Starting phenix.real_space_refine on Mon Aug 25 02:35:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3d_34464/08_2025/8h3d_34464.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3d_34464/08_2025/8h3d_34464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h3d_34464/08_2025/8h3d_34464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3d_34464/08_2025/8h3d_34464.map" model { file = "/net/cci-nas-00/data/ceres_data/8h3d_34464/08_2025/8h3d_34464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3d_34464/08_2025/8h3d_34464.cif" } resolution = 3.27 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= -0.001 sd= 0.099 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 112 5.16 5 C 15615 2.51 5 N 4038 2.21 5 O 4683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24448 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8005 Classifications: {'peptide': 1023} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 51, 'TRANS': 971} Chain breaks: 10 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8142 Classifications: {'peptide': 1041} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 51, 'TRANS': 989} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8119 Classifications: {'peptide': 1039} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 51, 'TRANS': 987} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 42 residue: pdb=" N ASN A 122 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN A 122 " occ=0.24 residue: pdb=" N GLU A 154 " occ=0.22 ... (7 atoms not shown) pdb=" OE2 GLU A 154 " occ=0.51 residue: pdb=" N PHE A 157 " occ=0.58 ... (9 atoms not shown) pdb=" CZ PHE A 157 " occ=0.16 residue: pdb=" N THR A 167 " occ=0.84 ... (5 atoms not shown) pdb=" CG2 THR A 167 " occ=0.32 residue: pdb=" N GLY A 199 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 199 " occ=0.81 residue: pdb=" N ASP A 215 " occ=0.63 ... (6 atoms not shown) pdb=" OD2 ASP A 215 " occ=0.41 residue: pdb=" N GLY A 219 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 219 " occ=0.85 residue: pdb=" N GLU A 340 " occ=0.18 ... (7 atoms not shown) pdb=" OE2 GLU A 340 " occ=0.39 residue: pdb=" N GLY A 446 " occ=0.84 ... (2 atoms not shown) pdb=" O GLY A 446 " occ=0.59 residue: pdb=" N GLY A 447 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 447 " occ=0.24 residue: pdb=" N THR A 470 " occ=0.63 ... (5 atoms not shown) pdb=" CG2 THR A 470 " occ=0.83 residue: pdb=" N GLY A 502 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 502 " occ=0.40 ... (remaining 30 not shown) Time building chain proxies: 4.89, per 1000 atoms: 0.20 Number of scatterers: 24448 At special positions: 0 Unit cell: (148.78, 151.36, 190.92, 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 112 16.00 O 4683 8.00 N 4038 7.00 C 15615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 657 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 657 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 657 " Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 912.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5812 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 53 sheets defined 19.8% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.602A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.888A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.440A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.721A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.597A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.614A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 770 removed outlier: 3.671A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 778 removed outlier: 4.053A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 783 removed outlier: 4.135A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 783 " --> pdb=" O GLN A 779 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 778 through 783' Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.701A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 817 through 822 removed outlier: 3.911A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 817 through 822' Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.634A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 874 removed outlier: 4.178A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.825A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 890' Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.773A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.786A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.599A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 965 removed outlier: 3.828A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 960 through 965' Processing helix chain 'A' and resid 988 through 993 removed outlier: 4.039A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1000 Processing helix chain 'A' and resid 1001 through 1019 removed outlier: 3.736A pdb=" N GLN A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1032 removed outlier: 3.549A pdb=" N ALA A1025 " --> pdb=" O SER A1021 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.516A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.893A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.541A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 765 Processing helix chain 'B' and resid 772 through 777 Processing helix chain 'B' and resid 777 through 782 removed outlier: 3.953A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 777 through 782' Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.912A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 818 through 823 removed outlier: 3.568A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 818 through 823' Processing helix chain 'B' and resid 852 through 856 removed outlier: 3.741A pdb=" N PHE B 855 " --> pdb=" O ALA B 852 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN B 856 " --> pdb=" O GLN B 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 852 through 856' Processing helix chain 'B' and resid 876 through 881 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.931A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 890' Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.590A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 931 Processing helix chain 'B' and resid 932 through 939 removed outlier: 3.949A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 965 removed outlier: 3.965A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (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 978 through 983 removed outlier: 3.977A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 993 removed outlier: 4.143A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1003 removed outlier: 4.132A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1015 Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.691A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B1025 " --> pdb=" O SER B1021 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B1026 " --> pdb=" O ALA B1022 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.835A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 4.052A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 338 through 343' Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.957A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.808A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.508A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 439 through 443 removed outlier: 4.007A pdb=" N SER C 443 " --> pdb=" O ASN C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.830A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.708A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 746 through 751' Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.841A pdb=" N GLN C 755 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR C 756 " --> pdb=" O LEU C 753 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 752 through 757' Processing helix chain 'C' and resid 762 through 770 removed outlier: 4.122A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 781 removed outlier: 3.721A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 822 removed outlier: 4.000A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 817 through 822' Processing helix chain 'C' and resid 822 through 827 removed outlier: 4.125A pdb=" N THR C 827 " --> pdb=" O PHE C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 856 removed outlier: 3.968A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 875 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.909A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 890' Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.802A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 932 Processing helix chain 'C' and resid 933 through 941 removed outlier: 3.996A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 958 removed outlier: 4.436A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 968 removed outlier: 3.585A pdb=" N LEU C 966 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER C 967 " --> pdb=" O LYS C 964 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER C 968 " --> pdb=" O GLN C 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 963 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.977A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1002 removed outlier: 3.769A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1015 removed outlier: 4.016A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1028 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.968A pdb=" N GLY C 566 " --> pdb=" O ALA C 575 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.798A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.891A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.533A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.759A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.241A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.415A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.771A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.533A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.866A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 193 through 196 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.703A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.608A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.608A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.889A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 539 through 542 Processing sheet with id=AB5, first strand: chain 'A' and resid 584 through 586 removed outlier: 3.615A pdb=" N ASP A 574 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.515A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 714 removed outlier: 3.772A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.626A pdb=" N ALA A1070 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.603A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 3.684A pdb=" N VAL A1096 " --> pdb=" O PHE A1103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.637A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.525A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.500A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 13.767A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.997A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.500A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.823A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 645 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 355 removed outlier: 3.899A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 removed outlier: 4.084A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.926A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 539 through 542 removed outlier: 3.905A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.521A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 702 removed outlier: 7.096A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.896A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 removed outlier: 3.681A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.584A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.964A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.133A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.133A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 51 removed outlier: 4.304A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.705A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.507A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.648A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.664A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.066A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.987A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 4.079A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 717 through 719 Processing sheet with id=AF5, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.647A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 734 through 735 removed outlier: 3.526A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1076 through 1077 removed outlier: 3.785A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.683A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) 513 hydrogen bonds defined for protein. 1335 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: 4.52 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4307 1.33 - 1.45: 6907 1.45 - 1.58: 13648 1.58 - 1.71: 1 1.71 - 1.83: 141 Bond restraints: 25004 Sorted by residual: bond pdb=" C PRO A 986 " pdb=" O PRO A 986 " ideal model delta sigma weight residual 1.240 1.198 0.042 1.12e-02 7.97e+03 1.42e+01 bond pdb=" C PRO B 986 " pdb=" O PRO B 986 " ideal model delta sigma weight residual 1.240 1.200 0.041 1.12e-02 7.97e+03 1.31e+01 bond pdb=" N VAL C 620 " pdb=" CA VAL C 620 " ideal model delta sigma weight residual 1.461 1.493 -0.033 9.10e-03 1.21e+04 1.31e+01 bond pdb=" N ILE A 326 " pdb=" CA ILE A 326 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.15e-02 7.56e+03 1.21e+01 bond pdb=" N VAL A 42 " pdb=" CA VAL A 42 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.22e-02 6.72e+03 8.72e+00 ... (remaining 24999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 33893 3.30 - 6.60: 109 6.60 - 9.90: 8 9.90 - 13.20: 1 13.20 - 16.50: 1 Bond angle restraints: 34012 Sorted by residual: angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 114.64 98.14 16.50 1.52e+00 4.33e-01 1.18e+02 angle pdb=" C TYR A 38 " pdb=" CA TYR A 38 " pdb=" CB TYR A 38 " ideal model delta sigma weight residual 110.08 101.78 8.30 1.15e+00 7.56e-01 5.21e+01 angle pdb=" C PRO B 561 " pdb=" CA PRO B 561 " pdb=" CB PRO B 561 " ideal model delta sigma weight residual 112.21 101.82 10.39 1.56e+00 4.11e-01 4.44e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 118.58 -7.88 1.22e+00 6.72e-01 4.17e+01 angle pdb=" N ILE C 993 " pdb=" CA ILE C 993 " pdb=" C ILE C 993 " ideal model delta sigma weight residual 112.96 107.81 5.15 1.00e+00 1.00e+00 2.66e+01 ... (remaining 34007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 12866 17.96 - 35.93: 1671 35.93 - 53.89: 428 53.89 - 71.86: 63 71.86 - 89.82: 27 Dihedral angle restraints: 15055 sinusoidal: 6026 harmonic: 9029 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 -177.18 -89.82 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -161.09 75.09 1 1.00e+01 1.00e-02 7.13e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 18.54 74.46 1 1.00e+01 1.00e-02 7.03e+01 ... (remaining 15052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3815 0.115 - 0.229: 65 0.229 - 0.344: 9 0.344 - 0.459: 1 0.459 - 0.574: 1 Chirality restraints: 3891 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.23e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA TYR A 38 " pdb=" N TYR A 38 " pdb=" C TYR A 38 " pdb=" CB TYR A 38 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 3888 not shown) Planarity restraints: 4404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 324 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.85e+00 pdb=" C GLU A 324 " 0.051 2.00e-02 2.50e+03 pdb=" O GLU A 324 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A 325 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 811 " 0.050 5.00e-02 4.00e+02 7.31e-02 8.54e+00 pdb=" N PRO B 812 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 812 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 812 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO C 986 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.031 5.00e-02 4.00e+02 ... (remaining 4401 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1146 2.72 - 3.26: 21880 3.26 - 3.81: 34535 3.81 - 4.35: 40041 4.35 - 4.90: 73063 Nonbonded interactions: 170665 Sorted by model distance: nonbonded pdb=" OD2 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.173 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.220 3.040 nonbonded pdb=" OG SER A 689 " pdb=" N GLN A 690 " model vdw 2.237 3.120 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR C 716 " pdb=" O GLN C1071 " model vdw 2.240 3.040 ... (remaining 170660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 67 or resid 81 through 175 or resid 186 through \ 263 or resid 265 through 622 or resid 639 through 675 or resid 690 through 829 \ or resid 849 through 1303)) selection = (chain 'B' and (resid 27 through 67 or resid 81 through 161 or resid 167 through \ 175 or resid 186 through 231 or resid 236 through 622 or resid 639 through 675 \ or resid 690 through 1303)) selection = (chain 'C' and (resid 27 through 161 or resid 167 through 175 or resid 186 throu \ gh 209 or resid 215 through 231 or resid 236 through 263 or resid 265 through 67 \ 5 or resid 690 through 1303)) } 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=0.00 max=1.00 mean=0.79 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.600 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 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 : 0.004 0.115 25055 Z= 0.180 Angle : 0.608 16.501 34127 Z= 0.335 Chirality : 0.048 0.574 3891 Planarity : 0.004 0.073 4391 Dihedral : 16.862 89.363 9129 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.36 % Favored : 93.60 % Rotamer: Outliers : 0.26 % Allowed : 29.38 % Favored : 70.36 % Cbeta Deviations : 0.10 % 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 aren not related in a simple way. whole: -3.11 (0.14), residues: 3049 helix: -2.95 (0.19), residues: 538 sheet: -0.83 (0.21), residues: 627 loop : -2.33 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 454 TYR 0.023 0.001 TYR A 38 PHE 0.018 0.001 PHE C 133 TRP 0.008 0.001 TRP A 353 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00358 (25004) covalent geometry : angle 0.59037 (34012) SS BOND : bond 0.00255 ( 38) SS BOND : angle 1.16335 ( 76) hydrogen bonds : bond 0.30633 ( 505) hydrogen bonds : angle 9.18401 ( 1335) link_NAG-ASN : bond 0.00800 ( 13) link_NAG-ASN : angle 4.14929 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 388 ASN cc_start: 0.8571 (m-40) cc_final: 0.8257 (m110) outliers start: 7 outliers final: 4 residues processed: 121 average time/residue: 0.1262 time to fit residues: 25.6309 Evaluate side-chains 112 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 392 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN B 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.108490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.071720 restraints weight = 57105.484| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.49 r_work: 0.2975 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2859 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2792 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25055 Z= 0.134 Angle : 0.573 11.677 34127 Z= 0.297 Chirality : 0.046 0.365 3891 Planarity : 0.004 0.057 4391 Dihedral : 6.047 59.137 3600 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.10 % Allowed : 27.75 % Favored : 69.14 % 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 aren not related in a simple way. whole: -2.98 (0.14), residues: 3049 helix: -2.61 (0.19), residues: 558 sheet: -0.59 (0.21), residues: 633 loop : -2.39 (0.13), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.015 0.001 TYR A1067 PHE 0.018 0.001 PHE C 133 TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00321 (25004) covalent geometry : angle 0.55516 (34012) SS BOND : bond 0.00296 ( 38) SS BOND : angle 1.06159 ( 76) hydrogen bonds : bond 0.05159 ( 505) hydrogen bonds : angle 6.53070 ( 1335) link_NAG-ASN : bond 0.00859 ( 13) link_NAG-ASN : angle 3.99356 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 117 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.5127 (OUTLIER) cc_final: 0.4722 (t80) REVERT: B 248 TYR cc_start: 0.5553 (t80) cc_final: 0.5251 (t80) REVERT: B 552 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8328 (mt) REVERT: B 571 ASP cc_start: 0.8849 (p0) cc_final: 0.8432 (p0) REVERT: C 324 GLU cc_start: 0.5928 (OUTLIER) cc_final: 0.5516 (pm20) REVERT: C 347 PHE cc_start: 0.4849 (OUTLIER) cc_final: 0.4521 (m-10) REVERT: C 388 ASN cc_start: 0.8675 (m-40) cc_final: 0.8366 (m110) outliers start: 84 outliers final: 37 residues processed: 189 average time/residue: 0.1267 time to fit residues: 41.4853 Evaluate side-chains 151 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 181 optimal weight: 0.0980 chunk 292 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 272 optimal weight: 4.9990 chunk 308 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 175 optimal weight: 0.0870 chunk 163 optimal weight: 4.9990 chunk 280 optimal weight: 0.0770 chunk 135 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN B 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.109692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.070624 restraints weight = 55757.342| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.45 r_work: 0.2960 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2792 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2854 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25055 Z= 0.102 Angle : 0.526 11.362 34127 Z= 0.269 Chirality : 0.045 0.356 3891 Planarity : 0.004 0.057 4391 Dihedral : 5.622 59.501 3596 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.40 % Allowed : 27.64 % Favored : 68.96 % 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 aren not related in a simple way. whole: -2.77 (0.14), residues: 3049 helix: -2.40 (0.20), residues: 547 sheet: -0.48 (0.21), residues: 643 loop : -2.26 (0.13), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.016 0.001 TYR C 396 PHE 0.019 0.001 PHE C 338 TRP 0.013 0.001 TRP B 104 HIS 0.005 0.000 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00243 (25004) covalent geometry : angle 0.50979 (34012) SS BOND : bond 0.00285 ( 38) SS BOND : angle 0.88438 ( 76) hydrogen bonds : bond 0.03795 ( 505) hydrogen bonds : angle 5.75522 ( 1335) link_NAG-ASN : bond 0.00828 ( 13) link_NAG-ASN : angle 3.78741 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 128 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.5138 (OUTLIER) cc_final: 0.4833 (t80) REVERT: A 622 VAL cc_start: 0.7985 (m) cc_final: 0.6584 (t) REVERT: B 248 TYR cc_start: 0.5615 (t80) cc_final: 0.5337 (t80) REVERT: B 552 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8219 (mt) REVERT: C 145 TYR cc_start: 0.2526 (OUTLIER) cc_final: 0.2128 (m-10) REVERT: C 324 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5684 (pm20) REVERT: C 347 PHE cc_start: 0.4725 (OUTLIER) cc_final: 0.4409 (m-10) REVERT: C 388 ASN cc_start: 0.8817 (m-40) cc_final: 0.8528 (m110) outliers start: 92 outliers final: 52 residues processed: 211 average time/residue: 0.1195 time to fit residues: 43.8791 Evaluate side-chains 171 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 114 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 79 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 202 optimal weight: 0.0870 chunk 246 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 302 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 275 optimal weight: 0.0270 chunk 22 optimal weight: 1.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN B 188 ASN B 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.111056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.069995 restraints weight = 55011.077| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.43 r_work: 0.2950 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2854 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2895 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 25055 Z= 0.095 Angle : 0.526 11.129 34127 Z= 0.265 Chirality : 0.045 0.355 3891 Planarity : 0.004 0.055 4391 Dihedral : 5.329 59.799 3594 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.14 % Allowed : 28.27 % Favored : 68.59 % 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 aren not related in a simple way. whole: -2.68 (0.14), residues: 3049 helix: -2.27 (0.20), residues: 553 sheet: -0.36 (0.21), residues: 632 loop : -2.24 (0.13), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.024 0.001 TYR B 160 PHE 0.023 0.001 PHE C 133 TRP 0.011 0.001 TRP B 436 HIS 0.005 0.000 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00229 (25004) covalent geometry : angle 0.50561 (34012) SS BOND : bond 0.00387 ( 38) SS BOND : angle 1.45443 ( 76) hydrogen bonds : bond 0.03386 ( 505) hydrogen bonds : angle 5.51848 ( 1335) link_NAG-ASN : bond 0.00848 ( 13) link_NAG-ASN : angle 3.85154 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 122 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6218 (m-80) cc_final: 0.5998 (m-80) REVERT: A 329 PHE cc_start: 0.5175 (OUTLIER) cc_final: 0.4933 (t80) REVERT: A 622 VAL cc_start: 0.8011 (m) cc_final: 0.6602 (t) REVERT: A 811 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.6934 (mtmt) REVERT: B 248 TYR cc_start: 0.5642 (t80) cc_final: 0.5393 (t80) REVERT: B 552 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8208 (mt) REVERT: C 96 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5483 (mp0) REVERT: C 248 TYR cc_start: 0.4425 (OUTLIER) cc_final: 0.3613 (m-80) REVERT: C 347 PHE cc_start: 0.4732 (OUTLIER) cc_final: 0.4441 (m-10) REVERT: C 382 VAL cc_start: 0.9193 (OUTLIER) cc_final: 0.8962 (p) REVERT: C 388 ASN cc_start: 0.8837 (m-40) cc_final: 0.8552 (m110) outliers start: 85 outliers final: 48 residues processed: 201 average time/residue: 0.1287 time to fit residues: 44.0012 Evaluate side-chains 169 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 114 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 28 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 245 optimal weight: 10.0000 chunk 301 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 295 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 211 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 126 optimal weight: 0.1980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN B 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.114695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.074256 restraints weight = 53890.600| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.40 r_work: 0.2976 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2895 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2890 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25055 Z= 0.109 Angle : 0.534 10.923 34127 Z= 0.270 Chirality : 0.045 0.351 3891 Planarity : 0.004 0.060 4391 Dihedral : 5.299 59.441 3593 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.77 % Allowed : 27.97 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.14), residues: 3049 helix: -2.24 (0.21), residues: 550 sheet: -0.37 (0.21), residues: 638 loop : -2.22 (0.13), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 328 TYR 0.020 0.001 TYR B 160 PHE 0.018 0.001 PHE C 338 TRP 0.011 0.001 TRP B 436 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00264 (25004) covalent geometry : angle 0.51579 (34012) SS BOND : bond 0.00413 ( 38) SS BOND : angle 1.41474 ( 76) hydrogen bonds : bond 0.03590 ( 505) hydrogen bonds : angle 5.37501 ( 1335) link_NAG-ASN : bond 0.00805 ( 13) link_NAG-ASN : angle 3.70114 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 119 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.5328 (OUTLIER) cc_final: 0.5072 (t80) REVERT: A 622 VAL cc_start: 0.8000 (m) cc_final: 0.6613 (t) REVERT: A 811 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.6936 (mtmt) REVERT: B 552 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8227 (mt) REVERT: B 906 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.6537 (t80) REVERT: C 96 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.5523 (mp0) REVERT: C 145 TYR cc_start: 0.2219 (OUTLIER) cc_final: 0.1808 (m-10) REVERT: C 241 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8125 (pp) REVERT: C 248 TYR cc_start: 0.4452 (OUTLIER) cc_final: 0.3215 (m-80) REVERT: C 347 PHE cc_start: 0.4695 (OUTLIER) cc_final: 0.4395 (m-10) REVERT: C 388 ASN cc_start: 0.8916 (m-40) cc_final: 0.8624 (m110) outliers start: 102 outliers final: 70 residues processed: 212 average time/residue: 0.1174 time to fit residues: 43.2687 Evaluate side-chains 196 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 117 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 257 optimal weight: 8.9990 chunk 283 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 268 optimal weight: 0.0370 chunk 69 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN B 115 GLN B 188 ASN B 501 ASN B 506 GLN B 955 ASN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.112636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.072306 restraints weight = 54397.796| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.78 r_work: 0.2920 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2890 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2916 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25055 Z= 0.175 Angle : 0.593 10.656 34127 Z= 0.304 Chirality : 0.047 0.341 3891 Planarity : 0.004 0.061 4391 Dihedral : 5.568 57.949 3593 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.25 % Allowed : 27.90 % Favored : 67.85 % 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 aren not related in a simple way. whole: -2.82 (0.14), residues: 3049 helix: -2.40 (0.20), residues: 556 sheet: -0.48 (0.21), residues: 619 loop : -2.30 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 328 TYR 0.020 0.001 TYR B 160 PHE 0.023 0.001 PHE C 133 TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00430 (25004) covalent geometry : angle 0.57595 (34012) SS BOND : bond 0.00530 ( 38) SS BOND : angle 1.57073 ( 76) hydrogen bonds : bond 0.04660 ( 505) hydrogen bonds : angle 5.61794 ( 1335) link_NAG-ASN : bond 0.00757 ( 13) link_NAG-ASN : angle 3.68539 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 114 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.5279 (OUTLIER) cc_final: 0.4947 (t80) REVERT: A 811 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7050 (mtmt) REVERT: B 188 ASN cc_start: 0.8173 (m-40) cc_final: 0.7955 (m110) REVERT: B 226 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6355 (mp) REVERT: B 552 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8298 (mt) REVERT: B 571 ASP cc_start: 0.8655 (p0) cc_final: 0.8232 (p0) REVERT: B 906 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.6721 (t80) REVERT: C 96 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5332 (mp0) REVERT: C 145 TYR cc_start: 0.2325 (OUTLIER) cc_final: 0.1843 (m-10) REVERT: C 248 TYR cc_start: 0.4503 (OUTLIER) cc_final: 0.3239 (m-80) REVERT: C 347 PHE cc_start: 0.4530 (OUTLIER) cc_final: 0.4283 (m-10) REVERT: C 388 ASN cc_start: 0.8895 (m-40) cc_final: 0.8592 (m110) REVERT: C 392 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7622 (p90) REVERT: C 780 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8863 (mt-10) REVERT: C 1010 GLN cc_start: 0.9169 (tp40) cc_final: 0.8954 (tp40) outliers start: 115 outliers final: 85 residues processed: 221 average time/residue: 0.1147 time to fit residues: 44.0726 Evaluate side-chains 204 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 109 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 0.9990 chunk 251 optimal weight: 0.9990 chunk 20 optimal weight: 0.0770 chunk 279 optimal weight: 4.9990 chunk 243 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 270 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN B 501 ASN B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.114297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.073415 restraints weight = 54020.971| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.40 r_work: 0.2970 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2916 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2936 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 25055 Z= 0.096 Angle : 0.532 11.413 34127 Z= 0.268 Chirality : 0.044 0.351 3891 Planarity : 0.004 0.060 4391 Dihedral : 5.221 56.897 3593 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.62 % Allowed : 28.42 % Favored : 67.96 % 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 aren not related in a simple way. whole: -2.66 (0.14), residues: 3049 helix: -2.21 (0.21), residues: 550 sheet: -0.44 (0.21), residues: 646 loop : -2.22 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.017 0.001 TYR B 160 PHE 0.016 0.001 PHE C 338 TRP 0.011 0.001 TRP B 436 HIS 0.005 0.000 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00233 (25004) covalent geometry : angle 0.51511 (34012) SS BOND : bond 0.00369 ( 38) SS BOND : angle 1.29886 ( 76) hydrogen bonds : bond 0.03240 ( 505) hydrogen bonds : angle 5.28606 ( 1335) link_NAG-ASN : bond 0.00807 ( 13) link_NAG-ASN : angle 3.62044 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 124 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8028 (tt) cc_final: 0.7766 (tp) REVERT: A 244 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.5798 (pp) REVERT: A 329 PHE cc_start: 0.5492 (OUTLIER) cc_final: 0.5138 (t80) REVERT: A 622 VAL cc_start: 0.7940 (m) cc_final: 0.6575 (t) REVERT: A 811 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7060 (mtmt) REVERT: A 995 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7781 (mtt-85) REVERT: B 188 ASN cc_start: 0.8168 (m-40) cc_final: 0.7961 (m110) REVERT: B 552 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8241 (mt) REVERT: B 906 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.6630 (t80) REVERT: C 96 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.5633 (mp0) REVERT: C 145 TYR cc_start: 0.2432 (OUTLIER) cc_final: 0.1936 (m-10) REVERT: C 241 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8158 (pp) REVERT: C 248 TYR cc_start: 0.4295 (OUTLIER) cc_final: 0.3333 (m-80) REVERT: C 347 PHE cc_start: 0.4614 (OUTLIER) cc_final: 0.4374 (m-10) REVERT: C 388 ASN cc_start: 0.8826 (m-40) cc_final: 0.8565 (m110) REVERT: C 392 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7360 (p90) REVERT: C 490 PHE cc_start: 0.5058 (m-80) cc_final: 0.4842 (m-10) REVERT: C 780 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8774 (mt-10) REVERT: C 1010 GLN cc_start: 0.9184 (tp40) cc_final: 0.8905 (tp40) outliers start: 98 outliers final: 70 residues processed: 216 average time/residue: 0.1220 time to fit residues: 45.0810 Evaluate side-chains 198 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 116 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 115 optimal weight: 20.0000 chunk 291 optimal weight: 3.9990 chunk 45 optimal weight: 0.0010 chunk 86 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 0.2980 chunk 184 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.113094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.071924 restraints weight = 53923.968| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.38 r_work: 0.2944 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2936 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2954 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 25055 Z= 0.143 Angle : 0.575 12.984 34127 Z= 0.291 Chirality : 0.046 0.414 3891 Planarity : 0.004 0.060 4391 Dihedral : 5.325 57.649 3593 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.58 % Allowed : 28.71 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.73 (0.14), residues: 3049 helix: -2.27 (0.21), residues: 551 sheet: -0.39 (0.21), residues: 621 loop : -2.28 (0.13), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.031 0.001 TYR B 160 PHE 0.020 0.001 PHE B 192 TRP 0.031 0.001 TRP B 104 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00352 (25004) covalent geometry : angle 0.55766 (34012) SS BOND : bond 0.00441 ( 38) SS BOND : angle 1.44407 ( 76) hydrogen bonds : bond 0.04097 ( 505) hydrogen bonds : angle 5.37224 ( 1335) link_NAG-ASN : bond 0.00767 ( 13) link_NAG-ASN : angle 3.79725 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 114 time to evaluate : 0.948 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: A 244 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.5921 (pp) REVERT: A 329 PHE cc_start: 0.5456 (OUTLIER) cc_final: 0.5194 (t80) REVERT: A 622 VAL cc_start: 0.7916 (m) cc_final: 0.6525 (t) REVERT: A 811 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7081 (mtmt) REVERT: A 878 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9214 (tt) REVERT: A 995 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7807 (mtt-85) REVERT: B 188 ASN cc_start: 0.8150 (m-40) cc_final: 0.7908 (m110) REVERT: B 226 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6301 (mp) REVERT: B 552 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8290 (mt) REVERT: B 906 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.6625 (t80) REVERT: C 96 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5462 (mp0) REVERT: C 145 TYR cc_start: 0.2696 (OUTLIER) cc_final: 0.2109 (m-10) REVERT: C 248 TYR cc_start: 0.4317 (OUTLIER) cc_final: 0.3045 (m-80) REVERT: C 347 PHE cc_start: 0.4478 (OUTLIER) cc_final: 0.4255 (m-10) REVERT: C 388 ASN cc_start: 0.8808 (m-40) cc_final: 0.8533 (m110) REVERT: C 392 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7197 (p90) REVERT: C 490 PHE cc_start: 0.5073 (OUTLIER) cc_final: 0.4834 (m-10) REVERT: C 1010 GLN cc_start: 0.9211 (tp40) cc_final: 0.8942 (tp40) outliers start: 97 outliers final: 76 residues processed: 204 average time/residue: 0.1188 time to fit residues: 41.7949 Evaluate side-chains 202 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 112 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 41 optimal weight: 20.0000 chunk 192 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 269 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 296 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 182 optimal weight: 0.3980 chunk 285 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.114414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.072738 restraints weight = 54049.821| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.39 r_work: 0.2965 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2954 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2958 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25055 Z= 0.106 Angle : 0.539 12.708 34127 Z= 0.270 Chirality : 0.045 0.368 3891 Planarity : 0.004 0.059 4391 Dihedral : 5.063 56.979 3593 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.73 % Allowed : 28.57 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.14), residues: 3049 helix: -2.15 (0.21), residues: 550 sheet: -0.43 (0.21), residues: 646 loop : -2.21 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 102 TYR 0.028 0.001 TYR B 160 PHE 0.016 0.001 PHE C 338 TRP 0.022 0.001 TRP B 104 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00259 (25004) covalent geometry : angle 0.52170 (34012) SS BOND : bond 0.00382 ( 38) SS BOND : angle 1.27195 ( 76) hydrogen bonds : bond 0.03315 ( 505) hydrogen bonds : angle 5.17190 ( 1335) link_NAG-ASN : bond 0.00796 ( 13) link_NAG-ASN : angle 3.74059 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 121 time to evaluate : 1.388 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: A 200 TYR cc_start: 0.6202 (m-80) cc_final: 0.5977 (m-80) REVERT: A 244 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.5870 (pp) REVERT: A 329 PHE cc_start: 0.5381 (OUTLIER) cc_final: 0.5088 (t80) REVERT: A 622 VAL cc_start: 0.7868 (m) cc_final: 0.6519 (t) REVERT: A 811 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7101 (mtmt) REVERT: A 995 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7794 (mtt-85) REVERT: B 188 ASN cc_start: 0.8109 (m-40) cc_final: 0.7868 (m110) REVERT: B 552 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8220 (mt) REVERT: B 906 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.6624 (t80) REVERT: C 96 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.5621 (mp0) REVERT: C 145 TYR cc_start: 0.2813 (OUTLIER) cc_final: 0.2171 (m-10) REVERT: C 241 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8193 (pp) REVERT: C 248 TYR cc_start: 0.4125 (OUTLIER) cc_final: 0.3040 (m-80) REVERT: C 347 PHE cc_start: 0.4653 (OUTLIER) cc_final: 0.4397 (m-10) REVERT: C 388 ASN cc_start: 0.8835 (m-40) cc_final: 0.8590 (m110) REVERT: C 392 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7151 (p90) REVERT: C 490 PHE cc_start: 0.5042 (m-80) cc_final: 0.4748 (m-10) REVERT: C 1010 GLN cc_start: 0.9206 (tp40) cc_final: 0.8923 (tp40) outliers start: 101 outliers final: 75 residues processed: 216 average time/residue: 0.1423 time to fit residues: 52.9599 Evaluate side-chains 206 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 119 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 7 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 161 optimal weight: 0.7980 chunk 31 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 257 optimal weight: 0.0270 chunk 252 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 238 optimal weight: 6.9990 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.112934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.071385 restraints weight = 53670.661| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.74 r_work: 0.2926 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2958 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2982 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 25055 Z= 0.161 Angle : 0.591 13.998 34127 Z= 0.300 Chirality : 0.046 0.339 3891 Planarity : 0.004 0.060 4391 Dihedral : 5.318 57.941 3593 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.51 % Allowed : 28.90 % Favored : 67.59 % 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 aren not related in a simple way. whole: -2.79 (0.14), residues: 3049 helix: -2.28 (0.20), residues: 556 sheet: -0.46 (0.21), residues: 615 loop : -2.31 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.029 0.001 TYR B 160 PHE 0.021 0.001 PHE B 192 TRP 0.023 0.001 TRP B 104 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00398 (25004) covalent geometry : angle 0.57413 (34012) SS BOND : bond 0.00457 ( 38) SS BOND : angle 1.48173 ( 76) hydrogen bonds : bond 0.04388 ( 505) hydrogen bonds : angle 5.42540 ( 1335) link_NAG-ASN : bond 0.00743 ( 13) link_NAG-ASN : angle 3.69526 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 111 time to evaluate : 0.959 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: A 244 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.5960 (pp) REVERT: A 329 PHE cc_start: 0.5350 (OUTLIER) cc_final: 0.5067 (t80) REVERT: A 811 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7155 (mtmt) REVERT: A 878 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9227 (tt) REVERT: A 995 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7858 (mtt-85) REVERT: B 188 ASN cc_start: 0.8095 (m-40) cc_final: 0.7837 (m110) REVERT: B 226 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6300 (mp) REVERT: B 248 TYR cc_start: 0.5258 (t80) cc_final: 0.4974 (t80) REVERT: B 552 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8339 (mt) REVERT: B 906 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.6697 (t80) REVERT: C 96 GLU cc_start: 0.6419 (OUTLIER) cc_final: 0.5720 (mp0) REVERT: C 145 TYR cc_start: 0.2792 (OUTLIER) cc_final: 0.2127 (m-10) REVERT: C 248 TYR cc_start: 0.4170 (OUTLIER) cc_final: 0.3054 (m-80) REVERT: C 347 PHE cc_start: 0.4499 (OUTLIER) cc_final: 0.4266 (m-10) REVERT: C 388 ASN cc_start: 0.8817 (m-40) cc_final: 0.8541 (m110) REVERT: C 392 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7204 (p90) REVERT: C 1010 GLN cc_start: 0.9245 (tp40) cc_final: 0.8968 (tp40) outliers start: 95 outliers final: 78 residues processed: 201 average time/residue: 0.1411 time to fit residues: 49.1507 Evaluate side-chains 202 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 111 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 181 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 282 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 276 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 233 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.113591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.071576 restraints weight = 53766.726| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.37 r_work: 0.2943 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2982 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3015 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25055 Z= 0.135 Angle : 0.572 13.749 34127 Z= 0.289 Chirality : 0.046 0.341 3891 Planarity : 0.004 0.060 4391 Dihedral : 5.246 57.659 3593 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.51 % Allowed : 28.86 % Favored : 67.63 % 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 aren not related in a simple way. whole: -2.77 (0.14), residues: 3049 helix: -2.25 (0.21), residues: 550 sheet: -0.49 (0.21), residues: 619 loop : -2.29 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.028 0.001 TYR B 160 PHE 0.023 0.001 PHE B 192 TRP 0.023 0.001 TRP B 104 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00331 (25004) covalent geometry : angle 0.55497 (34012) SS BOND : bond 0.00444 ( 38) SS BOND : angle 1.40451 ( 76) hydrogen bonds : bond 0.03941 ( 505) hydrogen bonds : angle 5.33974 ( 1335) link_NAG-ASN : bond 0.00761 ( 13) link_NAG-ASN : angle 3.66603 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7079.48 seconds wall clock time: 121 minutes 4.69 seconds (7264.69 seconds total)