Starting phenix.real_space_refine on Fri Mar 6 10:05:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ukl_26583/03_2026/7ukl_26583.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukl_26583/03_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_26583/03_2026/7ukl_26583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukl_26583/03_2026/7ukl_26583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ukl_26583/03_2026/7ukl_26583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukl_26583/03_2026/7ukl_26583.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 48 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 dihedrals: 48 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 dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 6.35, per 1000 atoms: 0.21 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: 2.80 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: 1.37 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: 8.47 Time building geometry restraints manager: 3.83 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: 17487 17.58 - 35.16: 1158 35.16 - 52.74: 232 52.74 - 70.32: 63 70.32 - 87.90: 29 Dihedral angle restraints: 18969 sinusoidal: 7968 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 18966 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: 8.420 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: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 31.650 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 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 : 12.695 87.897 11790 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 covalent geometry : bond 0.00532 (30912) covalent geometry : angle 0.86454 (42057) SS BOND : bond 0.01121 ( 45) SS BOND : angle 2.40358 ( 90) hydrogen bonds : bond 0.21375 ( 1167) hydrogen bonds : angle 8.92410 ( 3108) link_NAG-ASN : bond 0.02531 ( 48) link_NAG-ASN : angle 3.84673 ( 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 : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.2086 time to fit residues: 121.1398 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 : 0.943 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: Y 17 GLN B 164 ASN B 188 ASN B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN 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 Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.084092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.054879 restraints weight = 80113.795| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.29 r_work: 0.2775 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 31005 Z= 0.203 Angle : 0.630 9.486 42291 Z= 0.322 Chirality : 0.047 0.212 4866 Planarity : 0.004 0.067 5391 Dihedral : 5.984 59.998 5102 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.12 % Allowed : 6.23 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 3735 helix: 1.31 (0.21), residues: 657 sheet: -0.37 (0.16), residues: 948 loop : -0.54 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 93 TYR 0.022 0.001 TYR B 453 PHE 0.021 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 covalent geometry : bond 0.00475 (30912) covalent geometry : angle 0.61914 (42057) SS BOND : bond 0.00354 ( 45) SS BOND : angle 1.52124 ( 90) hydrogen bonds : bond 0.04479 ( 1167) hydrogen bonds : angle 6.36407 ( 3108) link_NAG-ASN : bond 0.00287 ( 48) link_NAG-ASN : angle 1.80982 ( 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 309 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 272 time to evaluate : 1.082 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: Y 32 TYR cc_start: 0.8160 (m-80) cc_final: 0.7839 (m-10) REVERT: Y 35 TRP cc_start: 0.8476 (m100) cc_final: 0.8002 (m100) REVERT: Y 53 LYS cc_start: 0.8578 (mttm) cc_final: 0.7939 (mttp) REVERT: Y 83 GLU cc_start: 0.9058 (tp30) cc_final: 0.8577 (mp0) REVERT: X 72 ASP cc_start: 0.8602 (t0) cc_final: 0.8224 (t0) REVERT: X 100 ASP cc_start: 0.8779 (t70) cc_final: 0.8512 (t70) REVERT: L 27 LYS cc_start: 0.9075 (mmmm) cc_final: 0.8871 (mmmm) REVERT: L 81 MET cc_start: 0.9257 (ppp) cc_final: 0.8660 (ppp) REVERT: C 417 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8885 (tptt) REVERT: C 902 MET cc_start: 0.9045 (tpp) cc_final: 0.8715 (tpt) REVERT: C 904 TYR cc_start: 0.8399 (t80) cc_final: 0.7998 (t80) REVERT: H 3 GLN cc_start: 0.7829 (pm20) cc_final: 0.6419 (pm20) REVERT: H 46 GLU cc_start: 0.9019 (tt0) cc_final: 0.8790 (tt0) REVERT: H 72 ASP cc_start: 0.8800 (t0) cc_final: 0.8548 (t0) REVERT: M 34 MET cc_start: 0.8575 (mmt) cc_final: 0.7462 (mmt) REVERT: M 46 GLU cc_start: 0.8602 (tt0) cc_final: 0.8091 (tt0) REVERT: M 64 LYS cc_start: 0.8181 (tttp) cc_final: 0.7887 (ttmm) REVERT: M 81 GLN cc_start: 0.8317 (mm-40) cc_final: 0.8106 (mm-40) REVERT: M 95 ASP cc_start: 0.8246 (m-30) cc_final: 0.7946 (m-30) REVERT: N 42 GLN cc_start: 0.8372 (mp10) cc_final: 0.8106 (mp10) REVERT: N 61 ARG cc_start: 0.8720 (ptt90) cc_final: 0.8201 (ptt90) REVERT: N 79 GLN cc_start: 0.7401 (mp10) cc_final: 0.7068 (mp10) REVERT: N 81 MET cc_start: 0.9112 (ptp) cc_final: 0.8430 (ppp) REVERT: N 82 ASP cc_start: 0.8725 (m-30) cc_final: 0.8227 (m-30) REVERT: N 85 ASP cc_start: 0.8231 (m-30) cc_final: 0.7341 (p0) REVERT: N 87 TYR cc_start: 0.9133 (m-80) cc_final: 0.8792 (m-80) REVERT: N 95 TYR cc_start: 0.7419 (t80) cc_final: 0.6944 (t80) outliers start: 37 outliers final: 24 residues processed: 295 average time/residue: 0.2026 time to fit residues: 94.5106 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 : 1.121 ------------------------------------------------------------------------------- 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 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 C residue 402 ILE 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 6 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 123 optimal weight: 0.6980 chunk 298 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 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: 0.8980 chunk 310 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 955 ASN C 87 ASN A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS M 35 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 = 0.3546 r_free = 0.3546 target = 0.082978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.053635 restraints weight = 80330.255| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.31 r_work: 0.2755 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 31005 Z= 0.207 Angle : 0.596 9.704 42291 Z= 0.305 Chirality : 0.046 0.228 4866 Planarity : 0.004 0.058 5391 Dihedral : 5.733 56.613 5102 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.67 % Allowed : 7.84 % 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: -0.17 (0.14), residues: 3735 helix: 1.55 (0.21), residues: 663 sheet: -0.31 (0.16), residues: 946 loop : -0.50 (0.13), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 16 TYR 0.021 0.001 TYR B 495 PHE 0.027 0.001 PHE B 490 TRP 0.009 0.001 TRP Y 35 HIS 0.003 0.001 HIS X 35 Details of bonding type rmsd covalent geometry : bond 0.00486 (30912) covalent geometry : angle 0.58624 (42057) SS BOND : bond 0.00350 ( 45) SS BOND : angle 1.41697 ( 90) hydrogen bonds : bond 0.04036 ( 1167) hydrogen bonds : angle 5.89071 ( 3108) link_NAG-ASN : bond 0.00237 ( 48) link_NAG-ASN : angle 1.64310 ( 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 322 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 267 time to evaluate : 1.362 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: Y 32 TYR cc_start: 0.8133 (m-80) cc_final: 0.7856 (m-80) REVERT: Y 35 TRP cc_start: 0.8592 (m100) cc_final: 0.7970 (m100) REVERT: Y 53 LYS cc_start: 0.8500 (mttm) cc_final: 0.7861 (mttp) REVERT: Y 79 GLN cc_start: 0.8045 (mp10) cc_final: 0.7824 (mp10) REVERT: Y 82 ASP cc_start: 0.7260 (m-30) cc_final: 0.6639 (m-30) REVERT: Y 83 GLU cc_start: 0.9073 (tp30) cc_final: 0.8702 (mp0) REVERT: Y 87 TYR cc_start: 0.9127 (m-80) cc_final: 0.8803 (m-80) REVERT: Y 92 ASP cc_start: 0.8508 (t0) cc_final: 0.8101 (t70) REVERT: B 360 ASN cc_start: 0.9186 (m-40) cc_final: 0.8756 (t0) REVERT: B 403 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6238 (mmm160) REVERT: B 497 PHE cc_start: 0.5146 (m-80) cc_final: 0.4349 (m-80) REVERT: X 61 ASP cc_start: 0.9321 (m-30) cc_final: 0.9052 (m-30) REVERT: X 64 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8657 (pttt) REVERT: X 72 ASP cc_start: 0.8560 (t0) cc_final: 0.8127 (t0) REVERT: X 100 ASP cc_start: 0.8799 (t70) cc_final: 0.8316 (t0) REVERT: L 27 LYS cc_start: 0.9136 (mmmm) cc_final: 0.8887 (mmmm) REVERT: L 42 GLN cc_start: 0.8820 (mp10) cc_final: 0.8488 (mp10) REVERT: L 81 MET cc_start: 0.9278 (ppp) cc_final: 0.8625 (ppp) REVERT: L 95 TYR cc_start: 0.8746 (t80) cc_final: 0.8540 (t80) REVERT: C 456 PHE cc_start: 0.8687 (m-80) cc_final: 0.8168 (m-80) REVERT: C 516 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8147 (mp0) REVERT: A 402 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7689 (tt) REVERT: H 46 GLU cc_start: 0.9002 (tt0) cc_final: 0.8761 (tt0) REVERT: H 72 ASP cc_start: 0.8856 (t0) cc_final: 0.8456 (t0) REVERT: H 82 MET cc_start: 0.8766 (mtm) cc_final: 0.8518 (mtm) REVERT: M 46 GLU cc_start: 0.8714 (tt0) cc_final: 0.8430 (tt0) REVERT: M 72 ASP cc_start: 0.8649 (t0) cc_final: 0.8264 (t0) REVERT: N 42 GLN cc_start: 0.8421 (mp10) cc_final: 0.8118 (mp10) REVERT: N 61 ARG cc_start: 0.8709 (ptt90) cc_final: 0.8225 (ptt90) REVERT: N 79 GLN cc_start: 0.7472 (mp10) cc_final: 0.7181 (mp10) REVERT: N 82 ASP cc_start: 0.8676 (m-30) cc_final: 0.8227 (m-30) REVERT: N 87 TYR cc_start: 0.9045 (m-80) cc_final: 0.8765 (m-80) REVERT: N 95 TYR cc_start: 0.7406 (t80) cc_final: 0.6988 (t80) outliers start: 55 outliers final: 34 residues processed: 302 average time/residue: 0.1958 time to fit residues: 93.4534 Evaluate side-chains 280 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 243 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 64 LYS 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 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 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 Chi-restraints excluded: chain N residue 104 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: 0.9980 chunk 296 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 37 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN C 196 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.082485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.053299 restraints weight = 80039.941| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.30 r_work: 0.2734 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 31005 Z= 0.212 Angle : 0.586 9.631 42291 Z= 0.299 Chirality : 0.045 0.236 4866 Planarity : 0.004 0.053 5391 Dihedral : 5.662 56.967 5102 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.85 % Allowed : 9.57 % Favored : 88.57 % 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: -0.10 (0.14), residues: 3735 helix: 1.69 (0.21), residues: 659 sheet: -0.34 (0.16), residues: 941 loop : -0.45 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 19 TYR 0.022 0.001 TYR B 453 PHE 0.026 0.001 PHE B 497 TRP 0.039 0.001 TRP C 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00499 (30912) covalent geometry : angle 0.57599 (42057) SS BOND : bond 0.00394 ( 45) SS BOND : angle 1.44708 ( 90) hydrogen bonds : bond 0.03812 ( 1167) hydrogen bonds : angle 5.72495 ( 3108) link_NAG-ASN : bond 0.00233 ( 48) link_NAG-ASN : angle 1.67664 ( 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 314 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 253 time to evaluate : 0.819 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: Y 32 TYR cc_start: 0.8135 (m-80) cc_final: 0.7888 (m-80) REVERT: Y 35 TRP cc_start: 0.8674 (m100) cc_final: 0.8103 (m100) REVERT: Y 37 GLN cc_start: 0.9064 (tt0) cc_final: 0.8859 (tt0) REVERT: Y 82 ASP cc_start: 0.7312 (m-30) cc_final: 0.6640 (m-30) REVERT: Y 83 GLU cc_start: 0.9084 (tp30) cc_final: 0.8867 (mp0) REVERT: Y 87 TYR cc_start: 0.9084 (m-80) cc_final: 0.8838 (m-80) REVERT: Y 92 ASP cc_start: 0.8486 (t0) cc_final: 0.8085 (t70) REVERT: B 360 ASN cc_start: 0.9208 (m-40) cc_final: 0.8743 (t0) REVERT: B 403 ARG cc_start: 0.6846 (mmt180) cc_final: 0.6588 (tpp80) REVERT: X 72 ASP cc_start: 0.8548 (t0) cc_final: 0.8095 (t0) REVERT: X 100 ASP cc_start: 0.8776 (t70) cc_final: 0.8262 (t0) REVERT: L 27 LYS cc_start: 0.9193 (mmmm) cc_final: 0.8966 (mmmm) REVERT: L 42 GLN cc_start: 0.8847 (mp10) cc_final: 0.8647 (mp10) REVERT: L 81 MET cc_start: 0.9241 (ppp) cc_final: 0.8610 (ppp) REVERT: C 417 LYS cc_start: 0.9247 (mmmm) cc_final: 0.8843 (tptt) REVERT: C 456 PHE cc_start: 0.8751 (m-80) cc_final: 0.8220 (m-80) REVERT: A 402 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7658 (tt) REVERT: H 46 GLU cc_start: 0.9028 (tt0) cc_final: 0.8747 (tt0) REVERT: H 72 ASP cc_start: 0.8885 (t0) cc_final: 0.8399 (t0) REVERT: H 82 MET cc_start: 0.8799 (mtm) cc_final: 0.8462 (mtm) REVERT: H 107 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8737 (p) REVERT: M 46 GLU cc_start: 0.8634 (tt0) cc_final: 0.8373 (tt0) REVERT: M 72 ASP cc_start: 0.8723 (t0) cc_final: 0.8328 (t0) REVERT: M 95 ASP cc_start: 0.8445 (m-30) cc_final: 0.8115 (m-30) REVERT: N 42 GLN cc_start: 0.8481 (mp10) cc_final: 0.8169 (mp10) REVERT: N 61 ARG cc_start: 0.8718 (ptt90) cc_final: 0.7918 (ptt180) REVERT: N 79 GLN cc_start: 0.7573 (mp10) cc_final: 0.7230 (mp10) REVERT: N 87 TYR cc_start: 0.9022 (m-80) cc_final: 0.8723 (m-80) REVERT: N 95 TYR cc_start: 0.7354 (t80) cc_final: 0.6920 (t80) outliers start: 61 outliers final: 41 residues processed: 295 average time/residue: 0.1958 time to fit residues: 91.5867 Evaluate side-chains 275 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 51 ASP 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 228 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 392 PHE 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 856 ASN Chi-restraints excluded: chain B residue 916 LEU 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 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 C residue 620 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 1132 ILE Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 4 LEU 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: 2.9990 chunk 50 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 190 optimal weight: 1.9990 chunk 361 optimal weight: 9.9990 chunk 366 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 270 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 79 GLN B 69 HIS B 218 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.081010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.051811 restraints weight = 80195.394| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.26 r_work: 0.2655 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 31005 Z= 0.244 Angle : 0.605 9.606 42291 Z= 0.308 Chirality : 0.046 0.238 4866 Planarity : 0.004 0.050 5391 Dihedral : 5.717 57.512 5102 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.31 % Allowed : 10.36 % Favored : 87.33 % 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: -0.11 (0.14), residues: 3735 helix: 1.67 (0.21), residues: 668 sheet: -0.41 (0.16), residues: 960 loop : -0.42 (0.14), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 83 TYR 0.022 0.001 TYR B 904 PHE 0.041 0.002 PHE B 497 TRP 0.035 0.001 TRP C 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00573 (30912) covalent geometry : angle 0.59359 (42057) SS BOND : bond 0.00362 ( 45) SS BOND : angle 1.58279 ( 90) hydrogen bonds : bond 0.03841 ( 1167) hydrogen bonds : angle 5.64552 ( 3108) link_NAG-ASN : bond 0.00273 ( 48) link_NAG-ASN : angle 1.74023 ( 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 319 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 243 time to evaluate : 1.146 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: Y 83 GLU cc_start: 0.8901 (tp30) cc_final: 0.8683 (mp0) REVERT: Y 92 ASP cc_start: 0.8480 (t0) cc_final: 0.8079 (t70) REVERT: B 360 ASN cc_start: 0.9228 (m-40) cc_final: 0.8731 (t0) REVERT: B 403 ARG cc_start: 0.6636 (mmt180) cc_final: 0.6159 (tpp80) REVERT: B 453 TYR cc_start: 0.7679 (OUTLIER) cc_final: 0.7460 (p90) REVERT: B 497 PHE cc_start: 0.6221 (m-80) cc_final: 0.5908 (m-80) REVERT: X 72 ASP cc_start: 0.8490 (t0) cc_final: 0.8156 (t0) REVERT: X 100 ASP cc_start: 0.8730 (t70) cc_final: 0.8146 (t0) REVERT: L 27 LYS cc_start: 0.9255 (mmmm) cc_final: 0.8997 (mmmm) REVERT: L 42 GLN cc_start: 0.8851 (mp10) cc_final: 0.8626 (mp10) REVERT: C 417 LYS cc_start: 0.9308 (mmmm) cc_final: 0.8864 (tptt) REVERT: C 425 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8097 (pp) REVERT: C 456 PHE cc_start: 0.8840 (m-80) cc_final: 0.8315 (m-80) REVERT: C 988 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8885 (pm20) REVERT: A 402 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7680 (tt) REVERT: A 740 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8942 (ttt) REVERT: H 46 GLU cc_start: 0.9055 (tt0) cc_final: 0.8762 (tt0) REVERT: H 72 ASP cc_start: 0.8875 (t0) cc_final: 0.8363 (t0) REVERT: H 107 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8716 (p) REVERT: M 13 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8509 (mm-40) REVERT: M 46 GLU cc_start: 0.8602 (tt0) cc_final: 0.8368 (tt0) REVERT: M 64 LYS cc_start: 0.8339 (tttp) cc_final: 0.8100 (mtmm) REVERT: M 72 ASP cc_start: 0.8775 (t0) cc_final: 0.8379 (t0) REVERT: N 42 GLN cc_start: 0.8478 (mp10) cc_final: 0.8131 (mp10) REVERT: N 79 GLN cc_start: 0.7447 (mp10) cc_final: 0.7070 (mp10) REVERT: N 81 MET cc_start: 0.9093 (ptp) cc_final: 0.8880 (pmm) REVERT: N 82 ASP cc_start: 0.8510 (m-30) cc_final: 0.7793 (m-30) REVERT: N 95 TYR cc_start: 0.7371 (t80) cc_final: 0.6930 (t80) outliers start: 76 outliers final: 52 residues processed: 300 average time/residue: 0.1888 time to fit residues: 90.5990 Evaluate side-chains 287 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 229 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 97 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 227 VAL Chi-restraints excluded: chain B residue 228 ASP 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 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 617 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 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 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 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 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 938 LEU 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 584 ILE 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 1132 ILE Chi-restraints excluded: chain H residue 107 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 248 optimal weight: 7.9990 chunk 212 optimal weight: 0.6980 chunk 265 optimal weight: 9.9990 chunk 373 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.080629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.051371 restraints weight = 80803.491| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.29 r_work: 0.2688 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 31005 Z= 0.301 Angle : 0.636 9.569 42291 Z= 0.324 Chirality : 0.047 0.256 4866 Planarity : 0.004 0.049 5391 Dihedral : 5.845 58.309 5102 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.40 % Allowed : 11.06 % Favored : 86.54 % 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: -0.16 (0.14), residues: 3735 helix: 1.69 (0.21), residues: 662 sheet: -0.40 (0.16), residues: 943 loop : -0.50 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 83 TYR 0.022 0.002 TYR B 904 PHE 0.032 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 covalent geometry : bond 0.00705 (30912) covalent geometry : angle 0.62322 (42057) SS BOND : bond 0.00385 ( 45) SS BOND : angle 1.83372 ( 90) hydrogen bonds : bond 0.03999 ( 1167) hydrogen bonds : angle 5.69164 ( 3108) link_NAG-ASN : bond 0.00356 ( 48) link_NAG-ASN : angle 1.85359 ( 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 318 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 239 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: symmetry clash REVERT: Y 92 ASP cc_start: 0.8511 (t0) cc_final: 0.8183 (t0) REVERT: Y 102 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8213 (m) REVERT: B 360 ASN cc_start: 0.9262 (m-40) cc_final: 0.8739 (t0) REVERT: B 403 ARG cc_start: 0.6457 (mmt180) cc_final: 0.5960 (tpp80) REVERT: X 72 ASP cc_start: 0.8642 (t0) cc_final: 0.8224 (t0) REVERT: X 100 ASP cc_start: 0.8785 (t70) cc_final: 0.8207 (t0) REVERT: L 27 LYS cc_start: 0.9244 (mmmm) cc_final: 0.8980 (mmmm) REVERT: L 42 GLN cc_start: 0.8904 (mp10) cc_final: 0.8649 (mp10) REVERT: L 69 ASN cc_start: 0.9159 (m-40) cc_final: 0.8937 (m-40) REVERT: C 425 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8256 (pp) REVERT: C 456 PHE cc_start: 0.8826 (m-80) cc_final: 0.8321 (m-80) REVERT: C 904 TYR cc_start: 0.8253 (t80) cc_final: 0.7935 (t80) REVERT: A 740 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.8989 (ttt) REVERT: H 46 GLU cc_start: 0.9027 (tt0) cc_final: 0.8724 (tt0) REVERT: H 72 ASP cc_start: 0.8996 (t0) cc_final: 0.8491 (t0) REVERT: M 13 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8595 (mm-40) REVERT: M 64 LYS cc_start: 0.8611 (tttp) cc_final: 0.8334 (mtmm) REVERT: M 72 ASP cc_start: 0.8826 (t0) cc_final: 0.8436 (t0) REVERT: N 42 GLN cc_start: 0.8496 (mp10) cc_final: 0.8134 (mp10) REVERT: N 61 ARG cc_start: 0.8662 (ptt90) cc_final: 0.8038 (ptt90) REVERT: N 79 GLN cc_start: 0.7529 (mp10) cc_final: 0.7176 (mp10) REVERT: N 85 ASP cc_start: 0.8107 (m-30) cc_final: 0.7390 (p0) REVERT: N 87 TYR cc_start: 0.9049 (m-80) cc_final: 0.8811 (m-10) REVERT: N 95 TYR cc_start: 0.7589 (t80) cc_final: 0.7241 (t80) outliers start: 79 outliers final: 60 residues processed: 300 average time/residue: 0.1913 time to fit residues: 91.9617 Evaluate side-chains 290 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 227 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 102 THR 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 228 ASP 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 430 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU 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 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 620 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 938 LEU 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 1132 ILE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 4 LEU 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: 9.9990 chunk 202 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 218 optimal weight: 0.9980 chunk 291 optimal weight: 1.9990 chunk 306 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 238 optimal weight: 0.7980 chunk 230 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.082984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.054072 restraints weight = 79867.737| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.29 r_work: 0.2760 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 31005 Z= 0.119 Angle : 0.553 9.616 42291 Z= 0.282 Chirality : 0.044 0.232 4866 Planarity : 0.004 0.046 5391 Dihedral : 5.451 55.186 5102 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.98 % Allowed : 11.94 % Favored : 86.08 % 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: 0.02 (0.14), residues: 3735 helix: 1.92 (0.21), residues: 665 sheet: -0.36 (0.16), residues: 945 loop : -0.37 (0.14), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 93 TYR 0.022 0.001 TYR B 904 PHE 0.028 0.001 PHE B 497 TRP 0.008 0.001 TRP N 35 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00274 (30912) covalent geometry : angle 0.54280 (42057) SS BOND : bond 0.00264 ( 45) SS BOND : angle 1.36644 ( 90) hydrogen bonds : bond 0.03377 ( 1167) hydrogen bonds : angle 5.41136 ( 3108) link_NAG-ASN : bond 0.00182 ( 48) link_NAG-ASN : angle 1.59529 ( 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: 65 poor density : 250 time to evaluate : 1.050 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: Y 35 TRP cc_start: 0.8821 (m100) cc_final: 0.8041 (m100) REVERT: Y 83 GLU cc_start: 0.9071 (tp30) cc_final: 0.8380 (mp0) REVERT: Y 87 TYR cc_start: 0.9050 (m-80) cc_final: 0.8820 (m-80) REVERT: Y 92 ASP cc_start: 0.8515 (t0) cc_final: 0.8151 (t70) REVERT: B 63 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8035 (p) REVERT: B 360 ASN cc_start: 0.9203 (m-40) cc_final: 0.8747 (t0) REVERT: B 403 ARG cc_start: 0.6408 (mmt180) cc_final: 0.6015 (tpp80) REVERT: B 453 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.7559 (p90) REVERT: B 823 PHE cc_start: 0.8690 (t80) cc_final: 0.8344 (m-80) REVERT: X 72 ASP cc_start: 0.8512 (t0) cc_final: 0.7777 (t0) REVERT: X 75 LYS cc_start: 0.9290 (mtmm) cc_final: 0.8800 (mtmm) REVERT: X 100 ASP cc_start: 0.8674 (t70) cc_final: 0.8191 (t0) REVERT: L 27 LYS cc_start: 0.9233 (mmmm) cc_final: 0.8961 (mmmm) REVERT: L 42 GLN cc_start: 0.8888 (mp10) cc_final: 0.8605 (mp10) REVERT: L 69 ASN cc_start: 0.9172 (m-40) cc_final: 0.8958 (m-40) REVERT: C 186 PHE cc_start: 0.8386 (m-80) cc_final: 0.8103 (m-80) REVERT: C 456 PHE cc_start: 0.8767 (m-80) cc_final: 0.8257 (m-80) REVERT: C 516 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8118 (mp0) REVERT: C 904 TYR cc_start: 0.8059 (t80) cc_final: 0.7836 (t80) REVERT: A 402 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.7820 (tt) REVERT: A 421 TYR cc_start: 0.9136 (m-10) cc_final: 0.8801 (m-80) REVERT: A 740 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8873 (ttt) REVERT: H 46 GLU cc_start: 0.9040 (tt0) cc_final: 0.8760 (tt0) REVERT: H 72 ASP cc_start: 0.8926 (t0) cc_final: 0.8420 (t0) REVERT: H 105 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8828 (mm-40) REVERT: M 13 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8585 (mm-40) REVERT: M 64 LYS cc_start: 0.8352 (tttp) cc_final: 0.8142 (mtmm) REVERT: M 72 ASP cc_start: 0.8819 (t0) cc_final: 0.8422 (t0) REVERT: M 95 ASP cc_start: 0.8465 (m-30) cc_final: 0.7953 (m-30) REVERT: N 42 GLN cc_start: 0.8616 (mp10) cc_final: 0.8294 (mp10) REVERT: N 61 ARG cc_start: 0.8712 (ptt90) cc_final: 0.8276 (ptt90) REVERT: N 79 GLN cc_start: 0.7665 (mp10) cc_final: 0.7416 (mp10) REVERT: N 81 MET cc_start: 0.9114 (ptp) cc_final: 0.8589 (pmm) REVERT: N 82 ASP cc_start: 0.8523 (m-30) cc_final: 0.7854 (m-30) REVERT: N 87 TYR cc_start: 0.8922 (m-80) cc_final: 0.8400 (m-10) REVERT: N 95 TYR cc_start: 0.7538 (t80) cc_final: 0.7129 (t80) outliers start: 65 outliers final: 49 residues processed: 298 average time/residue: 0.1873 time to fit residues: 89.7648 Evaluate side-chains 290 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 236 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 63 THR 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 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 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 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 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 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 512 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 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 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 1132 ILE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 18 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: 0.8980 chunk 283 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 371 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 270 optimal weight: 9.9990 chunk 293 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN M 56 ASN M 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.081272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.052224 restraints weight = 80734.643| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.27 r_work: 0.2715 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 31005 Z= 0.245 Angle : 0.604 9.550 42291 Z= 0.307 Chirality : 0.045 0.240 4866 Planarity : 0.004 0.047 5391 Dihedral : 5.603 57.648 5102 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.31 % Allowed : 12.15 % Favored : 85.54 % 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: -0.04 (0.14), residues: 3735 helix: 1.85 (0.21), residues: 667 sheet: -0.46 (0.16), residues: 978 loop : -0.37 (0.14), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 93 TYR 0.025 0.001 TYR B 904 PHE 0.026 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 covalent geometry : bond 0.00576 (30912) covalent geometry : angle 0.59295 (42057) SS BOND : bond 0.00351 ( 45) SS BOND : angle 1.58150 ( 90) hydrogen bonds : bond 0.03761 ( 1167) hydrogen bonds : angle 5.50292 ( 3108) link_NAG-ASN : bond 0.00271 ( 48) link_NAG-ASN : angle 1.72604 ( 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 316 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 240 time to evaluate : 0.931 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: Y 83 GLU cc_start: 0.9117 (tp30) cc_final: 0.8456 (mp0) REVERT: Y 92 ASP cc_start: 0.8548 (t0) cc_final: 0.8227 (t0) REVERT: B 360 ASN cc_start: 0.9237 (m-40) cc_final: 0.8706 (t0) REVERT: B 403 ARG cc_start: 0.6344 (mmt180) cc_final: 0.5894 (tpp80) REVERT: B 453 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.7502 (p90) REVERT: X 67 PHE cc_start: 0.9303 (m-10) cc_final: 0.8576 (m-10) REVERT: X 72 ASP cc_start: 0.8674 (t0) cc_final: 0.8112 (t0) REVERT: X 75 LYS cc_start: 0.9321 (mtmm) cc_final: 0.8950 (mtmm) REVERT: X 100 ASP cc_start: 0.8726 (t70) cc_final: 0.8137 (t0) REVERT: X 107 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8510 (p) REVERT: L 27 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8964 (mmmm) REVERT: L 42 GLN cc_start: 0.8927 (mp10) cc_final: 0.8667 (mp10) REVERT: L 69 ASN cc_start: 0.9174 (m-40) cc_final: 0.8950 (m-40) REVERT: C 456 PHE cc_start: 0.8751 (m-80) cc_final: 0.8215 (m-80) REVERT: C 904 TYR cc_start: 0.8224 (t80) cc_final: 0.7917 (t80) REVERT: A 402 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.7796 (tt) REVERT: A 421 TYR cc_start: 0.9138 (m-10) cc_final: 0.8744 (m-80) REVERT: A 740 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8947 (ttt) REVERT: H 46 GLU cc_start: 0.9004 (tt0) cc_final: 0.8698 (tt0) REVERT: H 72 ASP cc_start: 0.8969 (t0) cc_final: 0.8468 (t0) REVERT: M 13 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8598 (mm-40) REVERT: M 46 GLU cc_start: 0.8366 (tt0) cc_final: 0.8094 (pt0) REVERT: M 64 LYS cc_start: 0.8526 (tttp) cc_final: 0.8288 (mtmm) REVERT: M 72 ASP cc_start: 0.8850 (t0) cc_final: 0.8442 (t0) REVERT: M 95 ASP cc_start: 0.8504 (m-30) cc_final: 0.7962 (m-30) REVERT: N 42 GLN cc_start: 0.8612 (mp10) cc_final: 0.8299 (mp10) REVERT: N 61 ARG cc_start: 0.8711 (ptt90) cc_final: 0.8161 (ptt90) REVERT: N 79 GLN cc_start: 0.7652 (mp10) cc_final: 0.7390 (mp10) REVERT: N 81 MET cc_start: 0.9107 (ptp) cc_final: 0.8712 (pmm) REVERT: N 82 ASP cc_start: 0.8549 (m-30) cc_final: 0.7855 (m-30) REVERT: N 87 TYR cc_start: 0.8948 (m-80) cc_final: 0.8520 (m-80) outliers start: 76 outliers final: 59 residues processed: 297 average time/residue: 0.1956 time to fit residues: 93.2053 Evaluate side-chains 295 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 232 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 104 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 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 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 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 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 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 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 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 934 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain M residue 81 GLN Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 18 THR 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: 0.3980 chunk 170 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 253 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 294 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 287 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 50 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 M 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.083245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.054227 restraints weight = 79926.954| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.30 r_work: 0.2767 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31005 Z= 0.111 Angle : 0.557 9.602 42291 Z= 0.283 Chirality : 0.044 0.234 4866 Planarity : 0.004 0.045 5391 Dihedral : 5.367 55.302 5102 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.88 % Allowed : 12.49 % Favored : 85.63 % 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: 0.08 (0.14), residues: 3735 helix: 1.95 (0.21), residues: 671 sheet: -0.30 (0.16), residues: 954 loop : -0.35 (0.14), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 93 TYR 0.025 0.001 TYR B 904 PHE 0.027 0.001 PHE B 497 TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS X 35 Details of bonding type rmsd covalent geometry : bond 0.00254 (30912) covalent geometry : angle 0.54820 (42057) SS BOND : bond 0.00243 ( 45) SS BOND : angle 1.28283 ( 90) hydrogen bonds : bond 0.03368 ( 1167) hydrogen bonds : angle 5.33743 ( 3108) link_NAG-ASN : bond 0.00198 ( 48) link_NAG-ASN : angle 1.56290 ( 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 306 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 244 time to evaluate : 0.950 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 61 ARG cc_start: 0.8529 (ptt-90) cc_final: 0.7965 (ptt90) REVERT: Y 82 ASP cc_start: 0.7487 (m-30) cc_final: 0.6684 (m-30) REVERT: Y 83 GLU cc_start: 0.9095 (tp30) cc_final: 0.8391 (mp0) REVERT: Y 92 ASP cc_start: 0.8470 (t0) cc_final: 0.8105 (t70) REVERT: B 360 ASN cc_start: 0.9203 (m-40) cc_final: 0.8723 (t0) REVERT: B 403 ARG cc_start: 0.6305 (mmt180) cc_final: 0.5939 (tpp80) REVERT: B 417 LYS cc_start: 0.9162 (tptt) cc_final: 0.8953 (tptt) REVERT: B 453 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.7459 (p90) REVERT: B 490 PHE cc_start: 0.8530 (t80) cc_final: 0.8239 (t80) REVERT: B 823 PHE cc_start: 0.8657 (t80) cc_final: 0.8325 (m-80) REVERT: X 67 PHE cc_start: 0.9209 (m-10) cc_final: 0.8466 (m-10) REVERT: X 72 ASP cc_start: 0.8615 (t0) cc_final: 0.7851 (t0) REVERT: X 75 LYS cc_start: 0.9332 (mtmm) cc_final: 0.8828 (mtmm) REVERT: X 100 ASP cc_start: 0.8673 (t70) cc_final: 0.8193 (t0) REVERT: X 107 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8504 (p) REVERT: L 27 LYS cc_start: 0.9227 (mmmm) cc_final: 0.8961 (mmmm) REVERT: L 42 GLN cc_start: 0.8914 (mp10) cc_final: 0.8639 (mp10) REVERT: L 69 ASN cc_start: 0.9174 (m-40) cc_final: 0.8961 (m-40) REVERT: C 186 PHE cc_start: 0.8409 (m-80) cc_final: 0.8132 (m-80) REVERT: C 425 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8093 (pp) REVERT: C 456 PHE cc_start: 0.8759 (m-80) cc_final: 0.8213 (m-80) REVERT: C 516 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8104 (mp0) REVERT: C 904 TYR cc_start: 0.8102 (t80) cc_final: 0.7843 (t80) REVERT: A 421 TYR cc_start: 0.9149 (m-10) cc_final: 0.8712 (m-80) REVERT: H 46 GLU cc_start: 0.9012 (tt0) cc_final: 0.8724 (tt0) REVERT: H 72 ASP cc_start: 0.8934 (t0) cc_final: 0.8419 (t0) REVERT: H 105 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8806 (mm-40) REVERT: M 13 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8599 (mm-40) REVERT: M 46 GLU cc_start: 0.8298 (tt0) cc_final: 0.8037 (pt0) REVERT: M 57 ARG cc_start: 0.8645 (mtm180) cc_final: 0.8287 (mtm110) REVERT: M 64 LYS cc_start: 0.8362 (tttp) cc_final: 0.8161 (mtmm) REVERT: M 72 ASP cc_start: 0.8830 (t0) cc_final: 0.8411 (t0) REVERT: M 81 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7763 (tp40) REVERT: M 95 ASP cc_start: 0.8430 (m-30) cc_final: 0.7868 (m-30) REVERT: N 39 LYS cc_start: 0.8010 (mmmt) cc_final: 0.7578 (mmtt) REVERT: N 42 GLN cc_start: 0.8617 (mp10) cc_final: 0.8321 (mp10) REVERT: N 61 ARG cc_start: 0.8704 (ptt90) cc_final: 0.8440 (ptt90) REVERT: N 79 GLN cc_start: 0.7638 (mp10) cc_final: 0.7407 (mp10) REVERT: N 81 MET cc_start: 0.9088 (ptp) cc_final: 0.8701 (pmm) REVERT: N 82 ASP cc_start: 0.8590 (m-30) cc_final: 0.8111 (m-30) REVERT: N 87 TYR cc_start: 0.8871 (m-80) cc_final: 0.8429 (m-10) REVERT: N 95 TYR cc_start: 0.7559 (t80) cc_final: 0.7119 (t80) outliers start: 62 outliers final: 52 residues processed: 290 average time/residue: 0.1973 time to fit residues: 90.5671 Evaluate side-chains 296 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 239 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 50 GLN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 114 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 361 CYS Chi-restraints excluded: chain B residue 392 PHE 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 649 CYS Chi-restraints excluded: chain B residue 650 LEU 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 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 131 CYS 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 C residue 1145 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL 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 573 THR 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 1132 ILE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 81 GLN Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 18 THR 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: 0.5980 chunk 76 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 chunk 208 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 50 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.082947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.054038 restraints weight = 79750.714| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.28 r_work: 0.2760 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 31005 Z= 0.188 Angle : 0.715 59.200 42291 Z= 0.398 Chirality : 0.046 0.237 4866 Planarity : 0.004 0.143 5391 Dihedral : 5.360 55.341 5102 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.88 % Allowed : 12.82 % Favored : 85.29 % Cbeta Deviations : 0.06 % 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: 0.06 (0.14), residues: 3735 helix: 1.91 (0.21), residues: 671 sheet: -0.29 (0.16), residues: 954 loop : -0.36 (0.14), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 93 TYR 0.021 0.001 TYR B 904 PHE 0.025 0.001 PHE B 497 TRP 0.007 0.001 TRP B 436 HIS 0.006 0.001 HIS X 35 Details of bonding type rmsd covalent geometry : bond 0.00424 (30912) covalent geometry : angle 0.70729 (42057) SS BOND : bond 0.00332 ( 45) SS BOND : angle 1.50085 ( 90) hydrogen bonds : bond 0.03400 ( 1167) hydrogen bonds : angle 5.33323 ( 3108) link_NAG-ASN : bond 0.00208 ( 48) link_NAG-ASN : angle 1.56996 ( 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: 62 poor density : 239 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: Y 61 ARG cc_start: 0.8538 (ptt-90) cc_final: 0.7975 (ptt90) REVERT: Y 82 ASP cc_start: 0.7499 (m-30) cc_final: 0.6687 (m-30) REVERT: Y 83 GLU cc_start: 0.9102 (tp30) cc_final: 0.8396 (mp0) REVERT: Y 92 ASP cc_start: 0.8485 (t0) cc_final: 0.8122 (t70) REVERT: B 360 ASN cc_start: 0.9204 (m-40) cc_final: 0.8723 (t0) REVERT: B 403 ARG cc_start: 0.6313 (mmt180) cc_final: 0.5904 (tpp80) REVERT: B 490 PHE cc_start: 0.8528 (t80) cc_final: 0.8229 (t80) REVERT: B 823 PHE cc_start: 0.8657 (t80) cc_final: 0.8329 (m-80) REVERT: X 72 ASP cc_start: 0.8613 (t0) cc_final: 0.7852 (t0) REVERT: X 75 LYS cc_start: 0.9332 (mtmm) cc_final: 0.8834 (mtmm) REVERT: X 100 ASP cc_start: 0.8688 (t70) cc_final: 0.8197 (t0) REVERT: X 107 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8503 (p) REVERT: L 27 LYS cc_start: 0.9228 (mmmm) cc_final: 0.8960 (mmmm) REVERT: L 42 GLN cc_start: 0.8915 (mp10) cc_final: 0.8645 (mp10) REVERT: L 69 ASN cc_start: 0.9177 (m-40) cc_final: 0.8965 (m-40) REVERT: C 186 PHE cc_start: 0.8413 (m-80) cc_final: 0.8136 (m-80) REVERT: C 425 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8096 (pp) REVERT: C 456 PHE cc_start: 0.8746 (m-80) cc_final: 0.8202 (m-80) REVERT: C 516 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8104 (mp0) REVERT: C 904 TYR cc_start: 0.8110 (t80) cc_final: 0.7850 (t80) REVERT: A 421 TYR cc_start: 0.9153 (m-10) cc_final: 0.8717 (m-80) REVERT: H 46 GLU cc_start: 0.9008 (tt0) cc_final: 0.8718 (tt0) REVERT: H 72 ASP cc_start: 0.8935 (t0) cc_final: 0.8419 (t0) REVERT: H 105 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8808 (mm-40) REVERT: M 13 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8591 (mm-40) REVERT: M 46 GLU cc_start: 0.8295 (tt0) cc_final: 0.8036 (pt0) REVERT: M 57 ARG cc_start: 0.8634 (mtm180) cc_final: 0.8294 (mtm110) REVERT: M 72 ASP cc_start: 0.8831 (t0) cc_final: 0.8408 (t0) REVERT: M 95 ASP cc_start: 0.8427 (m-30) cc_final: 0.7877 (m-30) REVERT: N 39 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7579 (mmtt) REVERT: N 42 GLN cc_start: 0.8610 (mp10) cc_final: 0.8310 (mp10) REVERT: N 61 ARG cc_start: 0.8707 (ptt90) cc_final: 0.8436 (ptt90) REVERT: N 79 GLN cc_start: 0.7640 (mp10) cc_final: 0.7413 (mp10) REVERT: N 81 MET cc_start: 0.9089 (ptp) cc_final: 0.8712 (pmm) REVERT: N 82 ASP cc_start: 0.8599 (m-30) cc_final: 0.8117 (m-30) REVERT: N 87 TYR cc_start: 0.8867 (m-80) cc_final: 0.8431 (m-10) REVERT: N 95 TYR cc_start: 0.7559 (t80) cc_final: 0.7111 (t80) outliers start: 62 outliers final: 56 residues processed: 285 average time/residue: 0.1942 time to fit residues: 87.9054 Evaluate side-chains 294 residues out of total 3291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 235 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 114 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 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 945 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain X residue 107 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 131 CYS 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 1145 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL 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 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 934 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 105 GLN 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 18 THR 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: 5.9990 chunk 369 optimal weight: 0.9990 chunk 209 optimal weight: 0.0770 chunk 338 optimal weight: 0.0060 chunk 244 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 364 optimal weight: 0.9990 chunk 313 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 363 optimal weight: 0.9990 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 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 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.082915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.053915 restraints weight = 80387.316| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.30 r_work: 0.2759 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 31005 Z= 0.188 Angle : 0.715 59.200 42291 Z= 0.398 Chirality : 0.046 0.237 4866 Planarity : 0.004 0.143 5391 Dihedral : 5.360 55.341 5102 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.79 % Allowed : 12.79 % Favored : 85.41 % Cbeta Deviations : 0.06 % 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: 0.06 (0.14), residues: 3735 helix: 1.91 (0.21), residues: 671 sheet: -0.29 (0.16), residues: 954 loop : -0.36 (0.14), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 93 TYR 0.021 0.001 TYR B 904 PHE 0.025 0.001 PHE B 497 TRP 0.007 0.001 TRP B 436 HIS 0.006 0.001 HIS X 35 Details of bonding type rmsd covalent geometry : bond 0.00424 (30912) covalent geometry : angle 0.70729 (42057) SS BOND : bond 0.00332 ( 45) SS BOND : angle 1.50085 ( 90) hydrogen bonds : bond 0.03400 ( 1167) hydrogen bonds : angle 5.33323 ( 3108) link_NAG-ASN : bond 0.00208 ( 48) link_NAG-ASN : angle 1.56996 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8384.63 seconds wall clock time: 144 minutes 7.61 seconds (8647.61 seconds total)