Starting phenix.real_space_refine on Sun Jul 5 03:23:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xut_38683/07_2026/8xut_38683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xut_38683/07_2026/8xut_38683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xut_38683/07_2026/8xut_38683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xut_38683/07_2026/8xut_38683.map" model { file = "/net/cci-nas-00/data/ceres_data/8xut_38683/07_2026/8xut_38683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xut_38683/07_2026/8xut_38683.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.057 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 16038 2.51 5 N 4125 2.21 5 O 4874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25149 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 8154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8154 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 51, 'TRANS': 990} Chain breaks: 7 Chain: "A" Number of atoms: 8154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8154 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 51, 'TRANS': 990} Chain breaks: 7 Chain: "C" Number of atoms: 8154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8154 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 51, 'TRANS': 990} Chain breaks: 7 Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "A" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 239 Unusual residues: {'IDU': 1, 'NAG': 16} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 18 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 4.50, per 1000 atoms: 0.18 Number of scatterers: 25149 At special positions: 0 Unit cell: (140.896, 152.292, 165.76, 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 4874 8.00 N 4125 7.00 C 16038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.01 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 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 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 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 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1312 " - " ASN A 717 " " NAG A1313 " - " ASN A 801 " " NAG A1314 " - " ASN A1074 " " NAG A1315 " - " ASN A1098 " " NAG A1316 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG B1312 " - " ASN B 717 " " NAG B1313 " - " ASN B 801 " " NAG B1314 " - " ASN B1074 " " NAG B1315 " - " ASN B1098 " " NAG B1316 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 657 " " NAG C1311 " - " ASN C 709 " " NAG C1312 " - " ASN C 717 " " NAG C1313 " - " ASN C 801 " " NAG C1314 " - " ASN C1074 " " NAG C1315 " - " ASN C1098 " " NAG C1316 " - " ASN C1134 " Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 941.5 milliseconds 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 40 sheets defined 23.3% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.639A pdb=" N PHE B 371 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.512A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 4.782A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA B 411 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.545A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.888A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.008A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.534A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.444A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.047A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.977A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.680A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.586A pdb=" N ASN A 99 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 100 " --> pdb=" O LYS A 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 96 through 100' Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.566A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.186A pdb=" N ILE A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.627A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.571A pdb=" N ALA A 411 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.967A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.742A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 851 through 856 removed outlier: 3.865A pdb=" N PHE A 855 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.569A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.630A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.774A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.508A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 4.322A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 967 No H-bonds generated for 'chain 'A' and resid 965 through 967' Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.885A pdb=" N GLU A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'C' and resid 96 through 100 removed outlier: 3.900A pdb=" N ASN C 99 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 96 through 100' Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.548A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 4.546A pdb=" N ILE C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.102A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 411 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.721A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.501A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 852 through 856 removed outlier: 3.793A pdb=" N PHE C 855 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.238A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.830A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.609A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.598A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.857A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.112A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.794A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.718A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 55 removed outlier: 3.532A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'B' and resid 277 through 279 removed outlier: 6.837A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AA6, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.730A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 595 through 598 Processing sheet with id=AA8, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.951A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 672 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 703 through 704 removed outlier: 7.411A pdb=" N ASN B 703 " --> pdb=" O LYS A 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.743A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 718 through 723 Processing sheet with id=AB3, first strand: chain 'B' and resid 718 through 723 removed outlier: 7.189A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.277A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 789 through 790 removed outlier: 3.704A pdb=" N LYS B 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.734A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.685A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.574A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.995A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.558A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.625A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 565 through 567 removed outlier: 4.015A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 595 through 598 Processing sheet with id=AC6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.368A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.359A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.359A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A1113 " --> pdb=" O VAL A1104 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AD1, first strand: chain 'C' and resid 27 through 28 removed outlier: 3.833A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.930A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 52 through 55 removed outlier: 3.583A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.891A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 312 removed outlier: 4.128A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 325 through 327 Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.722A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.663A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 717 removed outlier: 6.377A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 720 through 728 removed outlier: 5.831A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1122 787 hydrogen bonds defined for protein. 2139 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.24 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4909 1.33 - 1.45: 6569 1.45 - 1.57: 14105 1.57 - 1.70: 1 1.70 - 1.82: 138 Bond restraints: 25722 Sorted by residual: bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.486 0.031 6.70e-03 2.23e+04 2.10e+01 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" N LEU B 560 " pdb=" CA LEU B 560 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.18e-02 7.18e+03 9.87e+00 bond pdb=" N VAL A 656 " pdb=" CA VAL A 656 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.23e-02 6.61e+03 9.83e+00 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.18e-02 7.18e+03 9.57e+00 ... (remaining 25717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 33483 1.85 - 3.70: 1384 3.70 - 5.56: 90 5.56 - 7.41: 16 7.41 - 9.26: 8 Bond angle restraints: 34981 Sorted by residual: angle pdb=" O PRO B 862 " pdb=" C PRO B 862 " pdb=" N PRO B 863 " ideal model delta sigma weight residual 121.15 118.78 2.37 4.70e-01 4.53e+00 2.55e+01 angle pdb=" N GLY C 799 " pdb=" CA GLY C 799 " pdb=" C GLY C 799 " ideal model delta sigma weight residual 115.31 109.62 5.69 1.24e+00 6.50e-01 2.11e+01 angle pdb=" N ASN B 556 " pdb=" CA ASN B 556 " pdb=" C ASN B 556 " ideal model delta sigma weight residual 114.39 107.90 6.49 1.45e+00 4.76e-01 2.00e+01 angle pdb=" N ILE A 666 " pdb=" CA ILE A 666 " pdb=" C ILE A 666 " ideal model delta sigma weight residual 111.62 108.58 3.04 7.90e-01 1.60e+00 1.48e+01 angle pdb=" N VAL B 341 " pdb=" CA VAL B 341 " pdb=" C VAL B 341 " ideal model delta sigma weight residual 112.80 108.40 4.40 1.15e+00 7.56e-01 1.47e+01 ... (remaining 34976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.11: 14421 23.11 - 46.22: 1262 46.22 - 69.34: 188 69.34 - 92.45: 42 92.45 - 115.56: 6 Dihedral angle restraints: 15919 sinusoidal: 6817 harmonic: 9102 Sorted by residual: dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -176.40 90.40 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -10.34 -75.66 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 27.75 65.25 1 1.00e+01 1.00e-02 5.58e+01 ... (remaining 15916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 4045 0.151 - 0.303: 42 0.303 - 0.454: 3 0.454 - 0.606: 0 0.606 - 0.757: 2 Chirality restraints: 4092 Sorted by residual: chirality pdb=" C1 NAG A1311 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1311 " pdb=" O5 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" C1 NAG B1314 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1314 " pdb=" O5 NAG B1314 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C1 NAG C1311 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1311 " pdb=" O5 NAG C1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.84e+00 ... (remaining 4089 not shown) Planarity restraints: 4495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1311 " -0.206 2.00e-02 2.50e+03 1.71e-01 3.66e+02 pdb=" C7 NAG A1311 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG A1311 " -0.149 2.00e-02 2.50e+03 pdb=" N2 NAG A1311 " 0.280 2.00e-02 2.50e+03 pdb=" O7 NAG A1311 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1311 " 0.178 2.00e-02 2.50e+03 1.48e-01 2.73e+02 pdb=" C7 NAG C1311 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG C1311 " 0.131 2.00e-02 2.50e+03 pdb=" N2 NAG C1311 " -0.240 2.00e-02 2.50e+03 pdb=" O7 NAG C1311 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " -0.064 2.00e-02 2.50e+03 5.41e-02 3.65e+01 pdb=" C7 NAG A1305 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " 0.017 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " 0.086 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " -0.052 2.00e-02 2.50e+03 ... (remaining 4492 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1757 2.73 - 3.27: 25657 3.27 - 3.82: 40376 3.82 - 4.36: 47944 4.36 - 4.90: 81240 Nonbonded interactions: 196974 Sorted by model distance: nonbonded pdb=" N GLU A 780 " pdb=" OE1 GLU A 780 " model vdw 2.192 3.120 nonbonded pdb=" O ASP A1041 " pdb=" OD1 ASP A1041 " model vdw 2.192 3.040 nonbonded pdb=" O LEU C 966 " pdb=" OG SER C 975 " model vdw 2.201 3.040 nonbonded pdb=" O THR A 250 " pdb=" OG SER A 254 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR C 393 " pdb=" O GLU C 516 " model vdw 2.204 3.040 ... (remaining 196969 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 26 through 1316) selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.200 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 25803 Z= 0.342 Angle : 0.775 9.261 35191 Z= 0.462 Chirality : 0.054 0.757 4092 Planarity : 0.007 0.176 4447 Dihedral : 16.645 115.560 9964 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.49 % Favored : 89.99 % Rotamer: Outliers : 0.77 % Allowed : 25.11 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.14), residues: 3078 helix: -0.18 (0.21), residues: 597 sheet: -1.22 (0.20), residues: 636 loop : -2.52 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 158 TYR 0.017 0.001 TYR B 796 PHE 0.019 0.001 PHE C1075 TRP 0.014 0.001 TRP A 886 HIS 0.003 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.34 (25722) covalent geometry : angle 0.75765 / 0.46 (34981) SS BOND : bond 0.00436 / 0.26 ( 33) SS BOND : angle 1.63092 / 1.07 ( 66) hydrogen bonds : bond 0.25766 / 17.02 ( 776) hydrogen bonds : angle 9.00558 / 6.20 ( 2139) link_NAG-ASN : bond 0.00461 / 0.29 ( 48) link_NAG-ASN : angle 2.45216 / 1.62 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 279 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 PHE cc_start: 0.6079 (m-80) cc_final: 0.5720 (m-80) REVERT: A 643 PHE cc_start: 0.6437 (t80) cc_final: 0.5862 (t80) REVERT: C 133 PHE cc_start: 0.5048 (m-80) cc_final: 0.4700 (m-80) outliers start: 21 outliers final: 9 residues processed: 291 average time/residue: 0.1441 time to fit residues: 70.3662 Evaluate side-chains 267 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 258 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 69 HIS B 81 ASN B 137 ASN B 317 ASN B 448 ASN B 804 GLN B 926 GLN B 957 GLN B1011 GLN B1106 GLN A 211 ASN A 354 ASN A 360 ASN A 448 ASN A 762 GLN A 774 GLN A 787 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 913 GLN A 926 GLN A1010 GLN A1011 GLN A1023 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 339 HIS C 448 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 751 ASN C 755 GLN C 762 GLN C 774 GLN C 872 GLN C 926 GLN C1011 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.176630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.135589 restraints weight = 42850.971| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 3.08 r_work: 0.3746 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25803 Z= 0.151 Angle : 0.639 8.273 35191 Z= 0.321 Chirality : 0.046 0.329 4092 Planarity : 0.004 0.053 4447 Dihedral : 7.622 100.507 4395 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.90 % Favored : 90.97 % Rotamer: Outliers : 4.41 % Allowed : 22.65 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.14), residues: 3078 helix: 0.52 (0.22), residues: 582 sheet: -1.07 (0.20), residues: 624 loop : -2.36 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.023 0.001 TYR B1067 PHE 0.018 0.001 PHE A 133 TRP 0.009 0.001 TRP A 633 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (25722) covalent geometry : angle 0.61919 / 0.32 (34981) SS BOND : bond 0.00373 / 0.26 ( 33) SS BOND : angle 1.29948 / 0.85 ( 66) hydrogen bonds : bond 0.05662 / 3.73 ( 776) hydrogen bonds : angle 6.33671 / 4.30 ( 2139) link_NAG-ASN : bond 0.00345 / 0.22 ( 48) link_NAG-ASN : angle 2.39805 / 1.58 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 297 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 116 SER cc_start: 0.7482 (OUTLIER) cc_final: 0.7267 (t) REVERT: B 519 HIS cc_start: 0.5036 (OUTLIER) cc_final: 0.4766 (m90) REVERT: B 747 THR cc_start: 0.7523 (m) cc_final: 0.6815 (p) REVERT: B 1017 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8262 (tm-30) REVERT: A 104 TRP cc_start: 0.5860 (OUTLIER) cc_final: 0.5583 (t60) REVERT: A 396 TYR cc_start: 0.5989 (m-10) cc_final: 0.5632 (m-10) REVERT: A 406 GLU cc_start: 0.4033 (mt-10) cc_final: 0.2545 (tt0) REVERT: C 66 HIS cc_start: 0.1908 (m-70) cc_final: 0.1685 (m-70) REVERT: C 133 PHE cc_start: 0.4935 (m-80) cc_final: 0.4682 (m-80) REVERT: C 796 TYR cc_start: 0.4919 (t80) cc_final: 0.4470 (t80) outliers start: 120 outliers final: 65 residues processed: 385 average time/residue: 0.1428 time to fit residues: 92.7154 Evaluate side-chains 326 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 258 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 22 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 221 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 ASN B 901 GLN B1048 HIS A 774 GLN A 787 GLN A 913 GLN A1005 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 777 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.169285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.130389 restraints weight = 43038.209| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.32 r_work: 0.3639 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 25803 Z= 0.236 Angle : 0.719 10.890 35191 Z= 0.360 Chirality : 0.049 0.282 4092 Planarity : 0.005 0.060 4447 Dihedral : 7.242 94.745 4388 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.94 % Favored : 89.93 % Rotamer: Outliers : 6.02 % Allowed : 22.36 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.14), residues: 3078 helix: 0.38 (0.22), residues: 585 sheet: -1.34 (0.19), residues: 684 loop : -2.46 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1039 TYR 0.026 0.002 TYR B1067 PHE 0.033 0.002 PHE B 782 TRP 0.015 0.002 TRP A 104 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 (25722) covalent geometry : angle 0.70088 / 0.36 (34981) SS BOND : bond 0.00467 / 0.31 ( 33) SS BOND : angle 1.59143 / 1.03 ( 66) hydrogen bonds : bond 0.04982 / 3.29 ( 776) hydrogen bonds : angle 6.05387 / 4.09 ( 2139) link_NAG-ASN : bond 0.00372 / 0.23 ( 48) link_NAG-ASN : angle 2.44573 / 1.62 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 291 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 275 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.6982 (t80) REVERT: B 304 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8241 (tttm) REVERT: B 324 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6396 (pm20) REVERT: B 519 HIS cc_start: 0.5682 (OUTLIER) cc_final: 0.4146 (t-90) REVERT: B 747 THR cc_start: 0.8105 (m) cc_final: 0.7644 (p) REVERT: B 748 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: B 1017 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8318 (tp30) REVERT: A 104 TRP cc_start: 0.6360 (OUTLIER) cc_final: 0.6151 (t60) REVERT: A 356 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6602 (mtmm) REVERT: A 393 THR cc_start: 0.8275 (t) cc_final: 0.7877 (p) REVERT: A 406 GLU cc_start: 0.4155 (mt-10) cc_final: 0.2533 (tt0) REVERT: A 418 ILE cc_start: 0.6243 (tp) cc_final: 0.5910 (tp) REVERT: A 444 LYS cc_start: 0.4787 (ttpt) cc_final: 0.4575 (mmtm) REVERT: A 495 TYR cc_start: 0.4517 (OUTLIER) cc_final: 0.3568 (t80) REVERT: A 525 CYS cc_start: 0.5625 (OUTLIER) cc_final: 0.5102 (m) REVERT: A 558 LYS cc_start: 0.6309 (tttt) cc_final: 0.5848 (mmmt) REVERT: A 564 GLN cc_start: 0.7750 (pm20) cc_final: 0.7209 (pm20) REVERT: A 1041 ASP cc_start: 0.7514 (t0) cc_final: 0.7307 (t0) REVERT: C 131 CYS cc_start: 0.3928 (OUTLIER) cc_final: 0.3332 (m) REVERT: C 133 PHE cc_start: 0.5414 (m-80) cc_final: 0.4844 (m-80) REVERT: C 319 ARG cc_start: 0.8045 (ppt170) cc_final: 0.7784 (ppt170) REVERT: C 396 TYR cc_start: 0.6743 (m-80) cc_final: 0.6490 (m-80) REVERT: C 429 PHE cc_start: 0.6791 (t80) cc_final: 0.6351 (t80) REVERT: C 493 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.6611 (tm-30) REVERT: C 501 TYR cc_start: 0.5828 (m-80) cc_final: 0.5474 (m-80) REVERT: C 767 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7822 (mt) REVERT: C 784 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8571 (mt0) REVERT: C 1005 GLN cc_start: 0.9045 (tp40) cc_final: 0.8834 (mm-40) outliers start: 164 outliers final: 94 residues processed: 428 average time/residue: 0.1433 time to fit residues: 101.6847 Evaluate side-chains 357 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 250 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 102 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 137 optimal weight: 0.0050 chunk 255 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 267 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN A 787 GLN A1005 GLN A1048 HIS C 66 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 774 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.172771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.132019 restraints weight = 42678.835| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 3.04 r_work: 0.3697 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25803 Z= 0.122 Angle : 0.608 9.864 35191 Z= 0.303 Chirality : 0.045 0.415 4092 Planarity : 0.004 0.054 4447 Dihedral : 6.622 90.237 4388 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.54 % Favored : 91.33 % Rotamer: Outliers : 5.36 % Allowed : 23.83 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.14), residues: 3078 helix: 0.71 (0.22), residues: 591 sheet: -1.23 (0.19), residues: 690 loop : -2.39 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 319 TYR 0.023 0.001 TYR C1110 PHE 0.022 0.001 PHE C 55 TRP 0.018 0.001 TRP C 64 HIS 0.004 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (25722) covalent geometry : angle 0.58930 / 0.30 (34981) SS BOND : bond 0.00277 / 0.19 ( 33) SS BOND : angle 1.38215 / 0.89 ( 66) hydrogen bonds : bond 0.04080 / 2.71 ( 776) hydrogen bonds : angle 5.70629 / 3.87 ( 2139) link_NAG-ASN : bond 0.00273 / 0.18 ( 48) link_NAG-ASN : angle 2.22666 / 1.47 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 272 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 275 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.6430 (t80) REVERT: B 304 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8173 (tttm) REVERT: B 519 HIS cc_start: 0.5568 (OUTLIER) cc_final: 0.4016 (t-90) REVERT: B 697 MET cc_start: 0.7214 (mmp) cc_final: 0.6575 (tpt) REVERT: B 747 THR cc_start: 0.7944 (m) cc_final: 0.7504 (p) REVERT: B 748 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: B 1017 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8297 (tp30) REVERT: A 104 TRP cc_start: 0.5983 (OUTLIER) cc_final: 0.5581 (t60) REVERT: A 406 GLU cc_start: 0.3957 (mt-10) cc_final: 0.2492 (tt0) REVERT: A 418 ILE cc_start: 0.6054 (tp) cc_final: 0.5757 (tp) REVERT: A 495 TYR cc_start: 0.4597 (OUTLIER) cc_final: 0.3625 (t80) REVERT: A 525 CYS cc_start: 0.5439 (OUTLIER) cc_final: 0.4435 (m) REVERT: A 558 LYS cc_start: 0.6073 (tttt) cc_final: 0.5647 (mmmt) REVERT: C 133 PHE cc_start: 0.5339 (m-80) cc_final: 0.4742 (m-80) REVERT: C 142 ASP cc_start: 0.2541 (OUTLIER) cc_final: 0.2280 (t70) REVERT: C 239 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6374 (mp-120) REVERT: C 319 ARG cc_start: 0.7967 (ppt170) cc_final: 0.7689 (ppt170) REVERT: C 493 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.6593 (tm-30) REVERT: C 501 TYR cc_start: 0.5692 (m-80) cc_final: 0.5449 (m-80) REVERT: C 726 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8441 (pp) REVERT: C 767 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7647 (mt) REVERT: C 775 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7505 (t0) REVERT: C 920 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8292 (tt0) outliers start: 146 outliers final: 78 residues processed: 397 average time/residue: 0.1413 time to fit residues: 93.0908 Evaluate side-chains 343 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 251 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 164 optimal weight: 0.0470 chunk 252 optimal weight: 9.9990 chunk 233 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 205 optimal weight: 0.8980 chunk 143 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 519 HIS A 774 GLN A 787 GLN A 901 GLN A 913 GLN A1005 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 774 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.171857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.132254 restraints weight = 42484.399| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 3.16 r_work: 0.3685 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25803 Z= 0.126 Angle : 0.602 10.550 35191 Z= 0.300 Chirality : 0.045 0.281 4092 Planarity : 0.004 0.054 4447 Dihedral : 6.277 84.118 4386 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.84 % Favored : 91.03 % Rotamer: Outliers : 4.81 % Allowed : 24.71 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.15), residues: 3078 helix: 0.90 (0.22), residues: 582 sheet: -1.16 (0.19), residues: 660 loop : -2.31 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.025 0.001 TYR C1110 PHE 0.032 0.001 PHE B 855 TRP 0.018 0.001 TRP C 64 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (25722) covalent geometry : angle 0.58473 / 0.30 (34981) SS BOND : bond 0.00284 / 0.18 ( 33) SS BOND : angle 1.45581 / 0.96 ( 66) hydrogen bonds : bond 0.03911 / 2.62 ( 776) hydrogen bonds : angle 5.55821 / 3.77 ( 2139) link_NAG-ASN : bond 0.00287 / 0.19 ( 48) link_NAG-ASN : angle 2.12376 / 1.40 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 267 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 275 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.6448 (t80) REVERT: B 304 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8159 (tttm) REVERT: B 519 HIS cc_start: 0.5688 (OUTLIER) cc_final: 0.4224 (t-90) REVERT: B 697 MET cc_start: 0.7270 (mmp) cc_final: 0.6405 (mmm) REVERT: B 747 THR cc_start: 0.7976 (m) cc_final: 0.7550 (p) REVERT: B 748 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: B 855 PHE cc_start: 0.6919 (t80) cc_final: 0.6693 (t80) REVERT: B 1017 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8431 (tp30) REVERT: A 104 TRP cc_start: 0.6190 (OUTLIER) cc_final: 0.5602 (t60) REVERT: A 406 GLU cc_start: 0.3870 (mt-10) cc_final: 0.2435 (tt0) REVERT: A 418 ILE cc_start: 0.6163 (tp) cc_final: 0.5725 (tp) REVERT: A 495 TYR cc_start: 0.4611 (OUTLIER) cc_final: 0.3647 (t80) REVERT: A 558 LYS cc_start: 0.5790 (tttt) cc_final: 0.5564 (mmmt) REVERT: A 643 PHE cc_start: 0.6294 (t80) cc_final: 0.5861 (t80) REVERT: A 740 MET cc_start: 0.8557 (tpp) cc_final: 0.7564 (tpt) REVERT: C 133 PHE cc_start: 0.5463 (m-80) cc_final: 0.4759 (m-80) REVERT: C 142 ASP cc_start: 0.2594 (OUTLIER) cc_final: 0.2345 (t70) REVERT: C 239 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.7097 (mp-120) REVERT: C 319 ARG cc_start: 0.7981 (ppt170) cc_final: 0.7720 (ppt170) REVERT: C 493 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6608 (tm-30) REVERT: C 501 TYR cc_start: 0.5804 (m-80) cc_final: 0.5485 (m-80) REVERT: C 519 HIS cc_start: 0.4656 (OUTLIER) cc_final: 0.4017 (t-90) REVERT: C 726 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8443 (pp) REVERT: C 767 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7657 (mm) outliers start: 131 outliers final: 93 residues processed: 377 average time/residue: 0.1440 time to fit residues: 90.2371 Evaluate side-chains 359 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 254 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 192 optimal weight: 8.9990 chunk 290 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 0.0770 chunk 148 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 285 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN A1005 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.167794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.128001 restraints weight = 42916.963| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 3.19 r_work: 0.3625 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25803 Z= 0.219 Angle : 0.677 11.120 35191 Z= 0.338 Chirality : 0.047 0.303 4092 Planarity : 0.004 0.056 4447 Dihedral : 6.513 75.657 4386 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.91 % Favored : 89.96 % Rotamer: Outliers : 5.91 % Allowed : 24.34 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.14), residues: 3078 helix: 0.65 (0.22), residues: 597 sheet: -1.29 (0.19), residues: 690 loop : -2.37 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 237 TYR 0.029 0.002 TYR C1110 PHE 0.029 0.002 PHE C 238 TRP 0.020 0.002 TRP C 64 HIS 0.005 0.001 HIS C 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (25722) covalent geometry : angle 0.65740 / 0.33 (34981) SS BOND : bond 0.00607 / 0.34 ( 33) SS BOND : angle 1.79478 / 1.23 ( 66) hydrogen bonds : bond 0.04394 / 2.94 ( 776) hydrogen bonds : angle 5.71868 / 3.87 ( 2139) link_NAG-ASN : bond 0.00331 / 0.22 ( 48) link_NAG-ASN : angle 2.34839 / 1.53 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 263 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.6565 (ppp) cc_final: 0.5923 (ppp) REVERT: B 275 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7028 (t80) REVERT: B 304 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8180 (tttm) REVERT: B 365 TYR cc_start: 0.5897 (t80) cc_final: 0.5611 (t80) REVERT: B 519 HIS cc_start: 0.5780 (OUTLIER) cc_final: 0.4344 (t-90) REVERT: B 747 THR cc_start: 0.8190 (m) cc_final: 0.7731 (p) REVERT: B 748 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: B 855 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.6597 (t80) REVERT: B 1017 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8277 (tp30) REVERT: A 406 GLU cc_start: 0.3960 (mt-10) cc_final: 0.2501 (tt0) REVERT: A 418 ILE cc_start: 0.5801 (tp) cc_final: 0.5398 (tp) REVERT: A 495 TYR cc_start: 0.4774 (OUTLIER) cc_final: 0.3751 (t80) REVERT: A 558 LYS cc_start: 0.5932 (tttt) cc_final: 0.5644 (mmmt) REVERT: A 564 GLN cc_start: 0.7744 (pm20) cc_final: 0.7410 (pm20) REVERT: A 950 ASP cc_start: 0.8060 (t0) cc_final: 0.7853 (t0) REVERT: A 990 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7911 (mm-30) REVERT: C 131 CYS cc_start: 0.3919 (OUTLIER) cc_final: 0.3081 (m) REVERT: C 133 PHE cc_start: 0.5641 (m-80) cc_final: 0.4887 (m-80) REVERT: C 142 ASP cc_start: 0.2199 (OUTLIER) cc_final: 0.1966 (t70) REVERT: C 319 ARG cc_start: 0.7943 (ppt170) cc_final: 0.7726 (ppt170) REVERT: C 396 TYR cc_start: 0.7037 (m-80) cc_final: 0.6807 (m-80) REVERT: C 493 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6611 (tm-30) REVERT: C 501 TYR cc_start: 0.5986 (m-80) cc_final: 0.5496 (m-80) REVERT: C 519 HIS cc_start: 0.4967 (OUTLIER) cc_final: 0.4260 (t-90) REVERT: C 726 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8454 (pp) REVERT: C 767 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7718 (mt) REVERT: C 775 ASP cc_start: 0.7792 (t0) cc_final: 0.7581 (t0) outliers start: 161 outliers final: 112 residues processed: 396 average time/residue: 0.1410 time to fit residues: 93.1346 Evaluate side-chains 365 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 240 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 8 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 242 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 306 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 chunk 224 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 281 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 307 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 955 ASN A 69 HIS A 913 GLN A1005 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 774 GLN C 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.170910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.131098 restraints weight = 42444.927| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.00 r_work: 0.3684 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25803 Z= 0.115 Angle : 0.608 11.415 35191 Z= 0.301 Chirality : 0.045 0.428 4092 Planarity : 0.004 0.054 4447 Dihedral : 6.100 67.936 4386 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.45 % Favored : 91.42 % Rotamer: Outliers : 4.77 % Allowed : 25.33 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.15), residues: 3078 helix: 0.90 (0.22), residues: 594 sheet: -1.01 (0.20), residues: 594 loop : -2.22 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.018 0.001 TYR B1067 PHE 0.024 0.001 PHE B 855 TRP 0.022 0.001 TRP C 64 HIS 0.007 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (25722) covalent geometry : angle 0.58875 / 0.30 (34981) SS BOND : bond 0.00278 / 0.19 ( 33) SS BOND : angle 1.50094 / 1.02 ( 66) hydrogen bonds : bond 0.03768 / 2.50 ( 776) hydrogen bonds : angle 5.53225 / 3.74 ( 2139) link_NAG-ASN : bond 0.00328 / 0.23 ( 48) link_NAG-ASN : angle 2.25332 / 1.47 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 263 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.6569 (ppp) cc_final: 0.5931 (ppp) REVERT: B 275 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.6516 (t80) REVERT: B 304 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8102 (tttm) REVERT: B 365 TYR cc_start: 0.5863 (t80) cc_final: 0.5551 (t80) REVERT: B 386 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6888 (mtpp) REVERT: B 519 HIS cc_start: 0.5776 (OUTLIER) cc_final: 0.4361 (t-90) REVERT: B 697 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6327 (mmm) REVERT: B 1017 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8328 (tp30) REVERT: B 1029 MET cc_start: 0.8562 (tpp) cc_final: 0.7552 (ttp) REVERT: A 104 TRP cc_start: 0.6250 (OUTLIER) cc_final: 0.5717 (t60) REVERT: A 340 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6544 (tm-30) REVERT: A 387 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7903 (mm) REVERT: A 406 GLU cc_start: 0.4040 (mt-10) cc_final: 0.2597 (tt0) REVERT: A 418 ILE cc_start: 0.5792 (tp) cc_final: 0.5283 (tp) REVERT: A 495 TYR cc_start: 0.4913 (OUTLIER) cc_final: 0.3882 (t80) REVERT: A 525 CYS cc_start: 0.5575 (OUTLIER) cc_final: 0.4983 (m) REVERT: A 564 GLN cc_start: 0.7828 (pm20) cc_final: 0.7361 (pm20) REVERT: A 1041 ASP cc_start: 0.7919 (m-30) cc_final: 0.7541 (t0) REVERT: C 133 PHE cc_start: 0.5555 (m-80) cc_final: 0.4753 (m-80) REVERT: C 142 ASP cc_start: 0.2733 (OUTLIER) cc_final: 0.2496 (t70) REVERT: C 239 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6539 (mp10) REVERT: C 319 ARG cc_start: 0.8017 (ppt170) cc_final: 0.7792 (ppt170) REVERT: C 396 TYR cc_start: 0.6990 (m-80) cc_final: 0.6782 (m-80) REVERT: C 493 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.6689 (tm-30) REVERT: C 501 TYR cc_start: 0.5834 (m-80) cc_final: 0.5517 (m-80) REVERT: C 519 HIS cc_start: 0.4863 (OUTLIER) cc_final: 0.4159 (t-90) REVERT: C 726 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8452 (pp) REVERT: C 767 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7500 (mt) REVERT: C 775 ASP cc_start: 0.7606 (t0) cc_final: 0.7385 (t0) outliers start: 130 outliers final: 94 residues processed: 376 average time/residue: 0.1438 time to fit residues: 89.7100 Evaluate side-chains 351 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 242 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 85 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 273 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 chunk 258 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 136 optimal weight: 0.0050 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN A 787 GLN A1005 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 774 GLN C 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.171349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.131557 restraints weight = 42566.022| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 3.01 r_work: 0.3692 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25803 Z= 0.113 Angle : 0.603 11.352 35191 Z= 0.299 Chirality : 0.045 0.382 4092 Planarity : 0.004 0.054 4447 Dihedral : 5.865 57.515 4386 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.23 % Favored : 90.64 % Rotamer: Outliers : 4.85 % Allowed : 25.48 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.15), residues: 3078 helix: 1.00 (0.22), residues: 594 sheet: -0.84 (0.21), residues: 564 loop : -2.13 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 44 TYR 0.017 0.001 TYR B1067 PHE 0.025 0.001 PHE C 817 TRP 0.021 0.001 TRP C 64 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (25722) covalent geometry : angle 0.58256 / 0.29 (34981) SS BOND : bond 0.00271 / 0.18 ( 33) SS BOND : angle 1.41717 / 0.97 ( 66) hydrogen bonds : bond 0.03629 / 2.42 ( 776) hydrogen bonds : angle 5.48117 / 3.69 ( 2139) link_NAG-ASN : bond 0.00327 / 0.22 ( 48) link_NAG-ASN : angle 2.32511 / 1.57 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 257 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.6566 (ppp) cc_final: 0.5927 (ppp) REVERT: B 275 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.6529 (t80) REVERT: B 304 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8099 (tttm) REVERT: B 365 TYR cc_start: 0.5873 (t80) cc_final: 0.5551 (t80) REVERT: B 383 SER cc_start: 0.7986 (p) cc_final: 0.7644 (t) REVERT: B 386 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6931 (mtpp) REVERT: B 519 HIS cc_start: 0.5738 (OUTLIER) cc_final: 0.4340 (t-90) REVERT: B 697 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6392 (mmm) REVERT: B 1017 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8390 (tp30) REVERT: B 1029 MET cc_start: 0.8555 (tpp) cc_final: 0.7522 (ttp) REVERT: A 104 TRP cc_start: 0.6315 (OUTLIER) cc_final: 0.5544 (t60) REVERT: A 340 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6557 (tm-30) REVERT: A 387 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7897 (mm) REVERT: A 406 GLU cc_start: 0.4132 (mt-10) cc_final: 0.2721 (tt0) REVERT: A 418 ILE cc_start: 0.5769 (tp) cc_final: 0.5234 (tp) REVERT: A 495 TYR cc_start: 0.4568 (OUTLIER) cc_final: 0.3661 (t80) REVERT: A 525 CYS cc_start: 0.5614 (OUTLIER) cc_final: 0.5011 (m) REVERT: A 564 GLN cc_start: 0.7790 (pm20) cc_final: 0.7388 (pm20) REVERT: A 1041 ASP cc_start: 0.7902 (m-30) cc_final: 0.7537 (t0) REVERT: C 133 PHE cc_start: 0.5575 (m-80) cc_final: 0.4783 (m-80) REVERT: C 142 ASP cc_start: 0.2836 (OUTLIER) cc_final: 0.2599 (t70) REVERT: C 239 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6646 (mp10) REVERT: C 319 ARG cc_start: 0.7954 (ppt170) cc_final: 0.7743 (ppt170) REVERT: C 493 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6713 (tm-30) REVERT: C 501 TYR cc_start: 0.5740 (m-80) cc_final: 0.5443 (m-80) REVERT: C 519 HIS cc_start: 0.4764 (OUTLIER) cc_final: 0.4099 (t-90) REVERT: C 726 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8428 (pp) REVERT: C 767 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7598 (mt) outliers start: 132 outliers final: 93 residues processed: 368 average time/residue: 0.1437 time to fit residues: 87.5165 Evaluate side-chains 353 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 245 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 267 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 146 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 288 optimal weight: 0.5980 chunk 219 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 117 optimal weight: 20.0000 chunk 264 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A1005 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 774 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.170558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.130863 restraints weight = 42750.893| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.98 r_work: 0.3687 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25803 Z= 0.126 Angle : 0.606 10.691 35191 Z= 0.301 Chirality : 0.045 0.334 4092 Planarity : 0.004 0.055 4447 Dihedral : 5.767 56.455 4386 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.03 % Favored : 90.84 % Rotamer: Outliers : 4.41 % Allowed : 25.77 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.15), residues: 3078 helix: 1.00 (0.22), residues: 597 sheet: -0.76 (0.21), residues: 564 loop : -2.14 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1019 TYR 0.019 0.001 TYR B1067 PHE 0.041 0.001 PHE C 817 TRP 0.022 0.001 TRP C 64 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (25722) covalent geometry : angle 0.58564 / 0.30 (34981) SS BOND : bond 0.00272 / 0.18 ( 33) SS BOND : angle 1.38520 / 0.94 ( 66) hydrogen bonds : bond 0.03666 / 2.46 ( 776) hydrogen bonds : angle 5.40677 / 3.65 ( 2139) link_NAG-ASN : bond 0.00319 / 0.21 ( 48) link_NAG-ASN : angle 2.33608 / 1.57 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 250 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.6695 (ppp) cc_final: 0.6053 (ppp) REVERT: B 275 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.6547 (t80) REVERT: B 304 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8122 (tttm) REVERT: B 365 TYR cc_start: 0.5841 (t80) cc_final: 0.5526 (t80) REVERT: B 386 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6964 (mtpp) REVERT: B 519 HIS cc_start: 0.5761 (OUTLIER) cc_final: 0.4367 (t-90) REVERT: B 697 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6323 (mmm) REVERT: B 1005 GLN cc_start: 0.8842 (tp40) cc_final: 0.8547 (tp40) REVERT: A 104 TRP cc_start: 0.6452 (OUTLIER) cc_final: 0.5653 (t60) REVERT: A 340 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6609 (tm-30) REVERT: A 387 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7970 (mm) REVERT: A 406 GLU cc_start: 0.4270 (mt-10) cc_final: 0.2770 (tt0) REVERT: A 418 ILE cc_start: 0.5769 (tp) cc_final: 0.5202 (tp) REVERT: A 495 TYR cc_start: 0.4670 (OUTLIER) cc_final: 0.3747 (t80) REVERT: A 525 CYS cc_start: 0.5707 (OUTLIER) cc_final: 0.5158 (m) REVERT: A 564 GLN cc_start: 0.7812 (pm20) cc_final: 0.7439 (pm20) REVERT: A 740 MET cc_start: 0.8391 (tpp) cc_final: 0.7606 (tpt) REVERT: A 1041 ASP cc_start: 0.7893 (m-30) cc_final: 0.7620 (t0) REVERT: C 133 PHE cc_start: 0.5599 (m-80) cc_final: 0.4813 (m-80) REVERT: C 142 ASP cc_start: 0.2893 (OUTLIER) cc_final: 0.2641 (t70) REVERT: C 493 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.6706 (tm-30) REVERT: C 501 TYR cc_start: 0.5677 (m-80) cc_final: 0.5429 (m-80) REVERT: C 519 HIS cc_start: 0.4637 (OUTLIER) cc_final: 0.3945 (t-90) REVERT: C 726 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8419 (pp) REVERT: C 767 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7675 (mt) REVERT: C 775 ASP cc_start: 0.7686 (t0) cc_final: 0.7431 (t0) outliers start: 120 outliers final: 97 residues processed: 349 average time/residue: 0.1447 time to fit residues: 84.0985 Evaluate side-chains 351 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 240 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 64 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 251 optimal weight: 0.3980 chunk 43 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 302 optimal weight: 5.9990 chunk 149 optimal weight: 30.0000 chunk 81 optimal weight: 0.9980 chunk 299 optimal weight: 0.6980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.170341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.130489 restraints weight = 42645.796| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 3.01 r_work: 0.3678 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25803 Z= 0.132 Angle : 0.615 12.748 35191 Z= 0.303 Chirality : 0.046 0.359 4092 Planarity : 0.004 0.056 4447 Dihedral : 6.045 57.653 4386 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.06 % Favored : 90.81 % Rotamer: Outliers : 4.37 % Allowed : 26.03 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.15), residues: 3078 helix: 1.02 (0.22), residues: 597 sheet: -0.73 (0.21), residues: 564 loop : -2.13 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1019 TYR 0.018 0.001 TYR B1067 PHE 0.037 0.001 PHE C 817 TRP 0.023 0.001 TRP C 64 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (25722) covalent geometry : angle 0.59749 / 0.30 (34981) SS BOND : bond 0.00289 / 0.19 ( 33) SS BOND : angle 1.41076 / 0.96 ( 66) hydrogen bonds : bond 0.03659 / 2.45 ( 776) hydrogen bonds : angle 5.40428 / 3.64 ( 2139) link_NAG-ASN : bond 0.00353 / 0.24 ( 48) link_NAG-ASN : angle 2.15607 / 1.41 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 243 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.6654 (ppp) cc_final: 0.6012 (ppp) REVERT: B 275 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.6511 (t80) REVERT: B 304 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8130 (tttm) REVERT: B 386 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6923 (mtpp) REVERT: B 519 HIS cc_start: 0.5589 (OUTLIER) cc_final: 0.4400 (t-90) REVERT: B 697 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6355 (mmm) REVERT: B 1005 GLN cc_start: 0.8881 (tp40) cc_final: 0.8567 (tp40) REVERT: A 104 TRP cc_start: 0.6454 (OUTLIER) cc_final: 0.5546 (t60) REVERT: A 340 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6697 (tm-30) REVERT: A 387 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7890 (mm) REVERT: A 406 GLU cc_start: 0.4187 (mt-10) cc_final: 0.2761 (tt0) REVERT: A 418 ILE cc_start: 0.5752 (tp) cc_final: 0.5192 (tp) REVERT: A 495 TYR cc_start: 0.4621 (OUTLIER) cc_final: 0.3712 (t80) REVERT: A 525 CYS cc_start: 0.5771 (OUTLIER) cc_final: 0.5105 (m) REVERT: A 564 GLN cc_start: 0.7820 (pm20) cc_final: 0.7403 (pm20) REVERT: A 1041 ASP cc_start: 0.7977 (m-30) cc_final: 0.7680 (t0) REVERT: C 133 PHE cc_start: 0.5692 (m-80) cc_final: 0.4804 (m-80) REVERT: C 142 ASP cc_start: 0.2818 (OUTLIER) cc_final: 0.2569 (t70) REVERT: C 493 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6716 (tm-30) REVERT: C 519 HIS cc_start: 0.4643 (OUTLIER) cc_final: 0.3971 (t-90) REVERT: C 726 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8434 (pp) REVERT: C 767 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7682 (mt) REVERT: C 775 ASP cc_start: 0.7730 (t0) cc_final: 0.7471 (t0) outliers start: 119 outliers final: 99 residues processed: 342 average time/residue: 0.1388 time to fit residues: 79.5094 Evaluate side-chains 350 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 237 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 52 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 235 optimal weight: 10.0000 chunk 305 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 304 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 260 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A1005 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.164184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.125426 restraints weight = 42645.390| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 3.10 r_work: 0.3595 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 25803 Z= 0.239 Angle : 0.737 10.851 35191 Z= 0.367 Chirality : 0.050 0.373 4092 Planarity : 0.005 0.063 4447 Dihedral : 6.749 61.365 4386 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.46 % Favored : 89.41 % Rotamer: Outliers : 4.70 % Allowed : 26.10 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.14), residues: 3078 helix: 0.63 (0.21), residues: 597 sheet: -0.98 (0.20), residues: 633 loop : -2.31 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 357 TYR 0.029 0.002 TYR C1110 PHE 0.041 0.002 PHE C 817 TRP 0.025 0.002 TRP C 64 HIS 0.007 0.001 HIS C 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.24 (25722) covalent geometry : angle 0.71705 / 0.36 (34981) SS BOND : bond 0.00367 / 0.24 ( 33) SS BOND : angle 1.83802 / 1.25 ( 66) hydrogen bonds : bond 0.04629 / 3.07 ( 776) hydrogen bonds : angle 5.76051 / 3.89 ( 2139) link_NAG-ASN : bond 0.00402 / 0.26 ( 48) link_NAG-ASN : angle 2.48118 / 1.60 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5822.18 seconds wall clock time: 100 minutes 49.58 seconds (6049.58 seconds total)