Starting phenix.real_space_refine on Thu Mar 5 17:25:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lym_23595/03_2026/7lym_23595.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lym_23595/03_2026/7lym_23595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lym_23595/03_2026/7lym_23595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lym_23595/03_2026/7lym_23595.map" model { file = "/net/cci-nas-00/data/ceres_data/7lym_23595/03_2026/7lym_23595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lym_23595/03_2026/7lym_23595.cif" } resolution = 3.57 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= 0.052 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 102 5.16 5 C 15258 2.51 5 N 3936 2.21 5 O 4620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 23916 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7818 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 954} Chain breaks: 7 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 7819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7819 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 47, 'TRANS': 954} Chain breaks: 7 Chain: "C" Number of atoms: 7817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7817 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 47, 'TRANS': 954} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.49, per 1000 atoms: 0.23 Number of scatterers: 23916 At special positions: 0 Unit cell: (128.28, 133.625, 175.316, 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 102 16.00 O 4620 8.00 N 3936 7.00 C 15258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 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=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.01 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 657 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B 801 " " NAG B1312 " - " ASN B1074 " " NAG B1313 " - " ASN B1134 " " NAG B1314 " - " ASN B 122 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " 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: 2.03 Conformation dependent library (CDL) restraints added in 1.7 seconds 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 47 sheets defined 27.7% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.605A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.150A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.523A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.916A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.949A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.326A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 removed outlier: 4.012A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 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 941 removed outlier: 3.741A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.577A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (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 984 removed outlier: 3.876A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.058A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.696A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.799A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.479A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.891A 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: 3.648A 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 616 through 620 removed outlier: 3.508A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.011A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.705A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.000A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.579A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.691A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.769A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.236A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.687A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.073A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.126A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.905A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.810A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.206A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.534A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.066A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.336A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.537A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.516A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.090A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.649A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.982A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.754A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.608A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.306A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.553A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.888A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.383A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.133A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.779A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.093A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.597A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.597A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.447A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.920A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.679A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.618A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.777A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.277A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.237A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.549A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.973A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.761A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.630A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.401A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.922A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.793A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.633A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN C 125 " --> pdb=" O ASN C 122 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 318 removed outlier: 6.911A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.989A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.697A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.940A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.990A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.482A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1067 hydrogen bonds defined for protein. 2901 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.68 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6252 1.33 - 1.46: 4575 1.46 - 1.58: 13488 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 24441 Sorted by residual: bond pdb=" CA PRO A 792 " pdb=" C PRO A 792 " ideal model delta sigma weight residual 1.514 1.541 -0.027 5.50e-03 3.31e+04 2.44e+01 bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.543 -0.026 6.70e-03 2.23e+04 1.54e+01 bond pdb=" C5 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C5 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 24436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 27823 2.44 - 4.87: 5223 4.87 - 7.31: 201 7.31 - 9.75: 1 9.75 - 12.19: 1 Bond angle restraints: 33249 Sorted by residual: angle pdb=" CA ASP C 796 " pdb=" CB ASP C 796 " pdb=" CG ASP C 796 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" CA ASP C 737 " pdb=" CB ASP C 737 " pdb=" CG ASP C 737 " ideal model delta sigma weight residual 112.60 107.16 5.44 1.00e+00 1.00e+00 2.96e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 119.14 -5.34 1.00e+00 1.00e+00 2.85e+01 angle pdb=" OE1 GLN B1106 " pdb=" CD GLN B1106 " pdb=" NE2 GLN B1106 " ideal model delta sigma weight residual 122.60 117.38 5.22 1.00e+00 1.00e+00 2.73e+01 angle pdb=" OE1 GLN B1054 " pdb=" CD GLN B1054 " pdb=" NE2 GLN B1054 " ideal model delta sigma weight residual 122.60 117.79 4.81 1.00e+00 1.00e+00 2.31e+01 ... (remaining 33244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 13944 17.73 - 35.46: 801 35.46 - 53.20: 128 53.20 - 70.93: 55 70.93 - 88.66: 36 Dihedral angle restraints: 14964 sinusoidal: 6228 harmonic: 8736 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -163.32 77.32 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -143.93 57.93 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CA PHE B 133 " pdb=" C PHE B 133 " pdb=" N GLN B 134 " pdb=" CA GLN B 134 " ideal model delta harmonic sigma weight residual 180.00 150.46 29.54 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 14961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.278: 3877 0.278 - 0.556: 16 0.556 - 0.834: 0 0.834 - 1.111: 0 1.111 - 1.389: 1 Chirality restraints: 3894 Sorted by residual: chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.01 -1.39 2.00e-01 2.50e+01 4.82e+01 chirality pdb=" CA ASP B 745 " pdb=" N ASP B 745 " pdb=" C ASP B 745 " pdb=" CB ASP B 745 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA ASN A 487 " pdb=" N ASN A 487 " pdb=" C ASN A 487 " pdb=" CB ASN A 487 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 3891 not shown) Planarity restraints: 4287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 886 " 0.257 2.00e-02 2.50e+03 1.38e-01 4.78e+02 pdb=" CG TRP B 886 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP B 886 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 TRP B 886 " -0.128 2.00e-02 2.50e+03 pdb=" NE1 TRP B 886 " -0.100 2.00e-02 2.50e+03 pdb=" CE2 TRP B 886 " -0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP B 886 " -0.201 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 886 " 0.154 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 886 " -0.054 2.00e-02 2.50e+03 pdb=" CH2 TRP B 886 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " 0.122 2.00e-02 2.50e+03 1.22e-01 1.86e+02 pdb=" CG ASN B 709 " -0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " -0.174 2.00e-02 2.50e+03 pdb=" C1 NAG B1309 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 904 " 0.154 2.00e-02 2.50e+03 8.47e-02 1.44e+02 pdb=" CG TYR A 904 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 904 " -0.069 2.00e-02 2.50e+03 pdb=" CD2 TYR A 904 " -0.076 2.00e-02 2.50e+03 pdb=" CE1 TYR A 904 " -0.054 2.00e-02 2.50e+03 pdb=" CE2 TYR A 904 " -0.046 2.00e-02 2.50e+03 pdb=" CZ TYR A 904 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 904 " 0.129 2.00e-02 2.50e+03 ... (remaining 4284 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 12536 3.01 - 3.48: 23138 3.48 - 3.95: 39207 3.95 - 4.43: 43141 4.43 - 4.90: 73318 Nonbonded interactions: 191340 Sorted by model distance: nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.536 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.538 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.539 3.040 nonbonded pdb=" OG SER B 813 " pdb=" OE1 GLU B 868 " model vdw 2.546 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.557 3.040 ... (remaining 191335 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 479 or (resid 480 and (name N or name CA or nam \ e C or name O or name CB )) or resid 481 through 589 or (resid 590 and (name N o \ r name CA or name C or name O or name CB )) or resid 591 through 1308)) selection = (chain 'B' and (resid 27 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 479 or (resid 480 and (name N o \ r name CA or name C or name O or name CB )) or resid 481 through 589 or (resid 5 \ 90 and (name N or name CA or name C or name O or name CB )) or resid 591 through \ 1308)) selection = (chain 'C' and (resid 27 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 1308)) } 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 group one per residue 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.050 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.013 0.076 24510 Z= 0.757 Angle : 1.747 12.187 33420 Z= 1.164 Chirality : 0.097 1.389 3894 Planarity : 0.013 0.138 4254 Dihedral : 12.920 88.659 9234 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 0.04 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.27 % Favored : 94.35 % Rotamer: Outliers : 0.84 % Allowed : 1.95 % Favored : 97.21 % Cbeta Deviations : 0.07 % 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: -1.08 (0.14), residues: 2958 helix: -1.24 (0.16), residues: 688 sheet: 0.24 (0.21), residues: 540 loop : -0.76 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 577 TYR 0.154 0.020 TYR A 904 PHE 0.071 0.011 PHE C 718 TRP 0.257 0.029 TRP B 886 HIS 0.010 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.01318 (24441) covalent geometry : angle 1.73230 (33249) SS BOND : bond 0.00958 ( 36) SS BOND : angle 1.77180 ( 72) hydrogen bonds : bond 0.16644 ( 1049) hydrogen bonds : angle 8.82460 ( 2901) link_NAG-ASN : bond 0.01398 ( 33) link_NAG-ASN : angle 4.42609 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 302 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8655 (m-10) cc_final: 0.8388 (m-80) REVERT: A 353 TRP cc_start: 0.8606 (p-90) cc_final: 0.8074 (p-90) REVERT: A 405 ASP cc_start: 0.6515 (m-30) cc_final: 0.6141 (m-30) REVERT: A 449 TYR cc_start: 0.7508 (m-80) cc_final: 0.7170 (m-80) REVERT: A 458 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8134 (tmtt) REVERT: A 902 MET cc_start: 0.9012 (mmm) cc_final: 0.8727 (tpt) REVERT: A 988 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.6768 (pm20) REVERT: B 347 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7268 (t80) REVERT: B 547 THR cc_start: 0.8612 (p) cc_final: 0.8359 (t) REVERT: C 994 ASP cc_start: 0.7777 (t70) cc_final: 0.7402 (t0) REVERT: C 1047 TYR cc_start: 0.8892 (m-80) cc_final: 0.8673 (m-80) outliers start: 22 outliers final: 5 residues processed: 322 average time/residue: 0.1627 time to fit residues: 81.6748 Evaluate side-chains 136 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN B 388 ASN B 957 GLN C 321 GLN C 394 ASN C 540 ASN C 675 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.142380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.104598 restraints weight = 45626.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.107181 restraints weight = 27791.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.107167 restraints weight = 18358.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107495 restraints weight = 15085.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.107598 restraints weight = 13997.969| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24510 Z= 0.180 Angle : 0.694 11.719 33420 Z= 0.365 Chirality : 0.048 0.292 3894 Planarity : 0.004 0.038 4254 Dihedral : 6.988 59.773 3918 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.37 % Favored : 97.60 % Rotamer: Outliers : 1.64 % Allowed : 5.88 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.13 (0.15), residues: 2958 helix: 0.77 (0.20), residues: 669 sheet: 0.05 (0.19), residues: 649 loop : -0.45 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 214 TYR 0.020 0.002 TYR A1067 PHE 0.025 0.002 PHE A 92 TRP 0.020 0.002 TRP B 64 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00403 (24441) covalent geometry : angle 0.67069 (33249) SS BOND : bond 0.00396 ( 36) SS BOND : angle 2.05486 ( 72) hydrogen bonds : bond 0.05088 ( 1049) hydrogen bonds : angle 6.48474 ( 2901) link_NAG-ASN : bond 0.00287 ( 33) link_NAG-ASN : angle 2.89354 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.6489 (t80) cc_final: 0.6035 (t80) REVERT: A 449 TYR cc_start: 0.7611 (m-80) cc_final: 0.7336 (m-10) REVERT: A 458 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8229 (tttt) REVERT: A 512 VAL cc_start: 0.8921 (t) cc_final: 0.8684 (p) REVERT: A 979 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7390 (t0) REVERT: B 347 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7135 (t80) REVERT: C 505 TYR cc_start: 0.5746 (OUTLIER) cc_final: 0.5059 (m-80) REVERT: C 979 ASP cc_start: 0.7244 (m-30) cc_final: 0.6899 (t0) REVERT: C 1047 TYR cc_start: 0.8934 (m-80) cc_final: 0.8727 (m-80) outliers start: 43 outliers final: 23 residues processed: 184 average time/residue: 0.1605 time to fit residues: 46.9563 Evaluate side-chains 138 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 289 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 66 optimal weight: 0.0770 chunk 59 optimal weight: 0.9990 chunk 151 optimal weight: 0.3980 chunk 295 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 139 optimal weight: 20.0000 chunk 294 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 417 ASN C 762 GLN C 907 ASN C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.143603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.105802 restraints weight = 45215.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.107784 restraints weight = 30224.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.108434 restraints weight = 17194.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.109583 restraints weight = 14929.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.109533 restraints weight = 13150.343| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 24510 Z= 0.115 Angle : 0.580 8.928 33420 Z= 0.304 Chirality : 0.045 0.273 3894 Planarity : 0.003 0.037 4254 Dihedral : 6.217 56.282 3913 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.68 % Allowed : 6.61 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.19 (0.15), residues: 2958 helix: 1.33 (0.20), residues: 680 sheet: 0.13 (0.19), residues: 654 loop : -0.33 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 983 TYR 0.021 0.001 TYR A1067 PHE 0.028 0.001 PHE A 92 TRP 0.016 0.002 TRP C 353 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00243 (24441) covalent geometry : angle 0.56243 (33249) SS BOND : bond 0.00276 ( 36) SS BOND : angle 1.62353 ( 72) hydrogen bonds : bond 0.04141 ( 1049) hydrogen bonds : angle 5.84681 ( 2901) link_NAG-ASN : bond 0.00261 ( 33) link_NAG-ASN : angle 2.33388 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.7608 (m-80) cc_final: 0.7357 (m-10) REVERT: A 458 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8089 (tmtt) REVERT: A 979 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7530 (t0) REVERT: B 347 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.6992 (t80) REVERT: B 902 MET cc_start: 0.8830 (tpt) cc_final: 0.8465 (tpt) REVERT: C 167 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8442 (t) REVERT: C 505 TYR cc_start: 0.5514 (OUTLIER) cc_final: 0.4906 (m-80) REVERT: C 979 ASP cc_start: 0.7269 (m-30) cc_final: 0.6841 (t0) REVERT: C 1047 TYR cc_start: 0.8934 (m-80) cc_final: 0.8724 (m-80) outliers start: 44 outliers final: 24 residues processed: 172 average time/residue: 0.1420 time to fit residues: 40.5341 Evaluate side-chains 141 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 71 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 216 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 195 optimal weight: 2.9990 chunk 250 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 213 optimal weight: 7.9990 chunk 239 optimal weight: 0.0010 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.140675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.102488 restraints weight = 45212.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.104736 restraints weight = 31647.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.104999 restraints weight = 19365.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.105408 restraints weight = 16083.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.105471 restraints weight = 15080.682| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24510 Z= 0.200 Angle : 0.620 13.240 33420 Z= 0.320 Chirality : 0.046 0.295 3894 Planarity : 0.004 0.049 4254 Dihedral : 6.137 56.592 3913 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.02 % Allowed : 7.41 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.15), residues: 2958 helix: 1.31 (0.20), residues: 672 sheet: -0.09 (0.19), residues: 698 loop : -0.39 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 408 TYR 0.022 0.001 TYR B1067 PHE 0.025 0.002 PHE C 140 TRP 0.015 0.002 TRP C 436 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00478 (24441) covalent geometry : angle 0.59914 (33249) SS BOND : bond 0.00335 ( 36) SS BOND : angle 2.42457 ( 72) hydrogen bonds : bond 0.04288 ( 1049) hydrogen bonds : angle 5.86907 ( 2901) link_NAG-ASN : bond 0.00239 ( 33) link_NAG-ASN : angle 2.24108 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 116 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7928 (tp-100) cc_final: 0.7679 (tp-100) REVERT: A 449 TYR cc_start: 0.7556 (m-80) cc_final: 0.7189 (m-10) REVERT: A 458 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8017 (tmtt) REVERT: B 347 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7005 (t80) REVERT: B 979 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7598 (t0) REVERT: C 212 LEU cc_start: 0.7845 (tp) cc_final: 0.7483 (tt) REVERT: C 505 TYR cc_start: 0.5305 (OUTLIER) cc_final: 0.4637 (m-80) REVERT: C 979 ASP cc_start: 0.7447 (m-30) cc_final: 0.7049 (t0) REVERT: C 1047 TYR cc_start: 0.9000 (m-80) cc_final: 0.8791 (m-80) outliers start: 53 outliers final: 37 residues processed: 158 average time/residue: 0.1424 time to fit residues: 38.0065 Evaluate side-chains 149 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 216 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 293 optimal weight: 0.0020 chunk 284 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 6 optimal weight: 30.0000 chunk 86 optimal weight: 0.7980 chunk 241 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 232 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN C 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.141590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.103435 restraints weight = 44879.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.105727 restraints weight = 30486.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.106193 restraints weight = 17270.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.106679 restraints weight = 15231.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.106641 restraints weight = 14152.266| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 24510 Z= 0.145 Angle : 0.573 11.139 33420 Z= 0.295 Chirality : 0.045 0.281 3894 Planarity : 0.003 0.042 4254 Dihedral : 5.900 55.135 3913 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.91 % Allowed : 8.09 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.15 (0.15), residues: 2958 helix: 1.53 (0.21), residues: 666 sheet: 0.03 (0.19), residues: 705 loop : -0.44 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.021 0.001 TYR A1067 PHE 0.025 0.001 PHE C 140 TRP 0.022 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00341 (24441) covalent geometry : angle 0.55223 (33249) SS BOND : bond 0.00290 ( 36) SS BOND : angle 2.35958 ( 72) hydrogen bonds : bond 0.04000 ( 1049) hydrogen bonds : angle 5.67461 ( 2901) link_NAG-ASN : bond 0.00181 ( 33) link_NAG-ASN : angle 2.04845 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.7665 (m-80) cc_final: 0.7247 (m-10) REVERT: A 458 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8017 (tmtt) REVERT: B 347 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.6936 (t80) REVERT: B 902 MET cc_start: 0.8890 (tpt) cc_final: 0.8411 (tpt) REVERT: C 493 GLN cc_start: 0.5183 (OUTLIER) cc_final: 0.3484 (mp10) REVERT: C 505 TYR cc_start: 0.5325 (OUTLIER) cc_final: 0.4726 (m-80) REVERT: C 979 ASP cc_start: 0.7417 (m-30) cc_final: 0.7110 (t0) outliers start: 50 outliers final: 33 residues processed: 166 average time/residue: 0.1369 time to fit residues: 38.2976 Evaluate side-chains 145 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 282 optimal weight: 4.9990 chunk 233 optimal weight: 7.9990 chunk 5 optimal weight: 30.0000 chunk 288 optimal weight: 0.8980 chunk 294 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 151 optimal weight: 0.0170 chunk 125 optimal weight: 9.9990 chunk 189 optimal weight: 0.4980 chunk 197 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 481 ASN C 907 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.143598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.106590 restraints weight = 45653.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.109424 restraints weight = 29637.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.109652 restraints weight = 17081.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.109887 restraints weight = 15306.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.109975 restraints weight = 14090.057| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 24510 Z= 0.109 Angle : 0.544 12.956 33420 Z= 0.282 Chirality : 0.044 0.269 3894 Planarity : 0.003 0.040 4254 Dihedral : 5.675 54.575 3913 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.87 % Allowed : 8.36 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.32 (0.15), residues: 2958 helix: 1.73 (0.21), residues: 672 sheet: 0.15 (0.19), residues: 693 loop : -0.37 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 408 TYR 0.020 0.001 TYR A1067 PHE 0.026 0.001 PHE C 140 TRP 0.021 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00247 (24441) covalent geometry : angle 0.52469 (33249) SS BOND : bond 0.00327 ( 36) SS BOND : angle 2.39687 ( 72) hydrogen bonds : bond 0.03677 ( 1049) hydrogen bonds : angle 5.49197 ( 2901) link_NAG-ASN : bond 0.00197 ( 33) link_NAG-ASN : angle 1.85444 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7476 (tp40) REVERT: A 449 TYR cc_start: 0.7547 (m-80) cc_final: 0.7130 (m-10) REVERT: A 458 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8001 (tmtt) REVERT: B 347 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.6862 (t80) REVERT: B 902 MET cc_start: 0.8766 (tpt) cc_final: 0.8336 (tpt) REVERT: B 1141 LEU cc_start: 0.8907 (tp) cc_final: 0.8628 (tt) REVERT: C 96 GLU cc_start: 0.4893 (OUTLIER) cc_final: 0.4568 (tp30) REVERT: C 493 GLN cc_start: 0.5416 (OUTLIER) cc_final: 0.3681 (mp10) REVERT: C 505 TYR cc_start: 0.5110 (OUTLIER) cc_final: 0.4520 (m-80) REVERT: C 515 PHE cc_start: 0.7995 (m-80) cc_final: 0.7703 (m-80) REVERT: C 900 MET cc_start: 0.8179 (mtp) cc_final: 0.7843 (mtm) outliers start: 49 outliers final: 34 residues processed: 165 average time/residue: 0.1421 time to fit residues: 39.4511 Evaluate side-chains 149 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 109 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 227 optimal weight: 0.1980 chunk 17 optimal weight: 30.0000 chunk 94 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 56 optimal weight: 8.9990 chunk 293 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.142020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.104410 restraints weight = 45565.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.106514 restraints weight = 29356.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.106805 restraints weight = 18583.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107261 restraints weight = 16951.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.107395 restraints weight = 14516.744| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24510 Z= 0.164 Angle : 0.561 10.773 33420 Z= 0.290 Chirality : 0.045 0.281 3894 Planarity : 0.003 0.039 4254 Dihedral : 5.662 55.284 3913 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.79 % Allowed : 9.13 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.21 (0.15), residues: 2958 helix: 1.64 (0.21), residues: 676 sheet: 0.05 (0.19), residues: 696 loop : -0.43 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 408 TYR 0.021 0.001 TYR B1067 PHE 0.027 0.001 PHE C 140 TRP 0.021 0.001 TRP C 436 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00391 (24441) covalent geometry : angle 0.54428 (33249) SS BOND : bond 0.00369 ( 36) SS BOND : angle 2.09664 ( 72) hydrogen bonds : bond 0.03854 ( 1049) hydrogen bonds : angle 5.51574 ( 2901) link_NAG-ASN : bond 0.00181 ( 33) link_NAG-ASN : angle 1.86993 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 112 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.7598 (m-80) cc_final: 0.7190 (m-10) REVERT: A 458 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8020 (tmtt) REVERT: B 347 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.6801 (t80) REVERT: B 1141 LEU cc_start: 0.8857 (tp) cc_final: 0.8560 (tt) REVERT: C 493 GLN cc_start: 0.5257 (OUTLIER) cc_final: 0.3553 (mp10) REVERT: C 505 TYR cc_start: 0.5191 (OUTLIER) cc_final: 0.4613 (m-80) REVERT: C 515 PHE cc_start: 0.8032 (m-80) cc_final: 0.7673 (m-80) REVERT: C 979 ASP cc_start: 0.7152 (t0) cc_final: 0.6813 (t0) outliers start: 47 outliers final: 38 residues processed: 152 average time/residue: 0.1379 time to fit residues: 35.4629 Evaluate side-chains 149 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 107 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 192 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 268 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 262 optimal weight: 0.5980 chunk 46 optimal weight: 8.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 481 ASN B 245 HIS B 394 ASN B 965 GLN C 907 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.140959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.099430 restraints weight = 44609.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.100346 restraints weight = 27379.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.101006 restraints weight = 18614.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.102467 restraints weight = 16095.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.102566 restraints weight = 13001.981| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 24510 Z= 0.235 Angle : 0.610 9.931 33420 Z= 0.315 Chirality : 0.046 0.303 3894 Planarity : 0.004 0.039 4254 Dihedral : 5.843 56.356 3913 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.02 % Allowed : 9.32 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.15), residues: 2958 helix: 1.47 (0.21), residues: 675 sheet: -0.03 (0.19), residues: 695 loop : -0.51 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 408 TYR 0.023 0.001 TYR B1067 PHE 0.028 0.002 PHE C 140 TRP 0.022 0.002 TRP C 436 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00566 (24441) covalent geometry : angle 0.59407 (33249) SS BOND : bond 0.00372 ( 36) SS BOND : angle 2.14028 ( 72) hydrogen bonds : bond 0.04228 ( 1049) hydrogen bonds : angle 5.65320 ( 2901) link_NAG-ASN : bond 0.00240 ( 33) link_NAG-ASN : angle 1.97512 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 104 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8101 (tp-100) cc_final: 0.7604 (tp40) REVERT: A 92 PHE cc_start: 0.7568 (t80) cc_final: 0.7316 (t80) REVERT: A 458 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8110 (tmtt) REVERT: B 347 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.6730 (t80) REVERT: B 979 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7393 (t0) REVERT: B 1141 LEU cc_start: 0.8868 (tp) cc_final: 0.8566 (tt) REVERT: C 493 GLN cc_start: 0.4973 (OUTLIER) cc_final: 0.3380 (mp10) REVERT: C 505 TYR cc_start: 0.5486 (OUTLIER) cc_final: 0.4859 (m-80) REVERT: C 515 PHE cc_start: 0.8117 (m-80) cc_final: 0.7718 (m-80) REVERT: C 900 MET cc_start: 0.8361 (mtp) cc_final: 0.8045 (mtm) outliers start: 53 outliers final: 41 residues processed: 149 average time/residue: 0.1436 time to fit residues: 36.2199 Evaluate side-chains 144 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 98 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 293 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 194 optimal weight: 0.4980 chunk 263 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 229 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 204 optimal weight: 0.6980 chunk 5 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN B 394 ASN C 69 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.142114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.104062 restraints weight = 45139.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.105621 restraints weight = 32768.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.106319 restraints weight = 18715.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.107297 restraints weight = 15768.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.107271 restraints weight = 14168.658| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24510 Z= 0.113 Angle : 0.546 10.270 33420 Z= 0.282 Chirality : 0.044 0.275 3894 Planarity : 0.003 0.040 4254 Dihedral : 5.648 55.520 3913 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.83 % Allowed : 9.85 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.24 (0.15), residues: 2958 helix: 1.75 (0.21), residues: 676 sheet: 0.05 (0.19), residues: 682 loop : -0.45 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 408 TYR 0.021 0.001 TYR A1067 PHE 0.039 0.001 PHE A 497 TRP 0.021 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00254 (24441) covalent geometry : angle 0.53125 (33249) SS BOND : bond 0.00358 ( 36) SS BOND : angle 1.89461 ( 72) hydrogen bonds : bond 0.03725 ( 1049) hydrogen bonds : angle 5.43779 ( 2901) link_NAG-ASN : bond 0.00233 ( 33) link_NAG-ASN : angle 1.79090 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 115 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8056 (tp-100) cc_final: 0.7570 (tp40) REVERT: A 92 PHE cc_start: 0.7330 (t80) cc_final: 0.7049 (t80) REVERT: A 458 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8091 (tmtt) REVERT: A 643 PHE cc_start: 0.7105 (t80) cc_final: 0.6766 (t80) REVERT: B 394 ASN cc_start: 0.7493 (OUTLIER) cc_final: 0.7240 (m-40) REVERT: B 902 MET cc_start: 0.8858 (tpt) cc_final: 0.8475 (tpt) REVERT: B 1141 LEU cc_start: 0.8824 (tp) cc_final: 0.8526 (tt) REVERT: C 493 GLN cc_start: 0.5329 (OUTLIER) cc_final: 0.3718 (mp10) REVERT: C 505 TYR cc_start: 0.5374 (OUTLIER) cc_final: 0.4746 (m-80) REVERT: C 515 PHE cc_start: 0.8047 (m-80) cc_final: 0.7725 (m-80) REVERT: C 900 MET cc_start: 0.8258 (mtp) cc_final: 0.7907 (mtm) REVERT: C 979 ASP cc_start: 0.7027 (t0) cc_final: 0.6809 (t0) outliers start: 48 outliers final: 36 residues processed: 156 average time/residue: 0.1478 time to fit residues: 37.8161 Evaluate side-chains 145 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 105 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 155 optimal weight: 0.8980 chunk 122 optimal weight: 0.0470 chunk 83 optimal weight: 0.9990 chunk 213 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN B 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.141149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.103804 restraints weight = 45769.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.105621 restraints weight = 27318.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.105947 restraints weight = 18151.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.106306 restraints weight = 16340.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.106350 restraints weight = 14790.715| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24510 Z= 0.156 Angle : 0.558 8.966 33420 Z= 0.288 Chirality : 0.045 0.282 3894 Planarity : 0.003 0.040 4254 Dihedral : 5.567 55.326 3911 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.57 % Allowed : 10.42 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.19 (0.15), residues: 2958 helix: 1.69 (0.21), residues: 676 sheet: 0.04 (0.19), residues: 682 loop : -0.47 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 408 TYR 0.022 0.001 TYR B1067 PHE 0.048 0.001 PHE A 497 TRP 0.021 0.001 TRP C 436 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00370 (24441) covalent geometry : angle 0.54350 (33249) SS BOND : bond 0.00346 ( 36) SS BOND : angle 1.91145 ( 72) hydrogen bonds : bond 0.03827 ( 1049) hydrogen bonds : angle 5.44189 ( 2901) link_NAG-ASN : bond 0.00195 ( 33) link_NAG-ASN : angle 1.80089 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7953 (tp-100) cc_final: 0.7353 (tp40) REVERT: A 458 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8089 (tmtt) REVERT: B 902 MET cc_start: 0.8959 (tpt) cc_final: 0.8509 (tpt) REVERT: B 1141 LEU cc_start: 0.8831 (tp) cc_final: 0.8531 (tt) REVERT: C 493 GLN cc_start: 0.5503 (OUTLIER) cc_final: 0.3830 (mp10) REVERT: C 505 TYR cc_start: 0.5253 (OUTLIER) cc_final: 0.4609 (m-80) REVERT: C 515 PHE cc_start: 0.8064 (m-80) cc_final: 0.7776 (m-80) REVERT: C 900 MET cc_start: 0.8274 (mtp) cc_final: 0.7897 (mtm) REVERT: C 979 ASP cc_start: 0.7177 (t0) cc_final: 0.6971 (t0) outliers start: 41 outliers final: 35 residues processed: 142 average time/residue: 0.1317 time to fit residues: 31.8245 Evaluate side-chains 140 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 106 optimal weight: 0.2980 chunk 113 optimal weight: 3.9990 chunk 228 optimal weight: 0.0870 chunk 204 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 15 optimal weight: 30.0000 chunk 74 optimal weight: 0.0870 overall best weight: 0.4940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.140907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.102695 restraints weight = 44973.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.104915 restraints weight = 31604.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.105328 restraints weight = 18218.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.105985 restraints weight = 15964.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.106084 restraints weight = 14777.041| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.292 24510 Z= 0.185 Angle : 0.723 59.184 33420 Z= 0.409 Chirality : 0.044 0.281 3894 Planarity : 0.004 0.072 4254 Dihedral : 5.579 55.329 3911 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.57 % Allowed : 10.46 % Favored : 87.97 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.20 (0.15), residues: 2958 helix: 1.70 (0.21), residues: 676 sheet: 0.03 (0.19), residues: 683 loop : -0.47 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.000 ARG A1107 TYR 0.114 0.001 TYR B 904 PHE 0.039 0.001 PHE A 497 TRP 0.021 0.001 TRP C 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00414 (24441) covalent geometry : angle 0.71328 (33249) SS BOND : bond 0.00353 ( 36) SS BOND : angle 1.86350 ( 72) hydrogen bonds : bond 0.03787 ( 1049) hydrogen bonds : angle 5.44224 ( 2901) link_NAG-ASN : bond 0.00194 ( 33) link_NAG-ASN : angle 1.80195 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3168.43 seconds wall clock time: 55 minutes 53.80 seconds (3353.80 seconds total)