Starting phenix.real_space_refine on Sat Jul 4 23:47:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7odl_12842/07_2026/7odl_12842.cif Found real_map, /net/cci-nas-00/data/ceres_data/7odl_12842/07_2026/7odl_12842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7odl_12842/07_2026/7odl_12842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7odl_12842/07_2026/7odl_12842.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7odl_12842/07_2026/7odl_12842.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7odl_12842/07_2026/7odl_12842.cif" model { file = "/net/cci-nas-00/data/ceres_data/7odl_12842/07_2026/7odl_12842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7odl_12842/07_2026/7odl_12842.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 111 5.16 5 C 15532 2.51 5 N 3999 2.21 5 O 4696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 24338 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7958 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 46, 'TRANS': 975} Chain breaks: 8 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7948 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 46, 'TRANS': 975} Chain breaks: 8 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 7952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7952 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 46, 'TRANS': 975} Chain breaks: 8 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 4.89, per 1000 atoms: 0.20 Number of scatterers: 24338 At special positions: 0 Unit cell: (139.65, 154.35, 162.75, 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 111 16.00 O 4696 8.00 N 3999 7.00 C 15532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 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 Atom "HETATM24336 O5 NAG C1311 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 717 " " NAG A1310 " - " ASN A 801 " " NAG A1311 " - " ASN A1074 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 717 " " NAG B1309 " - " ASN B 801 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B1134 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C1134 " Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5736 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 45 sheets defined 25.5% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 295 through 304 removed outlier: 4.152A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.803A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.808A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.298A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 759 removed outlier: 6.526A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.588A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.612A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 847 removed outlier: 3.731A pdb=" N CYS A 840 " --> pdb=" O TYR A 837 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 841 " --> pdb=" O GLY A 838 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY A 842 " --> pdb=" O ASP A 839 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ASP A 843 " --> pdb=" O CYS A 840 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 847 " --> pdb=" O ILE A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 938 removed outlier: 3.529A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 965 removed outlier: 4.009A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.871A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.004A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 5.355A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.782A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.685A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 758 removed outlier: 6.484A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 removed outlier: 4.040A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.583A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 840 removed outlier: 3.541A pdb=" N CYS B 840 " --> pdb=" O TYR B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 938 removed outlier: 3.507A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 965 removed outlier: 4.036A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.086A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.557A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.593A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.822A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.813A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.313A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.691A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 758 removed outlier: 3.680A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 754 through 758' Processing helix chain 'C' and resid 759 through 783 removed outlier: 3.682A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 836 through 841 removed outlier: 3.644A pdb=" N CYS C 840 " --> pdb=" O TYR C 837 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 841 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 847 removed outlier: 3.846A pdb=" N ARG C 847 " --> pdb=" O ILE C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.513A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.297A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 removed outlier: 3.579A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 4.249A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.750A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.899A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.280A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.356A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.539A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.873A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 11.362A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 13.236A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 13.000A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.166A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.277A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.070A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 11.362A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.679A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.313A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.770A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.393A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.673A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.673A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.606A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 31 removed outlier: 8.112A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.356A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 6.896A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.814A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 133 through 140 removed outlier: 6.728A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.330A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.055A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 removed outlier: 3.800A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.513A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.794A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.794A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.739A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.621A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.316A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.661A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 133 through 140 removed outlier: 9.129A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 11.095A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.083A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.490A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.559A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.360A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.515A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.836A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.836A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.654A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1121 through 1122 968 hydrogen bonds defined for protein. 2607 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: 5.65 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7733 1.34 - 1.46: 6073 1.46 - 1.59: 10922 1.59 - 1.71: 0 1.71 - 1.84: 135 Bond restraints: 24863 Sorted by residual: bond pdb=" N GLN A 271 " pdb=" CA GLN A 271 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.74e+01 bond pdb=" N VAL B 36 " pdb=" CA VAL B 36 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.18e-02 7.18e+03 1.04e+01 bond pdb=" N VAL C1133 " pdb=" CA VAL C1133 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.22e-02 6.72e+03 9.95e+00 bond pdb=" N VAL B 42 " pdb=" CA VAL B 42 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.20e-02 6.94e+03 8.56e+00 bond pdb=" N TYR A 269 " pdb=" CA TYR A 269 " ideal model delta sigma weight residual 1.454 1.488 -0.035 1.21e-02 6.83e+03 8.14e+00 ... (remaining 24858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 32796 1.54 - 3.07: 830 3.07 - 4.61: 146 4.61 - 6.15: 15 6.15 - 7.68: 13 Bond angle restraints: 33800 Sorted by residual: angle pdb=" N LEU A 293 " pdb=" CA LEU A 293 " pdb=" C LEU A 293 " ideal model delta sigma weight residual 113.88 106.20 7.68 1.23e+00 6.61e-01 3.90e+01 angle pdb=" CA GLY C 566 " pdb=" C GLY C 566 " pdb=" O GLY C 566 " ideal model delta sigma weight residual 120.94 117.40 3.54 7.80e-01 1.64e+00 2.06e+01 angle pdb=" N ILE B 666 " pdb=" CA ILE B 666 " pdb=" C ILE B 666 " ideal model delta sigma weight residual 112.96 109.06 3.90 1.00e+00 1.00e+00 1.52e+01 angle pdb=" N SER B 704 " pdb=" CA SER B 704 " pdb=" C SER B 704 " ideal model delta sigma weight residual 107.73 113.95 -6.22 1.61e+00 3.86e-01 1.49e+01 angle pdb=" C ASN A1135 " pdb=" CA ASN A1135 " pdb=" CB ASN A1135 " ideal model delta sigma weight residual 116.54 112.57 3.97 1.15e+00 7.56e-01 1.19e+01 ... (remaining 33795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 13060 17.91 - 35.81: 1186 35.81 - 53.72: 213 53.72 - 71.63: 50 71.63 - 89.53: 28 Dihedral angle restraints: 14537 sinusoidal: 5624 harmonic: 8913 Sorted by residual: dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual 93.00 38.34 54.66 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 38.78 54.22 1 1.00e+01 1.00e-02 3.99e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -32.39 -53.61 1 1.00e+01 1.00e-02 3.90e+01 ... (remaining 14534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3571 0.093 - 0.185: 348 0.185 - 0.278: 10 0.278 - 0.370: 0 0.370 - 0.463: 1 Chirality restraints: 3930 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA ASP A 294 " pdb=" N ASP A 294 " pdb=" C ASP A 294 " pdb=" CB ASP A 294 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3927 not shown) Planarity restraints: 4368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C1134 " 0.067 2.00e-02 2.50e+03 2.50e-01 7.83e+02 pdb=" CG ASN C1134 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN C1134 " 0.147 2.00e-02 2.50e+03 pdb=" ND2 ASN C1134 " -0.439 2.00e-02 2.50e+03 pdb=" C1 NAG C1311 " 0.298 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1302 " -0.065 2.00e-02 2.50e+03 5.40e-02 3.64e+01 pdb=" C7 NAG A1302 " 0.015 2.00e-02 2.50e+03 pdb=" C8 NAG A1302 " -0.049 2.00e-02 2.50e+03 pdb=" N2 NAG A1302 " 0.086 2.00e-02 2.50e+03 pdb=" O7 NAG A1302 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 216 " -0.043 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO B 217 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " -0.035 5.00e-02 4.00e+02 ... (remaining 4365 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 136 2.60 - 3.18: 19475 3.18 - 3.75: 32583 3.75 - 4.33: 49569 4.33 - 4.90: 84087 Nonbonded interactions: 185850 Sorted by model distance: nonbonded pdb=" O3 NAG B1302 " pdb=" O7 NAG B1302 " model vdw 2.028 3.040 nonbonded pdb=" O3 NAG C1311 " pdb=" O7 NAG C1311 " model vdw 2.086 3.040 nonbonded pdb=" O3 NAG C1303 " pdb=" O7 NAG C1303 " model vdw 2.189 3.040 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.200 3.120 nonbonded pdb=" O CYS B 617 " pdb=" OG1 THR B 618 " model vdw 2.203 3.040 ... (remaining 185845 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 95 or (resid 96 through 97 and (name N or name \ CA or name C or name O or name CB )) or resid 98 through 189 or (resid 190 and ( \ name N or name CA or name C or name O or name CB )) or resid 191 through 1311)) selection = chain 'B' selection = (chain 'C' and (resid 27 through 95 or (resid 96 through 97 and (name N or name \ CA or name C or name O or name CB )) or resid 98 through 1311)) } 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.790 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 24929 Z= 0.216 Angle : 0.636 20.795 33962 Z= 0.344 Chirality : 0.049 0.463 3930 Planarity : 0.003 0.064 4338 Dihedral : 14.568 89.532 8693 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.84 % Favored : 94.06 % Rotamer: Outliers : 0.64 % Allowed : 0.38 % Favored : 98.98 % 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: -1.28 (0.15), residues: 3012 helix: 0.64 (0.21), residues: 639 sheet: 0.43 (0.21), residues: 624 loop : -2.04 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1091 TYR 0.014 0.001 TYR B 91 PHE 0.017 0.001 PHE B 906 TRP 0.024 0.001 TRP A 886 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.21 (24863) covalent geometry : angle 0.60644 / 0.34 (33800) SS BOND : bond 0.00431 / 0.27 ( 36) SS BOND : angle 1.21468 / 0.82 ( 72) hydrogen bonds : bond 0.21096 / 13.76 ( 926) hydrogen bonds : angle 7.49694 / 5.15 ( 2607) link_NAG-ASN : bond 0.02382 / 1.72 ( 30) link_NAG-ASN : angle 3.65503 / 2.42 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 225 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1050 MET cc_start: 0.8581 (ptp) cc_final: 0.8303 (ptp) REVERT: A 1119 ASN cc_start: 0.7182 (p0) cc_final: 0.6651 (p0) REVERT: B 841 LEU cc_start: 0.7887 (tt) cc_final: 0.7654 (tt) REVERT: B 881 THR cc_start: 0.8834 (t) cc_final: 0.8583 (m) REVERT: B 1019 ARG cc_start: 0.7914 (ttm110) cc_final: 0.7631 (ttp-110) REVERT: C 202 LYS cc_start: 0.8688 (mttm) cc_final: 0.8362 (mttm) REVERT: C 357 ARG cc_start: 0.8185 (ttt90) cc_final: 0.7726 (ttm170) outliers start: 17 outliers final: 8 residues processed: 241 average time/residue: 0.1675 time to fit residues: 61.8612 Evaluate side-chains 206 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 198 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1135 ASN B 388 ASN B 675 GLN B 957 GLN C 334 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.129708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.101714 restraints weight = 30130.735| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.03 r_work: 0.2863 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24929 Z= 0.147 Angle : 0.617 21.052 33962 Z= 0.322 Chirality : 0.048 0.582 3930 Planarity : 0.004 0.053 4338 Dihedral : 6.889 73.144 3334 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.08 % Favored : 94.85 % Rotamer: Outliers : 0.68 % Allowed : 4.62 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.15), residues: 3012 helix: 0.76 (0.21), residues: 654 sheet: 0.88 (0.21), residues: 660 loop : -1.99 (0.13), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 765 TYR 0.018 0.001 TYR C1067 PHE 0.017 0.001 PHE C 592 TRP 0.018 0.001 TRP A 886 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (24863) covalent geometry : angle 0.58515 / 0.31 (33800) SS BOND : bond 0.00434 / 0.26 ( 36) SS BOND : angle 1.30698 / 0.88 ( 72) hydrogen bonds : bond 0.06077 / 3.93 ( 926) hydrogen bonds : angle 5.67117 / 3.91 ( 2607) link_NAG-ASN : bond 0.00530 / 0.36 ( 30) link_NAG-ASN : angle 3.72705 / 2.28 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 PHE cc_start: 0.6553 (m-80) cc_final: 0.6301 (m-10) REVERT: C 202 LYS cc_start: 0.8917 (mttm) cc_final: 0.8705 (mttt) outliers start: 18 outliers final: 15 residues processed: 213 average time/residue: 0.1702 time to fit residues: 55.3667 Evaluate side-chains 199 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 88 optimal weight: 0.7980 chunk 282 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 260 optimal weight: 0.8980 chunk 257 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 297 optimal weight: 5.9990 chunk 274 optimal weight: 0.6980 chunk 211 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN B 218 GLN B 388 ASN C 613 GLN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.128105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.100547 restraints weight = 30316.406| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.07 r_work: 0.2853 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24929 Z= 0.155 Angle : 0.616 21.366 33962 Z= 0.319 Chirality : 0.048 0.507 3930 Planarity : 0.004 0.056 4338 Dihedral : 6.772 64.896 3326 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.21 % Favored : 94.72 % Rotamer: Outliers : 1.14 % Allowed : 7.65 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.15), residues: 3012 helix: 0.76 (0.21), residues: 654 sheet: 0.99 (0.20), residues: 660 loop : -1.95 (0.13), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 815 TYR 0.020 0.002 TYR C1067 PHE 0.017 0.002 PHE C 592 TRP 0.018 0.001 TRP A 886 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (24863) covalent geometry : angle 0.58196 / 0.31 (33800) SS BOND : bond 0.00472 / 0.29 ( 36) SS BOND : angle 1.40740 / 0.95 ( 72) hydrogen bonds : bond 0.06207 / 4.02 ( 926) hydrogen bonds : angle 5.46683 / 3.78 ( 2607) link_NAG-ASN : bond 0.00461 / 0.30 ( 30) link_NAG-ASN : angle 3.82078 / 2.35 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 690 GLN cc_start: 0.5932 (OUTLIER) cc_final: 0.5597 (pm20) REVERT: A 986 LYS cc_start: 0.7788 (tttm) cc_final: 0.7302 (mmtm) REVERT: B 849 LEU cc_start: 0.8317 (tp) cc_final: 0.8048 (tt) outliers start: 30 outliers final: 20 residues processed: 224 average time/residue: 0.1651 time to fit residues: 56.4816 Evaluate side-chains 211 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 8 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 267 optimal weight: 8.9990 chunk 255 optimal weight: 6.9990 chunk 289 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 279 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN B 388 ASN B 690 GLN B 969 ASN C 440 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.125905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.098513 restraints weight = 30407.296| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.11 r_work: 0.2813 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 24929 Z= 0.233 Angle : 0.717 21.820 33962 Z= 0.369 Chirality : 0.051 0.515 3930 Planarity : 0.005 0.065 4338 Dihedral : 6.959 61.231 3324 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.08 % Favored : 93.86 % Rotamer: Outliers : 1.55 % Allowed : 10.08 % Favored : 88.37 % 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: -1.10 (0.14), residues: 3012 helix: 0.54 (0.21), residues: 645 sheet: 0.89 (0.20), residues: 648 loop : -2.02 (0.13), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 815 TYR 0.023 0.002 TYR C1067 PHE 0.023 0.002 PHE C 592 TRP 0.014 0.002 TRP A 886 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.23 (24863) covalent geometry : angle 0.68050 / 0.36 (33800) SS BOND : bond 0.00661 / 0.41 ( 36) SS BOND : angle 1.80386 / 1.20 ( 72) hydrogen bonds : bond 0.07409 / 4.81 ( 926) hydrogen bonds : angle 5.59465 / 3.86 ( 2607) link_NAG-ASN : bond 0.00487 / 0.32 ( 30) link_NAG-ASN : angle 4.17204 / 2.57 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.6028 (m170) cc_final: 0.5805 (m-70) REVERT: A 690 GLN cc_start: 0.6247 (OUTLIER) cc_final: 0.5872 (pm20) REVERT: A 790 LYS cc_start: 0.7524 (mmtt) cc_final: 0.7281 (mmmt) REVERT: B 1091 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.6876 (ptm160) outliers start: 41 outliers final: 32 residues processed: 222 average time/residue: 0.1597 time to fit residues: 54.7081 Evaluate side-chains 215 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 189 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 163 optimal weight: 0.0370 chunk 265 optimal weight: 0.0040 chunk 31 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 overall best weight: 0.9874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 613 GLN B 388 ASN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.130736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.102493 restraints weight = 30062.174| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.01 r_work: 0.2886 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24929 Z= 0.099 Angle : 0.534 20.032 33962 Z= 0.276 Chirality : 0.045 0.512 3930 Planarity : 0.004 0.048 4338 Dihedral : 6.217 58.707 3324 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 1.25 % Allowed : 11.29 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.15), residues: 3012 helix: 0.97 (0.21), residues: 648 sheet: 1.01 (0.20), residues: 672 loop : -1.85 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 102 TYR 0.016 0.001 TYR C1067 PHE 0.011 0.001 PHE C 592 TRP 0.010 0.001 TRP A 886 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (24863) covalent geometry : angle 0.50205 / 0.27 (33800) SS BOND : bond 0.00288 / 0.18 ( 36) SS BOND : angle 1.04275 / 0.71 ( 72) hydrogen bonds : bond 0.04738 / 3.05 ( 926) hydrogen bonds : angle 5.14156 / 3.57 ( 2607) link_NAG-ASN : bond 0.00491 / 0.33 ( 30) link_NAG-ASN : angle 3.50212 / 2.15 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 690 GLN cc_start: 0.5785 (OUTLIER) cc_final: 0.5482 (pm20) REVERT: A 790 LYS cc_start: 0.7276 (mmtt) cc_final: 0.7073 (mmtt) REVERT: B 660 TYR cc_start: 0.7717 (m-80) cc_final: 0.7305 (m-80) REVERT: B 765 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7782 (mtm-85) REVERT: B 849 LEU cc_start: 0.8310 (tp) cc_final: 0.8036 (tt) REVERT: B 1019 ARG cc_start: 0.8204 (ttm110) cc_final: 0.7927 (ttp-110) REVERT: B 1091 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7010 (ptm160) outliers start: 33 outliers final: 22 residues processed: 222 average time/residue: 0.1568 time to fit residues: 53.6936 Evaluate side-chains 212 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 290 optimal weight: 6.9990 chunk 292 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 253 optimal weight: 8.9990 chunk 201 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 162 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN B 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.127092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.099660 restraints weight = 30189.671| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.10 r_work: 0.2828 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24929 Z= 0.184 Angle : 0.646 20.768 33962 Z= 0.333 Chirality : 0.049 0.481 3930 Planarity : 0.004 0.059 4338 Dihedral : 6.550 59.799 3324 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.74 % Favored : 94.19 % Rotamer: Outliers : 1.78 % Allowed : 11.33 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.15), residues: 3012 helix: 0.81 (0.21), residues: 642 sheet: 0.99 (0.20), residues: 648 loop : -1.92 (0.13), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 815 TYR 0.022 0.002 TYR C1067 PHE 0.019 0.002 PHE C 592 TRP 0.010 0.001 TRP A 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.18 (24863) covalent geometry : angle 0.61244 / 0.32 (33800) SS BOND : bond 0.00551 / 0.34 ( 36) SS BOND : angle 1.55939 / 1.04 ( 72) hydrogen bonds : bond 0.06541 / 4.25 ( 926) hydrogen bonds : angle 5.34303 / 3.69 ( 2607) link_NAG-ASN : bond 0.00475 / 0.32 ( 30) link_NAG-ASN : angle 3.84823 / 2.37 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 690 GLN cc_start: 0.5999 (OUTLIER) cc_final: 0.5638 (pm20) REVERT: A 790 LYS cc_start: 0.7436 (mmtt) cc_final: 0.7212 (mmmt) REVERT: B 660 TYR cc_start: 0.7793 (m-80) cc_final: 0.7334 (m-80) REVERT: B 1091 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6706 (ptm160) outliers start: 47 outliers final: 39 residues processed: 219 average time/residue: 0.1565 time to fit residues: 53.5117 Evaluate side-chains 223 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 839 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 206 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 139 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.129048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.100720 restraints weight = 29987.146| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.04 r_work: 0.2822 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24929 Z= 0.140 Angle : 0.592 20.230 33962 Z= 0.305 Chirality : 0.047 0.508 3930 Planarity : 0.004 0.055 4338 Dihedral : 6.377 59.099 3324 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.01 % Favored : 94.92 % Rotamer: Outliers : 1.67 % Allowed : 12.01 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.15), residues: 3012 helix: 0.88 (0.21), residues: 642 sheet: 0.97 (0.20), residues: 669 loop : -1.88 (0.13), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.018 0.001 TYR C1067 PHE 0.016 0.001 PHE C 592 TRP 0.010 0.001 TRP A 886 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (24863) covalent geometry : angle 0.55859 / 0.30 (33800) SS BOND : bond 0.00425 / 0.27 ( 36) SS BOND : angle 1.34019 / 0.90 ( 72) hydrogen bonds : bond 0.05783 / 3.74 ( 926) hydrogen bonds : angle 5.25368 / 3.64 ( 2607) link_NAG-ASN : bond 0.00487 / 0.32 ( 30) link_NAG-ASN : angle 3.70511 / 2.28 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 690 GLN cc_start: 0.5988 (OUTLIER) cc_final: 0.5668 (pm20) REVERT: A 790 LYS cc_start: 0.7451 (mmtt) cc_final: 0.7216 (mmmt) REVERT: B 660 TYR cc_start: 0.7790 (m-80) cc_final: 0.7323 (m-80) REVERT: B 1091 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7066 (ptm160) outliers start: 44 outliers final: 34 residues processed: 222 average time/residue: 0.1538 time to fit residues: 53.3610 Evaluate side-chains 216 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 117 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 198 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 284 optimal weight: 5.9990 chunk 271 optimal weight: 8.9990 chunk 299 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A1135 ASN B 388 ASN B 474 GLN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.125913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.098588 restraints weight = 30116.498| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.03 r_work: 0.2802 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 24929 Z= 0.265 Angle : 0.744 21.194 33962 Z= 0.382 Chirality : 0.053 0.516 3930 Planarity : 0.005 0.065 4338 Dihedral : 6.919 58.577 3324 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.41 % Favored : 93.53 % Rotamer: Outliers : 2.31 % Allowed : 12.01 % Favored : 85.68 % 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: -1.20 (0.14), residues: 3012 helix: 0.43 (0.21), residues: 645 sheet: 0.73 (0.20), residues: 678 loop : -2.06 (0.13), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 815 TYR 0.024 0.002 TYR B 756 PHE 0.023 0.002 PHE C 86 TRP 0.009 0.002 TRP B 353 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.26 (24863) covalent geometry : angle 0.70859 / 0.37 (33800) SS BOND : bond 0.00729 / 0.45 ( 36) SS BOND : angle 1.91141 / 1.27 ( 72) hydrogen bonds : bond 0.07656 / 4.98 ( 926) hydrogen bonds : angle 5.56616 / 3.84 ( 2607) link_NAG-ASN : bond 0.00502 / 0.33 ( 30) link_NAG-ASN : angle 4.15903 / 2.56 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 185 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7090 (p0) cc_final: 0.6522 (p0) REVERT: A 690 GLN cc_start: 0.6324 (OUTLIER) cc_final: 0.5961 (pm20) REVERT: B 228 ASP cc_start: 0.8041 (p0) cc_final: 0.7787 (p0) REVERT: B 1091 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6845 (ptm160) outliers start: 61 outliers final: 51 residues processed: 231 average time/residue: 0.1571 time to fit residues: 57.1459 Evaluate side-chains 234 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 243 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 272 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 388 ASN C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.102419 restraints weight = 30263.364| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.00 r_work: 0.2868 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24929 Z= 0.115 Angle : 0.563 19.782 33962 Z= 0.290 Chirality : 0.046 0.527 3930 Planarity : 0.004 0.055 4338 Dihedral : 6.254 58.887 3320 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.45 % Rotamer: Outliers : 1.63 % Allowed : 12.73 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.15), residues: 3012 helix: 0.84 (0.21), residues: 648 sheet: 0.87 (0.20), residues: 699 loop : -1.91 (0.13), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 357 TYR 0.017 0.001 TYR C1067 PHE 0.013 0.001 PHE C 592 TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (24863) covalent geometry : angle 0.53097 / 0.28 (33800) SS BOND : bond 0.00415 / 0.25 ( 36) SS BOND : angle 1.24445 / 0.82 ( 72) hydrogen bonds : bond 0.05207 / 3.36 ( 926) hydrogen bonds : angle 5.19557 / 3.60 ( 2607) link_NAG-ASN : bond 0.00490 / 0.33 ( 30) link_NAG-ASN : angle 3.55524 / 2.19 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 690 GLN cc_start: 0.6111 (OUTLIER) cc_final: 0.5754 (pm20) REVERT: B 660 TYR cc_start: 0.7831 (m-80) cc_final: 0.7379 (m-80) REVERT: B 1091 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7118 (ptm160) outliers start: 43 outliers final: 36 residues processed: 220 average time/residue: 0.1709 time to fit residues: 58.6348 Evaluate side-chains 222 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 120 optimal weight: 7.9990 chunk 212 optimal weight: 8.9990 chunk 304 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 270 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 388 ASN C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.125455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.098341 restraints weight = 30274.512| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.07 r_work: 0.2759 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 24929 Z= 0.272 Angle : 0.751 20.945 33962 Z= 0.386 Chirality : 0.053 0.509 3930 Planarity : 0.005 0.065 4338 Dihedral : 6.853 58.633 3320 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.57 % Favored : 93.36 % Rotamer: Outliers : 1.74 % Allowed : 12.73 % Favored : 85.53 % 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: -1.19 (0.14), residues: 3012 helix: 0.43 (0.21), residues: 645 sheet: 0.75 (0.20), residues: 678 loop : -2.06 (0.13), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 815 TYR 0.025 0.003 TYR B 756 PHE 0.023 0.002 PHE C 86 TRP 0.009 0.002 TRP B 353 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.27 (24863) covalent geometry : angle 0.71689 / 0.38 (33800) SS BOND : bond 0.00772 / 0.48 ( 36) SS BOND : angle 1.94188 / 1.28 ( 72) hydrogen bonds : bond 0.07696 / 5.01 ( 926) hydrogen bonds : angle 5.55851 / 3.84 ( 2607) link_NAG-ASN : bond 0.00501 / 0.33 ( 30) link_NAG-ASN : angle 4.08374 / 2.52 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6024 Ramachandran restraints generated. 3012 Oldfield, 0 Emsley, 3012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.6976 (p0) cc_final: 0.6497 (p0) REVERT: A 690 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.5904 (pm20) REVERT: A 790 LYS cc_start: 0.7844 (mttt) cc_final: 0.7541 (mmmt) REVERT: B 228 ASP cc_start: 0.7856 (p0) cc_final: 0.7573 (p0) REVERT: B 1091 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6740 (ptm160) REVERT: C 808 ASP cc_start: 0.5948 (t0) cc_final: 0.5568 (p0) outliers start: 46 outliers final: 41 residues processed: 215 average time/residue: 0.1689 time to fit residues: 57.0557 Evaluate side-chains 223 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 215 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 222 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 chunk 284 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 280 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 388 ASN C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.127636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.100592 restraints weight = 30181.229| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.02 r_work: 0.2797 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24929 Z= 0.183 Angle : 0.658 20.317 33962 Z= 0.338 Chirality : 0.049 0.535 3930 Planarity : 0.005 0.062 4338 Dihedral : 6.663 58.009 3320 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.51 % Favored : 94.42 % Rotamer: Outliers : 1.89 % Allowed : 12.77 % Favored : 85.34 % 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: -1.10 (0.14), residues: 3012 helix: 0.57 (0.21), residues: 642 sheet: 0.78 (0.20), residues: 678 loop : -2.02 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 815 TYR 0.023 0.002 TYR A 660 PHE 0.019 0.002 PHE C 86 TRP 0.009 0.001 TRP A 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (24863) covalent geometry : angle 0.62526 / 0.33 (33800) SS BOND : bond 0.00558 / 0.35 ( 36) SS BOND : angle 1.60390 / 1.07 ( 72) hydrogen bonds : bond 0.06590 / 4.27 ( 926) hydrogen bonds : angle 5.43513 / 3.76 ( 2607) link_NAG-ASN : bond 0.00485 / 0.33 ( 30) link_NAG-ASN : angle 3.80185 / 2.34 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5446.40 seconds wall clock time: 93 minutes 58.53 seconds (5638.53 seconds total)