=" CA THR A 618 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 17958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.174: 4788 0.174 - 0.347: 69 0.347 - 0.521: 8 0.521 - 0.694: 0 0.694 - 0.868: 1 Chirality restraints: 4866 Sorted by residual: chirality pdb=" C1 NAG B1316 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1316 " pdb=" O5 NAG B1316 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.88e+01 chirality pdb=" C1 NAG A1311 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG A1311 " pdb=" O5 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CA PHE C 318 " pdb=" N PHE C 318 " pdb=" C PHE C 318 " pdb=" CB PHE C 318 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.20e+00 ... (remaining 4863 not shown) Planarity restraints: 5439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1314 " 0.338 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG B1314 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B1314 " 0.087 2.00e-02 2.50e+03 pdb=" N2 NAG B1314 " -0.522 2.00e-02 2.50e+03 pdb=" O7 NAG B1314 " 0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1311 " 0.342 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG B1311 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B1311 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG B1311 " -0.515 2.00e-02 2.50e+03 pdb=" O7 NAG B1311 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1316 " -0.331 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG A1316 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG A1316 " -0.119 2.00e-02 2.50e+03 pdb=" N2 NAG A1316 " 0.514 2.00e-02 2.50e+03 pdb=" O7 NAG A1316 " -0.141 2.00e-02 2.50e+03 ... (remaining 5436 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 712 2.69 - 3.24: 29428 3.24 - 3.80: 45578 3.80 - 4.35: 64591 4.35 - 4.90: 109211 Nonbonded interactions: 249520 Sorted by model distance: nonbonded pdb=" OG1 THR A 645 " pdb=" O GLY A 648 " model vdw 2.139 3.040 nonbonded pdb=" OD2 ASP M 100A" pdb=" OG1 THR M 100D" model vdw 2.150 3.040 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.164 3.040 nonbonded pdb=" OG SER A 555 " pdb=" O ILE A 584 " model vdw 2.200 3.040 nonbonded pdb=" OD2 ASP A 578 " pdb=" OG1 THR A 581 " model vdw 2.212 3.040 ... (remaining 249515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'X' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Y' } 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: 9.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.870 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 30.730 Find NCS groups from input model: 0.660 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: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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 : 0.005 0.080 31005 Z= 0.338 Angle : 0.898 13.945 42291 Z= 0.555 Chirality : 0.061 0.868 4866 Planarity : 0.015 0.294 5391 Dihedral : 12.934 87.897 10782 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.09 % Allowed : 1.00 % Favored : 98.91 % Cbeta Deviations : 0.09 % 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: -0.53 (0.14), residues: 3735 helix: 0.71 (0.21), residues: 635 sheet: -0.53 (0.16), residues: 957 loop : -0.53 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 454 TYR 0.024 0.001 TYR A 396 PHE 0.023 0.001 PHE C 515 TRP 0.015 0.001 TRP A 436 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.33 (30912) covalent geometry : angle 0.86454 / 0.55 (42057) SS BOND : bond 0.01121 / 0.77 ( 45) SS BOND : angle 2.40358 / 1.69 ( 90) hydrogen bonds : bond 0.21375 / 13.97 ( 1167) hydrogen bonds : angle 8.92410 / 6.19 ( 3108) link_NAG-ASN : bond 0.02531 / 1.63 ( 48) link_NAG-ASN : angle 3.84673 / 2.95 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 372 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 37 GLN cc_start: 0.7945 (tt0) cc_final: 0.7722 (tt0) REVERT: Y 82 ASP cc_start: 0.6262 (m-30) cc_final: 0.5943 (m-30) REVERT: C 455 LEU cc_start: 0.8479 (mt) cc_final: 0.8182 (mt) outliers start: 3 outliers final: 2 residues processed: 375 average time/residue: 0.1859 time to fit residues: 108.8383 Evaluate side-chains 255 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 253 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 17 GLN B 164 ASN B 188 ASN B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** X 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 388 ASN C 762 GLN C 779 GLN C 901 GLN A 81 ASN A 207 HIS A 913 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN M 76 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.084148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.055003 restraints weight = 79954.578| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.29 r_work: 0.2772 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 31005 Z= 0.206 Angle : 0.633 8.715 42291 Z= 0.324 Chirality : 0.047 0.222 4866 Planarity : 0.004 0.067 5391 Dihedral : 4.878 25.465 4094 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.09 % Allowed : 6.29 % Favored : 92.62 % 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: -0.31 (0.13), residues: 3735 helix: 1.33 (0.21), residues: 651 sheet: -0.41 (0.16), residues: 956 loop : -0.54 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 93 TYR 0.021 0.001 TYR B 453 PHE 0.022 0.002 PHE B 497 TRP 0.024 0.001 TRP Y 35 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (30912) covalent geometry : angle 0.62262 / 0.32 (42057) SS BOND : bond 0.00429 / 0.30 ( 45) SS BOND : angle 1.49401 / 1.13 ( 90) hydrogen bonds : bond 0.04471 / 2.99 ( 1167) hydrogen bonds : angle 6.39625 / 4.46 ( 3108) link_NAG-ASN : bond 0.00295 / 0.21 ( 48) link_NAG-ASN : angle 1.73768 / 1.30 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 271 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 32 TYR cc_start: 0.8173 (m-80) cc_final: 0.7807 (m-10) REVERT: Y 35 TRP cc_start: 0.8457 (m100) cc_final: 0.8025 (m100) REVERT: Y 53 LYS cc_start: 0.8569 (mttm) cc_final: 0.7941 (mttp) REVERT: Y 83 GLU cc_start: 0.9059 (tp30) cc_final: 0.8569 (mp0) REVERT: X 72 ASP cc_start: 0.8575 (t0) cc_final: 0.8176 (t0) REVERT: X 100 ASP cc_start: 0.8752 (t70) cc_final: 0.8463 (t70) REVERT: L 27 LYS cc_start: 0.9087 (mmmm) cc_final: 0.8876 (mmmm) REVERT: L 81 MET cc_start: 0.9251 (ppp) cc_final: 0.8665 (ppp) REVERT: C 902 MET cc_start: 0.9058 (tpp) cc_final: 0.8728 (tpt) REVERT: C 904 TYR cc_start: 0.8408 (t80) cc_final: 0.7987 (t80) REVERT: H 3 GLN cc_start: 0.7726 (pm20) cc_final: 0.6337 (pm20) REVERT: H 46 GLU cc_start: 0.9005 (tt0) cc_final: 0.8786 (tt0) REVERT: H 72 ASP cc_start: 0.8770 (t0) cc_final: 0.8525 (t0) REVERT: M 34 MET cc_start: 0.8628 (mmt) cc_final: 0.7501 (mmt) REVERT: M 46 GLU cc_start: 0.8593 (tt0) cc_final: 0.8047 (tt0) REVERT: M 64 LYS cc_start: 0.8160 (tttp) cc_final: 0.7861 (ttmm) REVERT: M 81 GLN cc_start: 0.8306 (mm-40) cc_final: 0.8096 (mm-40) REVERT: M 95 ASP cc_start: 0.8235 (m-30) cc_final: 0.7933 (m-30) REVERT: N 42 GLN cc_start: 0.8241 (mp10) cc_final: 0.7961 (mp10) REVERT: N 61 ARG cc_start: 0.8699 (ptt90) cc_final: 0.8178 (ptt90) REVERT: N 79 GLN cc_start: 0.7377 (mp10) cc_final: 0.7051 (mp10) REVERT: N 81 MET cc_start: 0.9124 (ptp) cc_final: 0.8459 (ppp) REVERT: N 82 ASP cc_start: 0.8723 (m-30) cc_final: 0.8222 (m-30) REVERT: N 85 ASP cc_start: 0.8220 (m-30) cc_final: 0.7329 (p0) REVERT: N 87 TYR cc_start: 0.9137 (m-80) cc_final: 0.8791 (m-80) REVERT: N 95 TYR cc_start: 0.7378 (t80) cc_final: 0.6910 (t80) outliers start: 36 outliers final: 24 residues processed: 293 average time/residue: 0.1890 time to fit residues: 87.5209 Evaluate side-chains 263 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 48 ILE Chi-restraints excluded: chain Y residue 51 ASP Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 4 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 123 optimal weight: 0.7980 chunk 298 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 955 ASN L 50 GLN C 87 ASN A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS N 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.081648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.052432 restraints weight = 80662.961| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.27 r_work: 0.2714 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 31005 Z= 0.289 Angle : 0.650 9.460 42291 Z= 0.332 Chirality : 0.047 0.236 4866 Planarity : 0.004 0.060 5391 Dihedral : 4.935 26.954 4094 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.82 % Allowed : 7.69 % Favored : 90.49 % 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: -0.27 (0.14), residues: 3735 helix: 1.44 (0.21), residues: 664 sheet: -0.39 (0.16), residues: 949 loop : -0.55 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 403 TYR 0.019 0.002 TYR A 421 PHE 0.026 0.002 PHE B 497 TRP 0.011 0.001 TRP C 886 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.29 (30912) covalent geometry : angle 0.63990 / 0.33 (42057) SS BOND : bond 0.00401 / 0.24 ( 45) SS BOND : angle 1.61605 / 1.18 ( 90) hydrogen bonds : bond 0.04312 / 2.87 ( 1167) hydrogen bonds : angle 5.99564 / 4.20 ( 3108) link_NAG-ASN : bond 0.00300 / 0.20 ( 48) link_NAG-ASN : angle 1.74186 / 1.21 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 259 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 32 TYR cc_start: 0.8171 (m-80) cc_final: 0.7865 (m-80) REVERT: Y 35 TRP cc_start: 0.8645 (m100) cc_final: 0.8016 (m100) REVERT: Y 53 LYS cc_start: 0.8553 (mttm) cc_final: 0.8306 (mttt) REVERT: Y 82 ASP cc_start: 0.7158 (m-30) cc_final: 0.6558 (m-30) REVERT: Y 83 GLU cc_start: 0.9050 (tp30) cc_final: 0.8712 (mp0) REVERT: Y 87 TYR cc_start: 0.9164 (m-80) cc_final: 0.8798 (m-80) REVERT: Y 92 ASP cc_start: 0.8509 (t0) cc_final: 0.8203 (t0) REVERT: X 13 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8612 (mm-40) REVERT: X 50 ILE cc_start: 0.9455 (tt) cc_final: 0.9236 (tt) REVERT: X 72 ASP cc_start: 0.8592 (t0) cc_final: 0.8181 (t0) REVERT: X 100 ASP cc_start: 0.8823 (t70) cc_final: 0.8337 (t0) REVERT: L 27 LYS cc_start: 0.9156 (mmmm) cc_final: 0.8912 (mmmm) REVERT: L 42 GLN cc_start: 0.8837 (mp10) cc_final: 0.8480 (mp10) REVERT: L 81 MET cc_start: 0.9275 (ppp) cc_final: 0.8547 (ppp) REVERT: C 417 LYS cc_start: 0.9226 (mmmm) cc_final: 0.8766 (tptt) REVERT: C 455 LEU cc_start: 0.9020 (mt) cc_final: 0.8809 (mp) REVERT: C 456 PHE cc_start: 0.8675 (m-80) cc_final: 0.8096 (m-80) REVERT: C 516 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8172 (mp0) REVERT: A 402 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7679 (tt) REVERT: H 46 GLU cc_start: 0.8998 (tt0) cc_final: 0.8746 (tt0) REVERT: H 72 ASP cc_start: 0.8877 (t0) cc_final: 0.8509 (t0) REVERT: M 46 GLU cc_start: 0.8723 (tt0) cc_final: 0.8460 (tt0) REVERT: M 64 LYS cc_start: 0.8497 (tttp) cc_final: 0.8210 (ttmm) REVERT: M 72 ASP cc_start: 0.8669 (t0) cc_final: 0.8301 (t0) REVERT: M 95 ASP cc_start: 0.8425 (m-30) cc_final: 0.8186 (m-30) REVERT: N 42 GLN cc_start: 0.8377 (mp10) cc_final: 0.8038 (mp10) REVERT: N 79 GLN cc_start: 0.7503 (mp10) cc_final: 0.7194 (mp10) REVERT: N 82 ASP cc_start: 0.8679 (m-30) cc_final: 0.8320 (m-30) REVERT: N 87 TYR cc_start: 0.9152 (m-80) cc_final: 0.8921 (m-80) REVERT: N 95 TYR cc_start: 0.7422 (t80) cc_final: 0.6997 (t80) outliers start: 60 outliers final: 40 residues processed: 299 average time/residue: 0.1793 time to fit residues: 85.2238 Evaluate side-chains 277 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 51 ASP Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 367 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 296 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 211 optimal weight: 0.4980 chunk 225 optimal weight: 0.7980 chunk 212 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.083198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.053912 restraints weight = 79756.893| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.32 r_work: 0.2755 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31005 Z= 0.141 Angle : 0.562 9.597 42291 Z= 0.288 Chirality : 0.045 0.241 4866 Planarity : 0.004 0.052 5391 Dihedral : 4.683 24.988 4094 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.73 % Allowed : 9.57 % Favored : 88.70 % 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: -0.08 (0.14), residues: 3735 helix: 1.74 (0.21), residues: 658 sheet: -0.35 (0.16), residues: 947 loop : -0.43 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 19 TYR 0.023 0.001 TYR B 453 PHE 0.034 0.001 PHE B 497 TRP 0.034 0.001 TRP C 886 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (30912) covalent geometry : angle 0.55289 / 0.29 (42057) SS BOND : bond 0.00305 / 0.19 ( 45) SS BOND : angle 1.30601 / 0.93 ( 90) hydrogen bonds : bond 0.03633 / 2.42 ( 1167) hydrogen bonds : angle 5.69761 / 3.99 ( 3108) link_NAG-ASN : bond 0.00189 / 0.13 ( 48) link_NAG-ASN : angle 1.54314 / 1.06 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 255 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 32 TYR cc_start: 0.8127 (m-80) cc_final: 0.7880 (m-80) REVERT: Y 35 TRP cc_start: 0.8673 (m100) cc_final: 0.8063 (m100) REVERT: Y 82 ASP cc_start: 0.7049 (m-30) cc_final: 0.6722 (m-30) REVERT: Y 83 GLU cc_start: 0.9074 (tp30) cc_final: 0.8852 (mp0) REVERT: Y 87 TYR cc_start: 0.9076 (m-80) cc_final: 0.8845 (m-80) REVERT: Y 92 ASP cc_start: 0.8499 (t0) cc_final: 0.8108 (t70) REVERT: B 360 ASN cc_start: 0.9163 (m-40) cc_final: 0.8755 (t0) REVERT: B 403 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6470 (tpp80) REVERT: B 497 PHE cc_start: 0.5606 (m-80) cc_final: 0.5390 (m-80) REVERT: X 72 ASP cc_start: 0.8539 (t0) cc_final: 0.8100 (t0) REVERT: X 100 ASP cc_start: 0.8779 (t70) cc_final: 0.8448 (t70) REVERT: L 27 LYS cc_start: 0.9178 (mmmm) cc_final: 0.8956 (mmmm) REVERT: L 42 GLN cc_start: 0.8822 (mp10) cc_final: 0.8613 (mp10) REVERT: L 81 MET cc_start: 0.9248 (ppp) cc_final: 0.8601 (ppp) REVERT: L 83 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8246 (mm-30) REVERT: C 417 LYS cc_start: 0.9273 (mmmm) cc_final: 0.8848 (tptt) REVERT: C 456 PHE cc_start: 0.8771 (m-80) cc_final: 0.8205 (m-80) REVERT: A 402 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7632 (tt) REVERT: H 46 GLU cc_start: 0.9037 (tt0) cc_final: 0.8772 (tt0) REVERT: H 72 ASP cc_start: 0.8851 (t0) cc_final: 0.8379 (t0) REVERT: M 46 GLU cc_start: 0.8666 (tt0) cc_final: 0.8408 (tt0) REVERT: M 72 ASP cc_start: 0.8739 (t0) cc_final: 0.8333 (t0) REVERT: M 82 MET cc_start: 0.8187 (mmt) cc_final: 0.7978 (mmt) REVERT: N 42 GLN cc_start: 0.8486 (mp10) cc_final: 0.8133 (mp10) REVERT: N 61 ARG cc_start: 0.8601 (ptt90) cc_final: 0.8115 (ptt90) REVERT: N 79 GLN cc_start: 0.7740 (mp10) cc_final: 0.7455 (mp10) REVERT: N 81 MET cc_start: 0.9123 (ptp) cc_final: 0.8810 (pmm) REVERT: N 82 ASP cc_start: 0.8689 (m-30) cc_final: 0.8079 (m-30) REVERT: N 87 TYR cc_start: 0.9081 (m-80) cc_final: 0.8863 (m-80) REVERT: N 95 TYR cc_start: 0.7311 (t80) cc_final: 0.6889 (t80) outliers start: 57 outliers final: 37 residues processed: 295 average time/residue: 0.1914 time to fit residues: 89.5087 Evaluate side-chains 268 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 229 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 51 ASP Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 240 optimal weight: 4.9990 chunk 294 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 190 optimal weight: 0.0670 chunk 361 optimal weight: 6.9990 chunk 366 optimal weight: 3.9990 chunk 164 optimal weight: 0.0670 chunk 73 optimal weight: 0.7980 chunk 270 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.082769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.053590 restraints weight = 79684.529| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.32 r_work: 0.2706 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31005 Z= 0.137 Angle : 0.551 9.583 42291 Z= 0.280 Chirality : 0.044 0.246 4866 Planarity : 0.004 0.049 5391 Dihedral : 4.523 25.512 4094 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.88 % Allowed : 10.36 % Favored : 87.75 % 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: 0.03 (0.14), residues: 3735 helix: 1.84 (0.21), residues: 662 sheet: -0.29 (0.16), residues: 949 loop : -0.37 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 83 TYR 0.019 0.001 TYR Y 95B PHE 0.029 0.001 PHE B 497 TRP 0.031 0.001 TRP C 886 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (30912) covalent geometry : angle 0.54222 / 0.28 (42057) SS BOND : bond 0.00287 / 0.18 ( 45) SS BOND : angle 1.32086 / 0.92 ( 90) hydrogen bonds : bond 0.03468 / 2.31 ( 1167) hydrogen bonds : angle 5.50455 / 3.86 ( 3108) link_NAG-ASN : bond 0.00178 / 0.13 ( 48) link_NAG-ASN : angle 1.48619 / 1.02 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 254 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 35 TRP cc_start: 0.8612 (m100) cc_final: 0.7968 (m100) REVERT: Y 79 GLN cc_start: 0.8072 (mp10) cc_final: 0.7772 (mp10) REVERT: Y 82 ASP cc_start: 0.6993 (m-30) cc_final: 0.6397 (m-30) REVERT: Y 87 TYR cc_start: 0.9132 (m-80) cc_final: 0.8803 (m-80) REVERT: Y 92 ASP cc_start: 0.8417 (t0) cc_final: 0.8014 (t70) REVERT: B 360 ASN cc_start: 0.9218 (m-40) cc_final: 0.8733 (t0) REVERT: B 403 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.6274 (tpp80) REVERT: B 497 PHE cc_start: 0.5731 (m-80) cc_final: 0.5491 (m-80) REVERT: X 67 PHE cc_start: 0.9255 (m-10) cc_final: 0.8493 (m-10) REVERT: X 72 ASP cc_start: 0.8396 (t0) cc_final: 0.8015 (t0) REVERT: X 100 ASP cc_start: 0.8636 (t70) cc_final: 0.8110 (t0) REVERT: L 27 LYS cc_start: 0.9273 (mmmm) cc_final: 0.8998 (mmmm) REVERT: L 42 GLN cc_start: 0.8787 (mp10) cc_final: 0.8258 (mp10) REVERT: L 83 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8077 (mm-30) REVERT: L 92 ASP cc_start: 0.8423 (t0) cc_final: 0.8031 (t0) REVERT: L 95 TYR cc_start: 0.8527 (t80) cc_final: 0.8289 (t80) REVERT: C 417 LYS cc_start: 0.9308 (mmmm) cc_final: 0.8916 (tptt) REVERT: C 456 PHE cc_start: 0.8801 (m-80) cc_final: 0.8275 (m-80) REVERT: C 988 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8899 (pm20) REVERT: A 402 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7615 (tt) REVERT: A 421 TYR cc_start: 0.9099 (m-10) cc_final: 0.8872 (m-10) REVERT: A 740 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8904 (ttt) REVERT: H 46 GLU cc_start: 0.9038 (tt0) cc_final: 0.8766 (tt0) REVERT: H 72 ASP cc_start: 0.8737 (t0) cc_final: 0.8205 (t0) REVERT: M 34 MET cc_start: 0.8505 (mmt) cc_final: 0.7429 (mmt) REVERT: M 46 GLU cc_start: 0.8631 (tt0) cc_final: 0.8376 (tt0) REVERT: M 72 ASP cc_start: 0.8704 (t0) cc_final: 0.8309 (t0) REVERT: M 95 ASP cc_start: 0.8315 (m-30) cc_final: 0.7534 (m-30) REVERT: N 42 GLN cc_start: 0.8518 (mp10) cc_final: 0.8207 (mp10) REVERT: N 61 ARG cc_start: 0.8573 (ptt90) cc_final: 0.7766 (ptt180) REVERT: N 79 GLN cc_start: 0.7739 (mp10) cc_final: 0.7429 (mp10) REVERT: N 82 ASP cc_start: 0.8594 (m-30) cc_final: 0.7841 (m-30) REVERT: N 87 TYR cc_start: 0.9082 (m-80) cc_final: 0.8852 (m-80) REVERT: N 95 TYR cc_start: 0.7231 (t80) cc_final: 0.6794 (t80) outliers start: 62 outliers final: 42 residues processed: 299 average time/residue: 0.1770 time to fit residues: 85.0196 Evaluate side-chains 280 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 248 optimal weight: 7.9990 chunk 212 optimal weight: 1.9990 chunk 265 optimal weight: 10.0000 chunk 373 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 255 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 37 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.082690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.053605 restraints weight = 79922.212| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.30 r_work: 0.2745 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 31005 Z= 0.178 Angle : 0.564 9.550 42291 Z= 0.287 Chirality : 0.045 0.247 4866 Planarity : 0.004 0.047 5391 Dihedral : 4.526 28.039 4094 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.13 % Allowed : 11.00 % Favored : 86.87 % 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: 0.04 (0.14), residues: 3735 helix: 1.84 (0.21), residues: 668 sheet: -0.26 (0.16), residues: 928 loop : -0.38 (0.14), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 83 TYR 0.019 0.001 TYR Y 95B PHE 0.026 0.001 PHE B 497 TRP 0.013 0.001 TRP C 886 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (30912) covalent geometry : angle 0.55448 / 0.28 (42057) SS BOND : bond 0.00278 / 0.17 ( 45) SS BOND : angle 1.44367 / 1.03 ( 90) hydrogen bonds : bond 0.03543 / 2.37 ( 1167) hydrogen bonds : angle 5.45780 / 3.83 ( 3108) link_NAG-ASN : bond 0.00187 / 0.13 ( 48) link_NAG-ASN : angle 1.51136 / 1.04 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 252 time to evaluate : 1.106 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: Y 35 TRP cc_start: 0.8706 (m100) cc_final: 0.8011 (m100) REVERT: Y 79 GLN cc_start: 0.8170 (mp10) cc_final: 0.7903 (mp10) REVERT: Y 82 ASP cc_start: 0.7190 (m-30) cc_final: 0.6947 (m-30) REVERT: Y 87 TYR cc_start: 0.9122 (m-80) cc_final: 0.8770 (m-80) REVERT: Y 92 ASP cc_start: 0.8468 (t0) cc_final: 0.8072 (t70) REVERT: B 360 ASN cc_start: 0.9245 (m-40) cc_final: 0.8731 (t0) REVERT: B 403 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.6140 (tpp80) REVERT: B 619 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8967 (pm20) REVERT: B 745 ASP cc_start: 0.8483 (t70) cc_final: 0.8272 (t70) REVERT: X 67 PHE cc_start: 0.9273 (m-10) cc_final: 0.8552 (m-10) REVERT: X 72 ASP cc_start: 0.8587 (t0) cc_final: 0.7854 (t0) REVERT: X 75 LYS cc_start: 0.9297 (mtmm) cc_final: 0.8775 (mtmm) REVERT: X 100 ASP cc_start: 0.8714 (t70) cc_final: 0.8165 (t0) REVERT: X 107 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8435 (p) REVERT: L 27 LYS cc_start: 0.9261 (mmmm) cc_final: 0.8993 (mmmm) REVERT: L 42 GLN cc_start: 0.8852 (mp10) cc_final: 0.8277 (mp10) REVERT: L 69 ASN cc_start: 0.9162 (m-40) cc_final: 0.8840 (m-40) REVERT: L 83 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8032 (mm-30) REVERT: L 92 ASP cc_start: 0.8515 (t0) cc_final: 0.8095 (t0) REVERT: C 417 LYS cc_start: 0.9307 (mmmm) cc_final: 0.8915 (tptt) REVERT: C 425 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8020 (pp) REVERT: C 456 PHE cc_start: 0.8872 (m-80) cc_final: 0.8359 (m-80) REVERT: C 516 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7941 (mp0) REVERT: A 402 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7698 (tt) REVERT: A 740 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.8907 (ttt) REVERT: H 46 GLU cc_start: 0.9014 (tt0) cc_final: 0.8713 (tt0) REVERT: H 72 ASP cc_start: 0.8909 (t0) cc_final: 0.8380 (t0) REVERT: M 34 MET cc_start: 0.8499 (mmt) cc_final: 0.7663 (mmt) REVERT: M 46 GLU cc_start: 0.8577 (tt0) cc_final: 0.8287 (tt0) REVERT: M 72 ASP cc_start: 0.8832 (t0) cc_final: 0.8488 (t0) REVERT: N 42 GLN cc_start: 0.8600 (mp10) cc_final: 0.8291 (mp10) REVERT: N 61 ARG cc_start: 0.8690 (ptt90) cc_final: 0.7902 (ptt180) REVERT: N 79 GLN cc_start: 0.7699 (mp10) cc_final: 0.7358 (mp10) REVERT: N 81 MET cc_start: 0.9097 (ptp) cc_final: 0.8627 (pmm) REVERT: N 82 ASP cc_start: 0.8620 (m-30) cc_final: 0.7830 (m-30) REVERT: N 95 TYR cc_start: 0.7397 (t80) cc_final: 0.6974 (t80) outliers start: 70 outliers final: 53 residues processed: 304 average time/residue: 0.2006 time to fit residues: 98.0720 Evaluate side-chains 293 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 234 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain X residue 107 THR Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 250 optimal weight: 10.0000 chunk 202 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 chunk 291 optimal weight: 2.9990 chunk 306 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 238 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.081970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.052811 restraints weight = 80358.129| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.28 r_work: 0.2725 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31005 Z= 0.210 Angle : 0.581 9.521 42291 Z= 0.295 Chirality : 0.045 0.247 4866 Planarity : 0.004 0.046 5391 Dihedral : 4.593 31.107 4094 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.16 % Allowed : 11.27 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.14), residues: 3735 helix: 1.81 (0.21), residues: 673 sheet: -0.33 (0.16), residues: 956 loop : -0.38 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 19 TYR 0.021 0.001 TYR B 904 PHE 0.039 0.001 PHE B 497 TRP 0.009 0.001 TRP L 91 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (30912) covalent geometry : angle 0.57083 / 0.29 (42057) SS BOND : bond 0.00322 / 0.20 ( 45) SS BOND : angle 1.56853 / 1.14 ( 90) hydrogen bonds : bond 0.03636 / 2.42 ( 1167) hydrogen bonds : angle 5.45563 / 3.83 ( 3108) link_NAG-ASN : bond 0.00215 / 0.15 ( 48) link_NAG-ASN : angle 1.57450 / 1.08 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 244 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 79 GLN cc_start: 0.8246 (mp10) cc_final: 0.7842 (mp10) REVERT: Y 82 ASP cc_start: 0.7277 (m-30) cc_final: 0.6539 (m-30) REVERT: Y 87 TYR cc_start: 0.9100 (m-80) cc_final: 0.8745 (m-80) REVERT: Y 92 ASP cc_start: 0.8478 (t0) cc_final: 0.8093 (t70) REVERT: B 360 ASN cc_start: 0.9255 (m-40) cc_final: 0.8696 (t0) REVERT: B 403 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.5907 (tpp80) REVERT: B 453 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.7591 (p90) REVERT: B 619 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8967 (pm20) REVERT: B 745 ASP cc_start: 0.8502 (t70) cc_final: 0.8298 (t70) REVERT: X 67 PHE cc_start: 0.9273 (m-10) cc_final: 0.8592 (m-10) REVERT: X 72 ASP cc_start: 0.8650 (t0) cc_final: 0.8365 (t0) REVERT: X 100 ASP cc_start: 0.8741 (t70) cc_final: 0.8181 (t0) REVERT: X 107 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8469 (p) REVERT: L 27 LYS cc_start: 0.9243 (mmmm) cc_final: 0.8988 (mmmm) REVERT: L 42 GLN cc_start: 0.8866 (mp10) cc_final: 0.8595 (mp10) REVERT: L 69 ASN cc_start: 0.9203 (m-40) cc_final: 0.8886 (m-40) REVERT: L 83 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8108 (mm-30) REVERT: L 92 ASP cc_start: 0.8510 (t0) cc_final: 0.8099 (t0) REVERT: C 425 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8095 (pp) REVERT: C 456 PHE cc_start: 0.8864 (m-80) cc_final: 0.8395 (m-80) REVERT: C 904 TYR cc_start: 0.8184 (t80) cc_final: 0.7887 (t80) REVERT: A 402 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7711 (tt) REVERT: A 421 TYR cc_start: 0.9144 (m-10) cc_final: 0.8819 (m-80) REVERT: A 740 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8909 (ttt) REVERT: H 46 GLU cc_start: 0.9013 (tt0) cc_final: 0.8711 (tt0) REVERT: H 72 ASP cc_start: 0.8953 (t0) cc_final: 0.8454 (t0) REVERT: M 46 GLU cc_start: 0.8480 (tt0) cc_final: 0.8186 (tt0) REVERT: M 72 ASP cc_start: 0.8821 (t0) cc_final: 0.8447 (t0) REVERT: M 95 ASP cc_start: 0.8499 (m-30) cc_final: 0.7970 (m-30) REVERT: N 39 LYS cc_start: 0.8032 (mmmt) cc_final: 0.7658 (mmtt) REVERT: N 42 GLN cc_start: 0.8615 (mp10) cc_final: 0.8302 (mp10) REVERT: N 61 ARG cc_start: 0.8698 (ptt90) cc_final: 0.8197 (ptt90) REVERT: N 79 GLN cc_start: 0.7624 (mp10) cc_final: 0.7346 (mp10) REVERT: N 81 MET cc_start: 0.9088 (ptp) cc_final: 0.8783 (pmm) REVERT: N 82 ASP cc_start: 0.8664 (m-30) cc_final: 0.8084 (m-30) REVERT: N 85 ASP cc_start: 0.8150 (m-30) cc_final: 0.7325 (p0) REVERT: N 87 TYR cc_start: 0.9047 (m-80) cc_final: 0.8691 (m-80) REVERT: N 95 TYR cc_start: 0.7481 (t80) cc_final: 0.7110 (t80) outliers start: 71 outliers final: 56 residues processed: 297 average time/residue: 0.1826 time to fit residues: 87.3705 Evaluate side-chains 296 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 233 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain X residue 107 THR Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 143 optimal weight: 4.9990 chunk 283 optimal weight: 8.9990 chunk 240 optimal weight: 4.9990 chunk 224 optimal weight: 0.7980 chunk 371 optimal weight: 20.0000 chunk 76 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 270 optimal weight: 10.0000 chunk 293 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 37 GLN B 69 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN M 56 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.081898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.052868 restraints weight = 80582.964| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.28 r_work: 0.2731 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 31005 Z= 0.206 Angle : 0.585 9.515 42291 Z= 0.296 Chirality : 0.045 0.245 4866 Planarity : 0.004 0.045 5391 Dihedral : 4.593 31.350 4094 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.40 % Allowed : 11.55 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.14), residues: 3735 helix: 1.88 (0.21), residues: 667 sheet: -0.33 (0.16), residues: 966 loop : -0.39 (0.14), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 93 TYR 0.024 0.001 TYR B 904 PHE 0.037 0.001 PHE B 497 TRP 0.009 0.001 TRP L 91 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (30912) covalent geometry : angle 0.57514 / 0.29 (42057) SS BOND : bond 0.00317 / 0.19 ( 45) SS BOND : angle 1.50279 / 1.09 ( 90) hydrogen bonds : bond 0.03606 / 2.40 ( 1167) hydrogen bonds : angle 5.43986 / 3.82 ( 3108) link_NAG-ASN : bond 0.00207 / 0.15 ( 48) link_NAG-ASN : angle 1.58480 / 1.09 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 236 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 79 GLN cc_start: 0.8329 (mp10) cc_final: 0.7913 (mp10) REVERT: Y 82 ASP cc_start: 0.7298 (m-30) cc_final: 0.6333 (m-30) REVERT: Y 87 TYR cc_start: 0.9037 (m-80) cc_final: 0.8704 (m-80) REVERT: Y 92 ASP cc_start: 0.8500 (t0) cc_final: 0.8186 (t0) REVERT: B 360 ASN cc_start: 0.9247 (m-40) cc_final: 0.8699 (t0) REVERT: B 403 ARG cc_start: 0.6324 (OUTLIER) cc_final: 0.5853 (tpp80) REVERT: B 453 TYR cc_start: 0.7722 (OUTLIER) cc_final: 0.7493 (p90) REVERT: X 67 PHE cc_start: 0.9269 (m-10) cc_final: 0.8668 (m-10) REVERT: X 72 ASP cc_start: 0.8629 (t0) cc_final: 0.8079 (t0) REVERT: X 75 LYS cc_start: 0.9317 (mtmm) cc_final: 0.8951 (mtmm) REVERT: X 100 ASP cc_start: 0.8748 (t70) cc_final: 0.8178 (t0) REVERT: X 107 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8463 (p) REVERT: L 27 LYS cc_start: 0.9242 (mmmm) cc_final: 0.8993 (mmmm) REVERT: L 42 GLN cc_start: 0.8886 (mp10) cc_final: 0.8608 (mp10) REVERT: L 83 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8158 (mm-30) REVERT: L 92 ASP cc_start: 0.8505 (t0) cc_final: 0.8092 (t0) REVERT: C 417 LYS cc_start: 0.9338 (mmmm) cc_final: 0.9130 (tptm) REVERT: C 425 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8162 (pp) REVERT: C 456 PHE cc_start: 0.8836 (m-80) cc_final: 0.8359 (m-80) REVERT: C 904 TYR cc_start: 0.8156 (t80) cc_final: 0.7860 (t80) REVERT: A 402 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7734 (tt) REVERT: A 421 TYR cc_start: 0.9126 (m-10) cc_final: 0.8781 (m-80) REVERT: A 740 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8917 (ttt) REVERT: H 46 GLU cc_start: 0.9017 (tt0) cc_final: 0.8713 (tt0) REVERT: H 72 ASP cc_start: 0.8964 (t0) cc_final: 0.8457 (t0) REVERT: M 46 GLU cc_start: 0.8443 (tt0) cc_final: 0.8141 (tt0) REVERT: M 72 ASP cc_start: 0.8858 (t0) cc_final: 0.8451 (t0) REVERT: M 95 ASP cc_start: 0.8479 (m-30) cc_final: 0.7929 (m-30) REVERT: N 39 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7599 (mmtt) REVERT: N 42 GLN cc_start: 0.8620 (mp10) cc_final: 0.8303 (mp10) REVERT: N 61 ARG cc_start: 0.8732 (ptt90) cc_final: 0.8173 (ptt90) REVERT: N 79 GLN cc_start: 0.7605 (mp10) cc_final: 0.7289 (mp10) REVERT: N 81 MET cc_start: 0.9059 (ptp) cc_final: 0.8784 (pmm) REVERT: N 82 ASP cc_start: 0.8662 (m-30) cc_final: 0.8022 (m-30) REVERT: N 87 TYR cc_start: 0.8996 (m-80) cc_final: 0.8623 (m-80) REVERT: N 95 TYR cc_start: 0.7537 (t80) cc_final: 0.7234 (t80) outliers start: 79 outliers final: 62 residues processed: 292 average time/residue: 0.2032 time to fit residues: 95.8413 Evaluate side-chains 302 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 234 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 51 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain X residue 107 THR Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 253 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 294 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 287 optimal weight: 6.9990 chunk 10 optimal weight: 0.0870 chunk 111 optimal weight: 0.9990 overall best weight: 0.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 37 GLN Y 50 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.083592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.054652 restraints weight = 79939.021| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.30 r_work: 0.2777 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31005 Z= 0.116 Angle : 0.544 9.517 42291 Z= 0.276 Chirality : 0.044 0.241 4866 Planarity : 0.004 0.044 5391 Dihedral : 4.377 30.724 4094 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.79 % Allowed : 12.15 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.14), residues: 3735 helix: 1.99 (0.21), residues: 672 sheet: -0.23 (0.16), residues: 945 loop : -0.33 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 93 TYR 0.027 0.001 TYR B 904 PHE 0.034 0.001 PHE B 497 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS X 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (30912) covalent geometry : angle 0.53618 / 0.27 (42057) SS BOND : bond 0.00249 / 0.15 ( 45) SS BOND : angle 1.27434 / 0.92 ( 90) hydrogen bonds : bond 0.03222 / 2.14 ( 1167) hydrogen bonds : angle 5.24684 / 3.68 ( 3108) link_NAG-ASN : bond 0.00186 / 0.14 ( 48) link_NAG-ASN : angle 1.41884 / 0.98 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 249 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 35 TRP cc_start: 0.8785 (m100) cc_final: 0.8104 (m100) REVERT: Y 53 LYS cc_start: 0.8566 (mttm) cc_final: 0.8280 (mttt) REVERT: Y 79 GLN cc_start: 0.8399 (mp10) cc_final: 0.8047 (mp10) REVERT: Y 82 ASP cc_start: 0.7120 (m-30) cc_final: 0.6180 (m-30) REVERT: Y 87 TYR cc_start: 0.8653 (m-80) cc_final: 0.8416 (m-80) REVERT: Y 92 ASP cc_start: 0.8489 (t0) cc_final: 0.8119 (t70) REVERT: B 186 PHE cc_start: 0.8621 (m-10) cc_final: 0.8411 (m-10) REVERT: B 346 ARG cc_start: 0.8883 (mtp-110) cc_final: 0.8682 (mmm160) REVERT: B 360 ASN cc_start: 0.9223 (m-40) cc_final: 0.8677 (t0) REVERT: B 403 ARG cc_start: 0.6295 (OUTLIER) cc_final: 0.5941 (tpp80) REVERT: B 453 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7470 (p90) REVERT: B 957 GLN cc_start: 0.8567 (tt0) cc_final: 0.8322 (tt0) REVERT: X 72 ASP cc_start: 0.8552 (t0) cc_final: 0.7804 (t0) REVERT: X 75 LYS cc_start: 0.9329 (mtmm) cc_final: 0.8817 (mtmm) REVERT: X 100 ASP cc_start: 0.8693 (t70) cc_final: 0.8207 (t0) REVERT: X 107 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8532 (p) REVERT: L 27 LYS cc_start: 0.9241 (mmmm) cc_final: 0.8972 (mmmm) REVERT: L 42 GLN cc_start: 0.8874 (mp10) cc_final: 0.8592 (mp10) REVERT: L 81 MET cc_start: 0.9218 (ppp) cc_final: 0.9003 (ppp) REVERT: L 83 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8076 (mm-30) REVERT: L 103 LYS cc_start: 0.9231 (tptm) cc_final: 0.8816 (tptp) REVERT: C 425 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8083 (pp) REVERT: C 456 PHE cc_start: 0.8793 (m-80) cc_final: 0.8310 (m-80) REVERT: C 904 TYR cc_start: 0.8065 (t80) cc_final: 0.7815 (t80) REVERT: A 421 TYR cc_start: 0.9146 (m-10) cc_final: 0.8753 (m-80) REVERT: H 46 GLU cc_start: 0.9015 (tt0) cc_final: 0.8730 (tt0) REVERT: H 72 ASP cc_start: 0.8912 (t0) cc_final: 0.8543 (t0) REVERT: M 46 GLU cc_start: 0.8464 (tt0) cc_final: 0.8190 (tt0) REVERT: M 72 ASP cc_start: 0.8846 (t0) cc_final: 0.8428 (t0) REVERT: M 95 ASP cc_start: 0.8410 (m-30) cc_final: 0.7851 (m-30) REVERT: N 39 LYS cc_start: 0.7989 (mmmt) cc_final: 0.7570 (mmtt) REVERT: N 42 GLN cc_start: 0.8621 (mp10) cc_final: 0.8335 (mp10) REVERT: N 61 ARG cc_start: 0.8737 (ptt90) cc_final: 0.8106 (ptt90) REVERT: N 79 GLN cc_start: 0.7617 (mp10) cc_final: 0.7276 (mp10) REVERT: N 81 MET cc_start: 0.9069 (ptp) cc_final: 0.8810 (pmm) REVERT: N 82 ASP cc_start: 0.8675 (m-30) cc_final: 0.7968 (m-30) REVERT: N 87 TYR cc_start: 0.8891 (m-80) cc_final: 0.8545 (m-80) REVERT: N 95 TYR cc_start: 0.7522 (t80) cc_final: 0.7174 (t80) outliers start: 59 outliers final: 47 residues processed: 289 average time/residue: 0.2042 time to fit residues: 95.1310 Evaluate side-chains 289 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain X residue 107 THR Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 86 optimal weight: 0.4980 chunk 208 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 37 GLN Y 50 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.082467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.053363 restraints weight = 79964.301| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.28 r_work: 0.2749 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31005 Z= 0.188 Angle : 0.576 11.600 42291 Z= 0.291 Chirality : 0.045 0.246 4866 Planarity : 0.004 0.044 5391 Dihedral : 4.457 30.630 4094 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.85 % Allowed : 12.31 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.14), residues: 3735 helix: 1.93 (0.21), residues: 680 sheet: -0.24 (0.16), residues: 942 loop : -0.36 (0.14), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 93 TYR 0.031 0.001 TYR B 904 PHE 0.033 0.001 PHE B 497 TRP 0.009 0.001 TRP L 91 HIS 0.004 0.001 HIS X 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (30912) covalent geometry : angle 0.56633 / 0.29 (42057) SS BOND : bond 0.00286 / 0.17 ( 45) SS BOND : angle 1.47565 / 1.07 ( 90) hydrogen bonds : bond 0.03465 / 2.31 ( 1167) hydrogen bonds : angle 5.29986 / 3.72 ( 3108) link_NAG-ASN : bond 0.00189 / 0.14 ( 48) link_NAG-ASN : angle 1.50677 / 1.04 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 240 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 53 LYS cc_start: 0.8668 (mttm) cc_final: 0.8406 (mttt) REVERT: Y 79 GLN cc_start: 0.8350 (mp10) cc_final: 0.7962 (mp10) REVERT: Y 82 ASP cc_start: 0.7305 (m-30) cc_final: 0.6043 (m-30) REVERT: Y 92 ASP cc_start: 0.8484 (t0) cc_final: 0.8159 (t0) REVERT: B 186 PHE cc_start: 0.8619 (m-10) cc_final: 0.8408 (m-10) REVERT: B 360 ASN cc_start: 0.9253 (m-40) cc_final: 0.8667 (t0) REVERT: B 403 ARG cc_start: 0.6347 (OUTLIER) cc_final: 0.5978 (tpp80) REVERT: B 957 GLN cc_start: 0.8601 (tt0) cc_final: 0.8356 (tt0) REVERT: X 72 ASP cc_start: 0.8612 (t0) cc_final: 0.7852 (t0) REVERT: X 75 LYS cc_start: 0.9334 (mtmm) cc_final: 0.8815 (mtmm) REVERT: X 100 ASP cc_start: 0.8742 (t70) cc_final: 0.8227 (t0) REVERT: X 107 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8592 (p) REVERT: L 27 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8982 (mmmm) REVERT: L 42 GLN cc_start: 0.8907 (mp10) cc_final: 0.8616 (mp10) REVERT: L 83 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8140 (mm-30) REVERT: L 92 ASP cc_start: 0.8510 (t0) cc_final: 0.8070 (t0) REVERT: C 425 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8132 (pp) REVERT: C 456 PHE cc_start: 0.8780 (m-80) cc_final: 0.8280 (m-80) REVERT: C 904 TYR cc_start: 0.8135 (t80) cc_final: 0.7844 (t80) REVERT: A 183 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8283 (tp-100) REVERT: A 421 TYR cc_start: 0.9155 (m-10) cc_final: 0.8746 (m-80) REVERT: A 740 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8895 (ttt) REVERT: H 46 GLU cc_start: 0.9021 (tt0) cc_final: 0.8718 (tt0) REVERT: H 72 ASP cc_start: 0.8953 (t0) cc_final: 0.8440 (t0) REVERT: M 46 GLU cc_start: 0.8432 (tt0) cc_final: 0.8146 (tt0) REVERT: M 72 ASP cc_start: 0.8875 (t0) cc_final: 0.8460 (t0) REVERT: M 95 ASP cc_start: 0.8443 (m-30) cc_final: 0.7994 (m-30) REVERT: N 39 LYS cc_start: 0.8022 (mmmt) cc_final: 0.7599 (mmtt) REVERT: N 42 GLN cc_start: 0.8643 (mp10) cc_final: 0.8362 (mp10) REVERT: N 79 GLN cc_start: 0.7578 (mp10) cc_final: 0.7137 (mp10) REVERT: N 81 MET cc_start: 0.9061 (ptp) cc_final: 0.8825 (pmm) REVERT: N 82 ASP cc_start: 0.8612 (m-30) cc_final: 0.8026 (m-30) REVERT: N 87 TYR cc_start: 0.8887 (m-80) cc_final: 0.8611 (m-80) outliers start: 61 outliers final: 52 residues processed: 285 average time/residue: 0.1918 time to fit residues: 88.5652 Evaluate side-chains 292 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 235 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain X residue 107 THR Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 101 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 369 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 338 optimal weight: 0.2980 chunk 244 optimal weight: 0.0070 chunk 105 optimal weight: 3.9990 chunk 364 optimal weight: 6.9990 chunk 313 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 363 optimal weight: 3.9990 overall best weight: 2.0604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 37 GLN B 422 ASN C 188 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.082550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.053482 restraints weight = 80481.911| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.27 r_work: 0.2745 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 31005 Z= 0.240 Angle : 0.702 59.140 42291 Z= 0.388 Chirality : 0.049 1.320 4866 Planarity : 0.004 0.100 5391 Dihedral : 4.489 36.494 4094 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 2.07 % Allowed : 12.12 % Favored : 85.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.14), residues: 3735 helix: 1.92 (0.21), residues: 680 sheet: -0.25 (0.16), residues: 942 loop : -0.37 (0.14), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG X 83 TYR 0.026 0.001 TYR B 453 PHE 0.030 0.001 PHE B 497 TRP 0.009 0.001 TRP L 91 HIS 0.008 0.001 HIS X 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 (30912) covalent geometry : angle 0.69472 / 0.39 (42057) SS BOND : bond 0.00296 / 0.18 ( 45) SS BOND : angle 1.46039 / 1.06 ( 90) hydrogen bonds : bond 0.03478 / 2.32 ( 1167) hydrogen bonds : angle 5.30044 / 3.72 ( 3108) link_NAG-ASN : bond 0.00192 / 0.14 ( 48) link_NAG-ASN : angle 1.50516 / 1.04 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7352.84 seconds wall clock time: 127 minutes 2.40 seconds (7622.40 seconds total)