Starting phenix.real_space_refine on Thu Mar 5 17:47:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7odl_12842/03_2026/7odl_12842.cif Found real_map, /net/cci-nas-00/data/ceres_data/7odl_12842/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7odl_12842/03_2026/7odl_12842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7odl_12842/03_2026/7odl_12842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7odl_12842/03_2026/7odl_12842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7odl_12842/03_2026/7odl_12842.map" } 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-5986/lib/python3.9/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 dihedrals: 30 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 dihedrals: 30 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.47, per 1000 atoms: 0.22 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: 1.97 Conformation dependent library (CDL) restraints added in 840.7 milliseconds 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: 1.09 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: 4.85 Time building geometry restraints manager: 2.63 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: 13608 17.91 - 35.81: 1218 35.81 - 53.72: 243 53.72 - 71.63: 70 71.63 - 89.53: 28 Dihedral angle restraints: 15167 sinusoidal: 6254 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 15164 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.850 Find NCS groups from input model: 0.440 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: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 14.657 89.532 9323 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 covalent geometry : bond 0.00380 (24863) covalent geometry : angle 0.60644 (33800) SS BOND : bond 0.00431 ( 36) SS BOND : angle 1.21468 ( 72) hydrogen bonds : bond 0.21096 ( 926) hydrogen bonds : angle 7.49694 ( 2607) link_NAG-ASN : bond 0.02382 ( 30) link_NAG-ASN : angle 3.65503 ( 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 : 0.931 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: 0.1814 time to fit residues: 66.5463 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 : 0.824 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 388 ASN B 675 GLN B 957 GLN C 334 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.101803 restraints weight = 30089.247| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.00 r_work: 0.2848 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0772 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 : 0.615 22.798 33962 Z= 0.321 Chirality : 0.048 0.627 3930 Planarity : 0.004 0.052 4338 Dihedral : 8.167 74.668 3964 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.08 % Favored : 94.85 % Rotamer: Outliers : 0.64 % Allowed : 4.58 % Favored : 94.77 % 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: -0.98 (0.15), residues: 3012 helix: 0.76 (0.21), residues: 654 sheet: 0.89 (0.21), residues: 660 loop : -1.99 (0.13), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 765 TYR 0.019 0.001 TYR C1067 PHE 0.016 0.001 PHE C 592 TRP 0.017 0.001 TRP A 886 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00338 (24863) covalent geometry : angle 0.58113 (33800) SS BOND : bond 0.00425 ( 36) SS BOND : angle 1.29309 ( 72) hydrogen bonds : bond 0.06331 ( 926) hydrogen bonds : angle 5.73163 ( 2607) link_NAG-ASN : bond 0.00463 ( 30) link_NAG-ASN : angle 3.82462 ( 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 215 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 PHE cc_start: 0.6495 (m-80) cc_final: 0.6253 (m-10) outliers start: 17 outliers final: 14 residues processed: 213 average time/residue: 0.1757 time to fit residues: 57.5185 Evaluate side-chains 199 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 282 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 260 optimal weight: 0.0870 chunk 257 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 297 optimal weight: 0.9990 chunk 274 optimal weight: 6.9990 chunk 211 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A1135 ASN B 218 GLN B 388 ASN C 613 GLN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.128209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.100110 restraints weight = 30308.398| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.17 r_work: 0.2808 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1007 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= 0.152 Angle : 0.612 21.111 33962 Z= 0.317 Chirality : 0.048 0.508 3930 Planarity : 0.004 0.055 4338 Dihedral : 7.692 64.409 3956 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 1.14 % Allowed : 7.31 % Favored : 91.55 % 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: -0.93 (0.15), residues: 3012 helix: 0.77 (0.21), residues: 654 sheet: 0.99 (0.21), residues: 645 loop : -1.94 (0.13), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 765 TYR 0.020 0.002 TYR C1067 PHE 0.016 0.002 PHE C 592 TRP 0.020 0.001 TRP A 886 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00356 (24863) covalent geometry : angle 0.57672 (33800) SS BOND : bond 0.00458 ( 36) SS BOND : angle 1.45353 ( 72) hydrogen bonds : bond 0.06173 ( 926) hydrogen bonds : angle 5.46227 ( 2607) link_NAG-ASN : bond 0.00467 ( 30) link_NAG-ASN : angle 3.81358 ( 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 231 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 690 GLN cc_start: 0.5868 (OUTLIER) cc_final: 0.5539 (pm20) REVERT: A 986 LYS cc_start: 0.7729 (tttm) cc_final: 0.7289 (mmtm) REVERT: B 849 LEU cc_start: 0.8154 (tp) cc_final: 0.7853 (tt) REVERT: C 207 HIS cc_start: 0.5599 (m-70) cc_final: 0.5385 (m90) outliers start: 30 outliers final: 21 residues processed: 225 average time/residue: 0.1791 time to fit residues: 61.5070 Evaluate side-chains 214 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 LEU 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 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 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 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 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: 4.9990 chunk 247 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 267 optimal weight: 1.9990 chunk 255 optimal weight: 0.0040 chunk 289 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 279 optimal weight: 7.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN B 388 ASN B 690 GLN B 969 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.127208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.099611 restraints weight = 30370.340| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.07 r_work: 0.2838 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24929 Z= 0.174 Angle : 0.639 20.917 33962 Z= 0.331 Chirality : 0.049 0.515 3930 Planarity : 0.004 0.059 4338 Dihedral : 7.590 59.421 3954 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.48 % Favored : 94.46 % Rotamer: Outliers : 1.48 % Allowed : 9.58 % Favored : 88.94 % 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: -0.93 (0.15), residues: 3012 helix: 0.77 (0.21), residues: 642 sheet: 0.99 (0.21), residues: 648 loop : -1.94 (0.13), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 815 TYR 0.021 0.002 TYR C1067 PHE 0.018 0.002 PHE C 592 TRP 0.013 0.001 TRP A 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00419 (24863) covalent geometry : angle 0.60451 (33800) SS BOND : bond 0.00520 ( 36) SS BOND : angle 1.53022 ( 72) hydrogen bonds : bond 0.06511 ( 926) hydrogen bonds : angle 5.43286 ( 2607) link_NAG-ASN : bond 0.00464 ( 30) link_NAG-ASN : angle 3.89283 ( 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 236 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 690 GLN cc_start: 0.5947 (OUTLIER) cc_final: 0.5634 (pm20) REVERT: A 986 LYS cc_start: 0.7706 (tttm) cc_final: 0.7268 (mmtm) REVERT: B 32 PHE cc_start: 0.6497 (m-80) cc_final: 0.6200 (m-80) REVERT: B 849 LEU cc_start: 0.8169 (tp) cc_final: 0.7886 (tt) REVERT: B 1091 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6697 (ptm160) REVERT: C 207 HIS cc_start: 0.5509 (m-70) cc_final: 0.5298 (m90) outliers start: 39 outliers final: 28 residues processed: 226 average time/residue: 0.1747 time to fit residues: 60.8951 Evaluate side-chains 216 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 95 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 1091 ARG 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 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 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: 2.9990 chunk 216 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 265 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 613 GLN B 388 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.100913 restraints weight = 30042.416| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.01 r_work: 0.2873 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24929 Z= 0.143 Angle : 0.596 20.214 33962 Z= 0.308 Chirality : 0.047 0.528 3930 Planarity : 0.004 0.056 4338 Dihedral : 7.265 59.314 3954 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.21 % Favored : 94.72 % Rotamer: Outliers : 1.67 % Allowed : 10.76 % Favored : 87.58 % 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: -0.86 (0.15), residues: 3012 helix: 0.86 (0.21), residues: 642 sheet: 1.02 (0.20), residues: 648 loop : -1.89 (0.13), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 102 TYR 0.019 0.001 TYR C1067 PHE 0.016 0.001 PHE C 592 TRP 0.011 0.001 TRP A 886 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00336 (24863) covalent geometry : angle 0.56109 (33800) SS BOND : bond 0.00432 ( 36) SS BOND : angle 1.36461 ( 72) hydrogen bonds : bond 0.05885 ( 926) hydrogen bonds : angle 5.30641 ( 2607) link_NAG-ASN : bond 0.00468 ( 30) link_NAG-ASN : angle 3.75476 ( 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 242 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 690 GLN cc_start: 0.6034 (OUTLIER) cc_final: 0.5702 (pm20) REVERT: A 790 LYS cc_start: 0.7391 (mmpt) cc_final: 0.7189 (mmmt) REVERT: A 986 LYS cc_start: 0.7786 (tttm) cc_final: 0.7356 (mmtm) REVERT: B 32 PHE cc_start: 0.6515 (m-80) cc_final: 0.6156 (m-80) REVERT: B 849 LEU cc_start: 0.8165 (tp) cc_final: 0.7881 (tt) REVERT: B 1091 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6816 (ptm160) outliers start: 44 outliers final: 34 residues processed: 231 average time/residue: 0.1699 time to fit residues: 60.5182 Evaluate side-chains 228 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL 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 A residue 719 THR Chi-restraints excluded: chain A residue 735 SER 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 207 HIS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 523 THR 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 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 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 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 42 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 290 optimal weight: 6.9990 chunk 292 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3391 r_free = 0.3391 target = 0.126174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.098211 restraints weight = 30196.951| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.16 r_work: 0.2819 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1325 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= 0.225 Angle : 0.700 20.663 33962 Z= 0.361 Chirality : 0.051 0.536 3930 Planarity : 0.005 0.064 4338 Dihedral : 7.685 58.993 3954 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.21 % Favored : 93.69 % Rotamer: Outliers : 2.20 % Allowed : 11.10 % Favored : 86.70 % 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: -1.10 (0.14), residues: 3012 helix: 0.56 (0.21), residues: 645 sheet: 0.79 (0.20), residues: 678 loop : -2.02 (0.13), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 815 TYR 0.023 0.002 TYR C1067 PHE 0.022 0.002 PHE C 592 TRP 0.010 0.002 TRP A 886 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00552 (24863) covalent geometry : angle 0.66456 (33800) SS BOND : bond 0.00644 ( 36) SS BOND : angle 1.77596 ( 72) hydrogen bonds : bond 0.07252 ( 926) hydrogen bonds : angle 5.50757 ( 2607) link_NAG-ASN : bond 0.00471 ( 30) link_NAG-ASN : angle 4.09370 ( 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 241 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 183 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 690 GLN cc_start: 0.6250 (OUTLIER) cc_final: 0.5878 (pm20) REVERT: B 32 PHE cc_start: 0.6602 (m-80) cc_final: 0.6231 (m-80) REVERT: B 849 LEU cc_start: 0.8181 (tp) cc_final: 0.7870 (tt) REVERT: B 1091 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.6810 (ptm160) outliers start: 58 outliers final: 47 residues processed: 229 average time/residue: 0.1684 time to fit residues: 60.0067 Evaluate side-chains 227 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 208 THR 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 1120 THR 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 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 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 1117 THR 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 206 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 193 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 243 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN B 164 ASN B 388 ASN C 164 ASN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.130132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.101949 restraints weight = 30061.144| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.02 r_work: 0.2855 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1386 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= 0.103 Angle : 0.543 19.207 33962 Z= 0.281 Chirality : 0.045 0.539 3930 Planarity : 0.004 0.051 4338 Dihedral : 6.886 58.799 3954 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 1.82 % Allowed : 11.97 % Favored : 86.21 % 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: -0.76 (0.15), residues: 3012 helix: 0.95 (0.21), residues: 648 sheet: 1.02 (0.20), residues: 669 loop : -1.85 (0.13), residues: 1695 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 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00217 (24863) covalent geometry : angle 0.50983 (33800) SS BOND : bond 0.00317 ( 36) SS BOND : angle 1.12850 ( 72) hydrogen bonds : bond 0.04939 ( 926) hydrogen bonds : angle 5.13390 ( 2607) link_NAG-ASN : bond 0.00487 ( 30) link_NAG-ASN : angle 3.52514 ( 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 242 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 690 GLN cc_start: 0.5975 (OUTLIER) cc_final: 0.5662 (pm20) REVERT: B 32 PHE cc_start: 0.6496 (m-80) cc_final: 0.6096 (m-80) REVERT: B 765 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7852 (mtm-85) REVERT: B 849 LEU cc_start: 0.8141 (tp) cc_final: 0.7835 (tt) REVERT: B 1019 ARG cc_start: 0.8414 (ttm110) cc_final: 0.8138 (ttp-110) REVERT: B 1091 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7139 (ptm160) outliers start: 48 outliers final: 36 residues processed: 231 average time/residue: 0.1732 time to fit residues: 61.8631 Evaluate side-chains 225 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR 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 735 SER 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 90 VAL 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 373 SER Chi-restraints excluded: chain B residue 569 ILE 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 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 394 ASN 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 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 Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 117 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 chunk 198 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 chunk 271 optimal weight: 9.9990 chunk 299 optimal weight: 1.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN B 388 ASN C 440 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.127908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.100066 restraints weight = 30003.112| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.98 r_work: 0.2842 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24929 Z= 0.172 Angle : 0.627 19.702 33962 Z= 0.324 Chirality : 0.048 0.511 3930 Planarity : 0.004 0.058 4338 Dihedral : 7.194 59.181 3954 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.22 % Rotamer: Outliers : 1.78 % Allowed : 12.12 % Favored : 86.10 % 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: -0.88 (0.15), residues: 3012 helix: 0.84 (0.21), residues: 642 sheet: 0.96 (0.20), residues: 654 loop : -1.89 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 815 TYR 0.022 0.002 TYR C1067 PHE 0.018 0.002 PHE C 592 TRP 0.009 0.001 TRP A 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00414 (24863) covalent geometry : angle 0.59344 (33800) SS BOND : bond 0.00514 ( 36) SS BOND : angle 1.50610 ( 72) hydrogen bonds : bond 0.06326 ( 926) hydrogen bonds : angle 5.29571 ( 2607) link_NAG-ASN : bond 0.00466 ( 30) link_NAG-ASN : angle 3.80199 ( 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 228 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 181 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 690 GLN cc_start: 0.6058 (OUTLIER) cc_final: 0.5696 (pm20) REVERT: A 790 LYS cc_start: 0.7880 (mttt) cc_final: 0.7656 (mtpt) REVERT: B 849 LEU cc_start: 0.8147 (tp) cc_final: 0.7857 (tt) REVERT: B 1091 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6787 (ptm160) outliers start: 47 outliers final: 40 residues processed: 221 average time/residue: 0.1648 time to fit residues: 56.9420 Evaluate side-chains 217 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 293 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 827 THR Chi-restraints excluded: chain A residue 1120 THR 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 207 HIS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 373 SER 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 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 394 ASN 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 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: 1.9990 chunk 175 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 166 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 272 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3438 r_free = 0.3438 target = 0.129819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.101716 restraints weight = 30218.131| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.00 r_work: 0.2859 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24929 Z= 0.110 Angle : 0.543 18.922 33962 Z= 0.281 Chirality : 0.046 0.520 3930 Planarity : 0.004 0.053 4338 Dihedral : 6.731 59.243 3954 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 1.55 % Allowed : 12.65 % Favored : 85.80 % 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: -0.70 (0.15), residues: 3012 helix: 1.03 (0.21), residues: 648 sheet: 1.05 (0.20), residues: 669 loop : -1.81 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 765 TYR 0.017 0.001 TYR C1067 PHE 0.013 0.001 PHE C 592 TRP 0.009 0.001 TRP A 886 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00244 (24863) covalent geometry : angle 0.51122 (33800) SS BOND : bond 0.00348 ( 36) SS BOND : angle 1.18343 ( 72) hydrogen bonds : bond 0.04984 ( 926) hydrogen bonds : angle 5.08810 ( 2607) link_NAG-ASN : bond 0.00484 ( 30) link_NAG-ASN : angle 3.48581 ( 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 228 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 790 LYS cc_start: 0.7795 (mttt) cc_final: 0.7402 (mmmt) REVERT: B 765 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7858 (mtm-85) REVERT: B 849 LEU cc_start: 0.8133 (tp) cc_final: 0.7845 (tt) REVERT: B 1019 ARG cc_start: 0.8402 (ttm110) cc_final: 0.8117 (ttp-110) REVERT: B 1091 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7135 (ptm160) outliers start: 41 outliers final: 34 residues processed: 220 average time/residue: 0.1724 time to fit residues: 58.3841 Evaluate side-chains 221 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1120 THR 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 127 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 588 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 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 719 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 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: 5.9990 chunk 212 optimal weight: 5.9990 chunk 304 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 270 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 658 ASN A1135 ASN B 164 ASN B 388 ASN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.127191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.099902 restraints weight = 30150.797| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.03 r_work: 0.2810 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24929 Z= 0.213 Angle : 0.673 19.595 33962 Z= 0.347 Chirality : 0.050 0.515 3930 Planarity : 0.005 0.060 4338 Dihedral : 7.322 59.264 3954 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.91 % Favored : 94.06 % Rotamer: Outliers : 1.93 % Allowed : 12.31 % Favored : 85.76 % 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: 0.69 (0.21), residues: 645 sheet: 0.81 (0.20), residues: 684 loop : -1.95 (0.13), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 815 TYR 0.023 0.002 TYR C1067 PHE 0.021 0.002 PHE C 86 TRP 0.010 0.002 TRP B 353 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00522 (24863) covalent geometry : angle 0.63870 (33800) SS BOND : bond 0.00625 ( 36) SS BOND : angle 1.69404 ( 72) hydrogen bonds : bond 0.06921 ( 926) hydrogen bonds : angle 5.38515 ( 2607) link_NAG-ASN : bond 0.00466 ( 30) link_NAG-ASN : angle 3.91197 ( 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 233 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7062 (p0) cc_final: 0.6467 (p0) REVERT: A 690 GLN cc_start: 0.6160 (OUTLIER) cc_final: 0.5807 (pm20) REVERT: A 790 LYS cc_start: 0.7921 (mttt) cc_final: 0.7626 (mmmt) REVERT: B 849 LEU cc_start: 0.8187 (tp) cc_final: 0.7905 (tt) REVERT: B 1091 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6787 (ptm160) outliers start: 51 outliers final: 45 residues processed: 221 average time/residue: 0.1630 time to fit residues: 56.1275 Evaluate side-chains 226 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 658 ASN 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 1120 THR Chi-restraints excluded: chain A residue 1122 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 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 588 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 215 optimal weight: 0.9990 chunk 102 optimal weight: 20.0000 chunk 222 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 chunk 284 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3414 r_free = 0.3414 target = 0.127978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.100644 restraints weight = 30142.321| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.98 r_work: 0.2813 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.198 24929 Z= 0.233 Angle : 0.798 59.186 33962 Z= 0.441 Chirality : 0.053 1.179 3930 Planarity : 0.005 0.060 4338 Dihedral : 7.338 59.270 3954 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.94 % Favored : 93.99 % Rotamer: Outliers : 1.89 % Allowed : 12.39 % Favored : 85.72 % Cbeta Deviations : 0.03 % 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: -1.01 (0.15), residues: 3012 helix: 0.67 (0.21), residues: 645 sheet: 0.81 (0.20), residues: 684 loop : -1.97 (0.13), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 815 TYR 0.023 0.002 TYR C1067 PHE 0.020 0.002 PHE C 592 TRP 0.010 0.002 TRP B 353 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00552 (24863) covalent geometry : angle 0.77023 (33800) SS BOND : bond 0.00617 ( 36) SS BOND : angle 1.68808 ( 72) hydrogen bonds : bond 0.06917 ( 926) hydrogen bonds : angle 5.38528 ( 2607) link_NAG-ASN : bond 0.00466 ( 30) link_NAG-ASN : angle 3.91223 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5752.60 seconds wall clock time: 98 minutes 57.68 seconds (5937.68 seconds total)