Starting phenix.real_space_refine on Fri May 23 15:04:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xm5_38463/05_2025/8xm5_38463.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xm5_38463/05_2025/8xm5_38463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xm5_38463/05_2025/8xm5_38463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xm5_38463/05_2025/8xm5_38463.map" model { file = "/net/cci-nas-00/data/ceres_data/8xm5_38463/05_2025/8xm5_38463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xm5_38463/05_2025/8xm5_38463.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.018 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 108 5.16 5 C 15476 2.51 5 N 4001 2.21 5 O 4641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24226 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 7992 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 55, 'TRANS': 965} Chain breaks: 7 Chain: "B" Number of atoms: 7894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7894 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 55, 'TRANS': 952} Chain breaks: 9 Chain: "C" Number of atoms: 7962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7962 Classifications: {'peptide': 1018} Link IDs: {'PTRANS': 55, 'TRANS': 962} Chain breaks: 8 Chain: "A" 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 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 16.28, per 1000 atoms: 0.67 Number of scatterers: 24226 At special positions: 0 Unit cell: (133.32, 134.936, 166.448, 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 108 16.00 O 4641 8.00 N 4001 7.00 C 15476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 717 " " NAG A1308 " - " ASN A 801 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A 61 " " NAG A1311 " - " ASN A1134 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B1134 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B 61 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C1134 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 717 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C 61 " Time building additional restraints: 5.93 Conformation dependent library (CDL) restraints added in 3.1 seconds 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5726 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 45 sheets defined 23.8% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.892A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.643A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.950A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.724A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.059A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.769A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (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 966 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.707A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.554A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.024A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.645A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) 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 966 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.609A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.625A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.197A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.512A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.820A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 852 through 856 removed outlier: 3.578A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.816A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.592A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (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 982 Processing helix chain 'C' and resid 985 through 1032 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 30 removed outlier: 7.941A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS A 69 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY A 261 " --> pdb=" O HIS A 69 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.810A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.023A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.539A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 135 removed outlier: 7.533A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.857A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.150A 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: 3.503A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.965A 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 removed outlier: 3.624A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.784A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.784A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.434A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.756A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB8, first strand: chain 'B' and resid 23 through 30 Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.560A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.662A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 224 through 227 removed outlier: 6.668A pdb=" N SER B 205 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 134 through 135 removed outlier: 7.598A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.471A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.067A 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 327 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: 6.813A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.366A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.534A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.534A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (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 1121 Processing sheet with id=AD6, first strand: chain 'C' and resid 23 through 30 removed outlier: 7.805A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.928A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 169 through 172 removed outlier: 5.621A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 206 through 207 removed outlier: 3.869A pdb=" N HIS C 207 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.841A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.829A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 4.050A pdb=" N CYS C 525 " --> pdb=" O CYS C 361 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.592A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.638A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.638A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.381A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1121 995 hydrogen bonds defined for protein. 2778 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: 11.30 Time building geometry restraints manager: 6.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4210 1.32 - 1.45: 6792 1.45 - 1.58: 13646 1.58 - 1.70: 0 1.70 - 1.83: 135 Bond restraints: 24783 Sorted by residual: bond pdb=" C PRO C 230 " pdb=" O PRO C 230 " ideal model delta sigma weight residual 1.233 1.203 0.030 9.60e-03 1.09e+04 9.55e+00 bond pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.29e+00 bond pdb=" N LEU B 441 " pdb=" CA LEU B 441 " ideal model delta sigma weight residual 1.459 1.493 -0.035 1.22e-02 6.72e+03 8.04e+00 bond pdb=" C PRO C 209 " pdb=" O PRO C 209 " ideal model delta sigma weight residual 1.233 1.198 0.035 1.23e-02 6.61e+03 8.01e+00 bond pdb=" N GLU B 213 " pdb=" CA GLU B 213 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.31e-02 5.83e+03 7.81e+00 ... (remaining 24778 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 33132 2.14 - 4.27: 547 4.27 - 6.41: 37 6.41 - 8.54: 4 8.54 - 10.68: 4 Bond angle restraints: 33724 Sorted by residual: angle pdb=" C VAL A 524 " pdb=" N CYS A 525 " pdb=" CA CYS A 525 " ideal model delta sigma weight residual 121.64 110.96 10.68 1.20e+00 6.94e-01 7.92e+01 angle pdb=" C ILE B 231 " pdb=" CA ILE B 231 " pdb=" CB ILE B 231 " ideal model delta sigma weight residual 111.45 102.72 8.73 1.12e+00 7.97e-01 6.08e+01 angle pdb=" CA ASN A 122 " pdb=" CB ASN A 122 " pdb=" CG ASN A 122 " ideal model delta sigma weight residual 112.60 118.94 -6.34 1.00e+00 1.00e+00 4.02e+01 angle pdb=" CA PHE A 562 " pdb=" CB PHE A 562 " pdb=" CG PHE A 562 " ideal model delta sigma weight residual 113.80 119.85 -6.05 1.00e+00 1.00e+00 3.66e+01 angle pdb=" C PRO A 561 " pdb=" CA PRO A 561 " pdb=" CB PRO A 561 " ideal model delta sigma weight residual 112.26 121.21 -8.95 1.67e+00 3.59e-01 2.87e+01 ... (remaining 33719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 13861 17.80 - 35.60: 1048 35.60 - 53.40: 178 53.40 - 71.20: 38 71.20 - 89.00: 24 Dihedral angle restraints: 15149 sinusoidal: 6266 harmonic: 8883 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 0.99 -86.99 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 16.57 76.43 1 1.00e+01 1.00e-02 7.35e+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 -19.65 -66.35 1 1.00e+01 1.00e-02 5.75e+01 ... (remaining 15146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.204: 3892 0.204 - 0.408: 17 0.408 - 0.611: 2 0.611 - 0.815: 1 0.815 - 1.019: 1 Chirality restraints: 3913 Sorted by residual: chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 717 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-01 2.50e+01 2.59e+01 chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CA PRO A 561 " pdb=" N PRO A 561 " pdb=" C PRO A 561 " pdb=" CB PRO A 561 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.67e+00 ... (remaining 3910 not shown) Planarity restraints: 4348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1303 " 0.349 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG A1303 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A1303 " 0.104 2.00e-02 2.50e+03 pdb=" N2 NAG A1303 " -0.536 2.00e-02 2.50e+03 pdb=" O7 NAG A1303 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1310 " -0.336 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG A1310 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1310 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG A1310 " 0.510 2.00e-02 2.50e+03 pdb=" O7 NAG A1310 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " -0.284 2.00e-02 2.50e+03 2.38e-01 7.09e+02 pdb=" C7 NAG A1304 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " 0.404 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " -0.011 2.00e-02 2.50e+03 ... (remaining 4345 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 204 2.60 - 3.18: 20269 3.18 - 3.75: 36443 3.75 - 4.33: 51715 4.33 - 4.90: 85216 Nonbonded interactions: 193847 Sorted by model distance: nonbonded pdb=" O THR B 124 " pdb=" OD1 ASN B 125 " model vdw 2.026 3.040 nonbonded pdb=" O THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.055 3.040 nonbonded pdb=" O THR C 124 " pdb=" OD1 ASN C 125 " model vdw 2.129 3.040 nonbonded pdb=" ND2 ASN B 20 " pdb=" OD1 ASN B 137 " model vdw 2.204 3.120 nonbonded pdb=" OG SER C 884 " pdb=" OG1 THR C 887 " model vdw 2.213 3.040 ... (remaining 193842 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 19 through 197 or resid 201 through 210 or resid 216 throu \ gh 243 or resid 264 through 330 or resid 332 through 620 or resid 641 through 67 \ 6 or resid 691 through 1139 or resid 1301 through 1307)) selection = (chain 'B' and (resid 19 through 210 or resid 216 through 676 or resid 691 throu \ gh 826 or resid 855 through 1139 or resid 1301 through 1307)) selection = (chain 'C' and (resid 19 through 197 or resid 201 through 243 or resid 264 throu \ gh 330 or resid 332 through 676 or resid 691 through 826 or resid 855 through 11 \ 39 or resid 1301 through 1307)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.060 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 58.600 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.100 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:14.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24847 Z= 0.213 Angle : 0.674 16.371 33879 Z= 0.385 Chirality : 0.054 1.019 3913 Planarity : 0.010 0.302 4321 Dihedral : 12.960 89.003 9312 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.34 % Favored : 95.56 % Rotamer: Outliers : 0.11 % Allowed : 0.60 % Favored : 99.29 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 2993 helix: 1.81 (0.21), residues: 641 sheet: 0.30 (0.19), residues: 656 loop : -0.66 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 886 HIS 0.003 0.001 HIS C 66 PHE 0.029 0.001 PHE A 562 TYR 0.021 0.001 TYR A 904 ARG 0.004 0.000 ARG C 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00842 ( 27) link_NAG-ASN : angle 4.31023 ( 81) hydrogen bonds : bond 0.13949 ( 959) hydrogen bonds : angle 7.26876 ( 2778) SS BOND : bond 0.00313 ( 37) SS BOND : angle 1.47527 ( 74) covalent geometry : bond 0.00389 (24783) covalent geometry : angle 0.63841 (33724) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 700 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8413 (m-80) cc_final: 0.8101 (m-80) REVERT: A 294 ASP cc_start: 0.7760 (p0) cc_final: 0.7558 (p0) REVERT: A 555 SER cc_start: 0.8644 (t) cc_final: 0.8380 (p) REVERT: A 574 ASP cc_start: 0.7181 (t70) cc_final: 0.6773 (t0) REVERT: A 583 GLU cc_start: 0.6404 (pm20) cc_final: 0.6006 (pm20) REVERT: A 737 ASP cc_start: 0.7532 (t0) cc_final: 0.7224 (t0) REVERT: A 994 ASP cc_start: 0.7634 (m-30) cc_final: 0.7343 (m-30) REVERT: A 1041 ASP cc_start: 0.7797 (m-30) cc_final: 0.7115 (m-30) REVERT: A 1045 LYS cc_start: 0.7800 (mmtm) cc_final: 0.7297 (mmtm) REVERT: A 1138 TYR cc_start: 0.7894 (t80) cc_final: 0.7666 (t80) REVERT: B 129 LYS cc_start: 0.7990 (mtmm) cc_final: 0.7774 (mtmm) REVERT: B 231 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7776 (pt) REVERT: B 512 VAL cc_start: 0.8086 (t) cc_final: 0.7817 (p) REVERT: B 543 PHE cc_start: 0.7059 (m-10) cc_final: 0.6232 (m-80) REVERT: B 607 GLN cc_start: 0.8359 (mt0) cc_final: 0.8139 (mt0) REVERT: B 745 ASP cc_start: 0.7393 (t0) cc_final: 0.7142 (t0) REVERT: B 790 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8131 (mtmt) REVERT: B 808 ASP cc_start: 0.7643 (t70) cc_final: 0.7344 (t0) REVERT: B 868 GLU cc_start: 0.7528 (mp0) cc_final: 0.7286 (mp0) REVERT: B 981 LEU cc_start: 0.7473 (mt) cc_final: 0.7261 (mm) REVERT: B 1010 GLN cc_start: 0.7662 (tp40) cc_final: 0.7438 (tp40) REVERT: B 1014 ARG cc_start: 0.7910 (ttm110) cc_final: 0.7439 (mtm180) REVERT: B 1031 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7670 (mt-10) REVERT: C 65 PHE cc_start: 0.8004 (m-10) cc_final: 0.7779 (m-80) REVERT: C 113 LYS cc_start: 0.7513 (tmtt) cc_final: 0.7255 (tmtt) REVERT: C 203 ILE cc_start: 0.7497 (tt) cc_final: 0.5780 (tp) REVERT: C 207 HIS cc_start: 0.6686 (m170) cc_final: 0.6354 (m170) REVERT: C 237 ARG cc_start: 0.7995 (mtp180) cc_final: 0.7731 (mtp180) REVERT: C 307 THR cc_start: 0.8594 (t) cc_final: 0.8305 (m) REVERT: C 574 ASP cc_start: 0.6944 (m-30) cc_final: 0.6686 (m-30) REVERT: C 583 GLU cc_start: 0.7348 (tp30) cc_final: 0.7120 (tp30) REVERT: C 735 SER cc_start: 0.8536 (p) cc_final: 0.8331 (p) REVERT: C 814 LYS cc_start: 0.7991 (mmtm) cc_final: 0.7685 (mmtm) REVERT: C 819 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7742 (tt0) REVERT: C 858 LEU cc_start: 0.8743 (mt) cc_final: 0.8524 (mt) REVERT: C 868 GLU cc_start: 0.7346 (mp0) cc_final: 0.7074 (mp0) REVERT: C 1017 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7012 (mm-30) REVERT: C 1094 VAL cc_start: 0.8465 (m) cc_final: 0.8219 (p) outliers start: 3 outliers final: 5 residues processed: 703 average time/residue: 1.2572 time to fit residues: 1021.6728 Evaluate side-chains 568 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 562 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 122 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 1.9990 chunk 229 optimal weight: 0.0370 chunk 127 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 122 optimal weight: 0.4980 chunk 237 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 144 optimal weight: 0.0010 chunk 176 optimal weight: 0.8980 chunk 275 optimal weight: 1.9990 overall best weight: 0.4464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 762 GLN A 779 GLN A 804 GLN A 824 ASN A 949 GLN A 955 ASN B 314 GLN B 422 ASN B 755 GLN B 787 GLN B 907 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 317 ASN C 360 ASN C 751 ASN C 777 ASN C 872 GLN C 907 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.167107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.140557 restraints weight = 34240.874| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.10 r_work: 0.3743 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 24847 Z= 0.156 Angle : 0.624 13.395 33879 Z= 0.323 Chirality : 0.047 0.319 3913 Planarity : 0.005 0.055 4321 Dihedral : 6.483 59.020 3836 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.73 % Allowed : 9.93 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 2993 helix: 2.40 (0.20), residues: 643 sheet: 0.34 (0.19), residues: 683 loop : -0.66 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.005 0.001 HIS C 207 PHE 0.018 0.001 PHE B 342 TYR 0.019 0.001 TYR B1067 ARG 0.007 0.001 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 27) link_NAG-ASN : angle 2.41575 ( 81) hydrogen bonds : bond 0.05056 ( 959) hydrogen bonds : angle 5.79071 ( 2778) SS BOND : bond 0.00621 ( 37) SS BOND : angle 2.93309 ( 74) covalent geometry : bond 0.00361 (24783) covalent geometry : angle 0.59827 (33724) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 556 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8450 (m-80) cc_final: 0.8167 (m-80) REVERT: A 555 SER cc_start: 0.8578 (t) cc_final: 0.8262 (p) REVERT: A 574 ASP cc_start: 0.7473 (t70) cc_final: 0.7100 (t0) REVERT: A 933 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8273 (mtmm) REVERT: A 990 GLU cc_start: 0.6567 (mm-30) cc_final: 0.6340 (tp30) REVERT: A 994 ASP cc_start: 0.7548 (m-30) cc_final: 0.7284 (m-30) REVERT: A 1041 ASP cc_start: 0.8078 (m-30) cc_final: 0.7262 (m-30) REVERT: A 1045 LYS cc_start: 0.8070 (mmtm) cc_final: 0.7496 (mmtm) REVERT: A 1138 TYR cc_start: 0.7904 (t80) cc_final: 0.7697 (t80) REVERT: B 511 VAL cc_start: 0.8053 (t) cc_final: 0.7767 (p) REVERT: B 512 VAL cc_start: 0.8129 (t) cc_final: 0.7880 (p) REVERT: B 583 GLU cc_start: 0.6141 (tm-30) cc_final: 0.5910 (tm-30) REVERT: B 607 GLN cc_start: 0.8729 (mt0) cc_final: 0.8501 (mt0) REVERT: B 791 THR cc_start: 0.8673 (m) cc_final: 0.8450 (p) REVERT: B 808 ASP cc_start: 0.8032 (t70) cc_final: 0.7700 (t0) REVERT: B 868 GLU cc_start: 0.7751 (mp0) cc_final: 0.7496 (mp0) REVERT: B 900 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8261 (mtt) REVERT: B 1010 GLN cc_start: 0.7948 (tp40) cc_final: 0.7711 (tp40) REVERT: B 1014 ARG cc_start: 0.8262 (ttm110) cc_final: 0.7855 (mtm180) REVERT: B 1031 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7571 (mt-10) REVERT: B 1072 GLU cc_start: 0.8342 (pm20) cc_final: 0.8016 (pm20) REVERT: C 113 LYS cc_start: 0.7544 (tmtt) cc_final: 0.7298 (tmtt) REVERT: C 191 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6713 (tm-30) REVERT: C 202 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8076 (mttm) REVERT: C 203 ILE cc_start: 0.7372 (tt) cc_final: 0.5822 (tp) REVERT: C 237 ARG cc_start: 0.8245 (mtp180) cc_final: 0.7932 (mtp180) REVERT: C 583 GLU cc_start: 0.7561 (tp30) cc_final: 0.7327 (tp30) REVERT: C 747 THR cc_start: 0.8149 (p) cc_final: 0.7941 (t) REVERT: C 814 LYS cc_start: 0.8067 (mmtm) cc_final: 0.7850 (mppt) REVERT: C 819 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7783 (mt-10) REVERT: C 858 LEU cc_start: 0.8714 (mt) cc_final: 0.8498 (mt) REVERT: C 868 GLU cc_start: 0.7801 (mp0) cc_final: 0.7542 (mp0) REVERT: C 900 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8251 (mtp) REVERT: C 918 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7643 (mt-10) REVERT: C 1010 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7659 (mp10) REVERT: C 1017 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7493 (mm-30) outliers start: 73 outliers final: 35 residues processed: 581 average time/residue: 1.2599 time to fit residues: 850.5735 Evaluate side-chains 565 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 525 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 52 optimal weight: 1.9990 chunk 259 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 258 optimal weight: 0.5980 chunk 295 optimal weight: 0.0270 chunk 230 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 219 optimal weight: 0.0370 chunk 110 optimal weight: 8.9990 chunk 160 optimal weight: 0.0010 overall best weight: 0.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 955 ASN A 965 GLN B 282 ASN B 317 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 751 ASN C 787 GLN C 907 ASN C 955 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.166306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.139904 restraints weight = 34133.392| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.09 r_work: 0.3746 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 24847 Z= 0.131 Angle : 0.593 12.684 33879 Z= 0.306 Chirality : 0.046 0.283 3913 Planarity : 0.004 0.051 4321 Dihedral : 6.189 59.950 3832 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.11 % Allowed : 12.25 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 2993 helix: 2.56 (0.20), residues: 639 sheet: 0.37 (0.19), residues: 675 loop : -0.63 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 886 HIS 0.004 0.001 HIS C 207 PHE 0.017 0.001 PHE A 238 TYR 0.019 0.001 TYR B1067 ARG 0.008 0.001 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 27) link_NAG-ASN : angle 2.66690 ( 81) hydrogen bonds : bond 0.04488 ( 959) hydrogen bonds : angle 5.51821 ( 2778) SS BOND : bond 0.00391 ( 37) SS BOND : angle 2.55416 ( 74) covalent geometry : bond 0.00301 (24783) covalent geometry : angle 0.56685 (33724) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 543 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8454 (m-80) cc_final: 0.8095 (m-80) REVERT: A 138 ASP cc_start: 0.7795 (t0) cc_final: 0.7545 (t0) REVERT: A 574 ASP cc_start: 0.7535 (t70) cc_final: 0.7150 (t0) REVERT: A 660 TYR cc_start: 0.8619 (m-80) cc_final: 0.8175 (m-80) REVERT: A 737 ASP cc_start: 0.7602 (t0) cc_final: 0.7224 (t0) REVERT: A 900 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7945 (mtt) REVERT: A 933 LYS cc_start: 0.8526 (ttmm) cc_final: 0.8277 (mtmm) REVERT: A 945 LEU cc_start: 0.7522 (mp) cc_final: 0.7315 (mm) REVERT: A 990 GLU cc_start: 0.6563 (mm-30) cc_final: 0.6337 (tp30) REVERT: A 994 ASP cc_start: 0.7486 (m-30) cc_final: 0.7244 (m-30) REVERT: A 1041 ASP cc_start: 0.8025 (m-30) cc_final: 0.6984 (m-30) REVERT: A 1045 LYS cc_start: 0.8059 (mmtm) cc_final: 0.7217 (mmtm) REVERT: A 1138 TYR cc_start: 0.7889 (t80) cc_final: 0.7686 (t80) REVERT: B 117 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8050 (tt) REVERT: B 512 VAL cc_start: 0.8129 (t) cc_final: 0.7877 (p) REVERT: B 553 THR cc_start: 0.8072 (m) cc_final: 0.7562 (t) REVERT: B 558 LYS cc_start: 0.8213 (mmmt) cc_final: 0.7788 (mmmt) REVERT: B 583 GLU cc_start: 0.6160 (tm-30) cc_final: 0.5794 (tm-30) REVERT: B 607 GLN cc_start: 0.8735 (mt0) cc_final: 0.8499 (mt0) REVERT: B 791 THR cc_start: 0.8676 (m) cc_final: 0.8465 (p) REVERT: B 808 ASP cc_start: 0.8078 (t70) cc_final: 0.7757 (t0) REVERT: B 868 GLU cc_start: 0.7726 (mp0) cc_final: 0.7468 (mp0) REVERT: B 900 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8193 (mtt) REVERT: B 994 ASP cc_start: 0.7543 (t70) cc_final: 0.7310 (t0) REVERT: B 1010 GLN cc_start: 0.7942 (tp40) cc_final: 0.7738 (tp40) REVERT: B 1014 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7709 (mtt180) REVERT: B 1031 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7556 (mt-10) REVERT: C 113 LYS cc_start: 0.7630 (tmtt) cc_final: 0.7375 (tmtt) REVERT: C 129 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7722 (ttmm) REVERT: C 191 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6755 (tm-30) REVERT: C 202 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7949 (mttm) REVERT: C 203 ILE cc_start: 0.7223 (tt) cc_final: 0.6260 (tt) REVERT: C 317 ASN cc_start: 0.8019 (m-40) cc_final: 0.7521 (m-40) REVERT: C 583 GLU cc_start: 0.7602 (tp30) cc_final: 0.7324 (tp30) REVERT: C 703 ASN cc_start: 0.8296 (t0) cc_final: 0.8072 (t0) REVERT: C 814 LYS cc_start: 0.8016 (mmtm) cc_final: 0.7806 (mppt) REVERT: C 819 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7774 (mt-10) REVERT: C 821 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8149 (tp) REVERT: C 868 GLU cc_start: 0.7717 (mp0) cc_final: 0.7467 (mp0) REVERT: C 900 MET cc_start: 0.8476 (mtm) cc_final: 0.8272 (mtp) REVERT: C 918 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7694 (mt-10) REVERT: C 1010 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: C 1091 ARG cc_start: 0.7936 (mtm-85) cc_final: 0.7731 (mtm-85) REVERT: C 1092 GLU cc_start: 0.6954 (pm20) cc_final: 0.6723 (pm20) REVERT: C 1138 TYR cc_start: 0.7948 (t80) cc_final: 0.7699 (t80) outliers start: 83 outliers final: 40 residues processed: 572 average time/residue: 1.2759 time to fit residues: 841.8479 Evaluate side-chains 569 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 522 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 149 optimal weight: 0.5980 chunk 270 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 127 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 219 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 273 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 245 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 564 GLN A 955 ASN A 965 GLN B 317 ASN B 787 GLN B 935 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 907 ASN C 913 GLN C 955 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.164044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.137364 restraints weight = 34233.135| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.11 r_work: 0.3711 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24847 Z= 0.182 Angle : 0.628 14.829 33879 Z= 0.320 Chirality : 0.048 0.286 3913 Planarity : 0.004 0.063 4321 Dihedral : 6.065 57.741 3832 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.45 % Allowed : 13.26 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 2993 helix: 2.38 (0.20), residues: 645 sheet: 0.35 (0.19), residues: 660 loop : -0.73 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.006 0.001 HIS C 207 PHE 0.021 0.002 PHE B 342 TYR 0.021 0.002 TYR B 266 ARG 0.009 0.001 ARG A1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 27) link_NAG-ASN : angle 3.25268 ( 81) hydrogen bonds : bond 0.04823 ( 959) hydrogen bonds : angle 5.51237 ( 2778) SS BOND : bond 0.00465 ( 37) SS BOND : angle 2.44401 ( 74) covalent geometry : bond 0.00432 (24783) covalent geometry : angle 0.59812 (33724) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 538 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7764 (t) REVERT: A 574 ASP cc_start: 0.7552 (t70) cc_final: 0.7168 (t0) REVERT: A 660 TYR cc_start: 0.8589 (m-80) cc_final: 0.8192 (m-80) REVERT: A 900 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8012 (mtt) REVERT: A 933 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8310 (mtmm) REVERT: A 1041 ASP cc_start: 0.8067 (m-30) cc_final: 0.7192 (m-30) REVERT: A 1045 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7273 (mmtm) REVERT: B 117 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8078 (tt) REVERT: B 126 VAL cc_start: 0.7936 (OUTLIER) cc_final: 0.7684 (m) REVERT: B 140 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.6912 (p90) REVERT: B 379 CYS cc_start: 0.5390 (m) cc_final: 0.5124 (m) REVERT: B 512 VAL cc_start: 0.8193 (t) cc_final: 0.7945 (p) REVERT: B 553 THR cc_start: 0.8099 (m) cc_final: 0.7560 (t) REVERT: B 558 LYS cc_start: 0.8292 (mmmt) cc_final: 0.7890 (mmmt) REVERT: B 808 ASP cc_start: 0.8121 (t70) cc_final: 0.7822 (t0) REVERT: B 820 ASP cc_start: 0.7811 (m-30) cc_final: 0.7555 (m-30) REVERT: B 868 GLU cc_start: 0.7768 (mp0) cc_final: 0.7503 (mp0) REVERT: B 900 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8285 (ttm) REVERT: B 988 GLU cc_start: 0.7514 (tm-30) cc_final: 0.6961 (tm-30) REVERT: B 994 ASP cc_start: 0.7583 (t70) cc_final: 0.7348 (t0) REVERT: B 1010 GLN cc_start: 0.7979 (tp40) cc_final: 0.7771 (tp40) REVERT: B 1014 ARG cc_start: 0.8240 (ttm110) cc_final: 0.7759 (mtm-85) REVERT: B 1031 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7706 (mt-10) REVERT: B 1072 GLU cc_start: 0.8388 (pm20) cc_final: 0.8178 (pm20) REVERT: B 1107 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7978 (mtt180) REVERT: C 100 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8068 (mp) REVERT: C 113 LYS cc_start: 0.7677 (tmtt) cc_final: 0.7422 (tmtt) REVERT: C 129 LYS cc_start: 0.7946 (mtpp) cc_final: 0.7716 (mtpp) REVERT: C 191 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6796 (tm-30) REVERT: C 202 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8053 (mttm) REVERT: C 203 ILE cc_start: 0.7278 (tt) cc_final: 0.6460 (tt) REVERT: C 235 ILE cc_start: 0.8441 (mm) cc_final: 0.8181 (tp) REVERT: C 317 ASN cc_start: 0.8038 (m-40) cc_final: 0.7671 (m-40) REVERT: C 356 LYS cc_start: 0.8348 (tppp) cc_final: 0.8081 (tppp) REVERT: C 583 GLU cc_start: 0.7603 (tp30) cc_final: 0.7360 (tp30) REVERT: C 588 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8138 (t) REVERT: C 703 ASN cc_start: 0.8364 (t0) cc_final: 0.8143 (t0) REVERT: C 811 LYS cc_start: 0.7672 (ptpt) cc_final: 0.7327 (ptpp) REVERT: C 814 LYS cc_start: 0.8001 (mmtm) cc_final: 0.7796 (mppt) REVERT: C 868 GLU cc_start: 0.7744 (mp0) cc_final: 0.7472 (mp0) REVERT: C 918 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: C 1010 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7657 (mp10) REVERT: C 1091 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7773 (mtm-85) REVERT: C 1092 GLU cc_start: 0.7047 (pm20) cc_final: 0.6824 (pm20) REVERT: C 1094 VAL cc_start: 0.8331 (m) cc_final: 0.8121 (p) outliers start: 92 outliers final: 47 residues processed: 574 average time/residue: 1.2570 time to fit residues: 839.2918 Evaluate side-chains 586 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 527 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 57 optimal weight: 0.9980 chunk 253 optimal weight: 3.9990 chunk 216 optimal weight: 0.5980 chunk 229 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 180 optimal weight: 0.3980 chunk 111 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 762 GLN A 955 ASN B 239 GLN B 317 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 907 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.163587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.136977 restraints weight = 34277.635| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.13 r_work: 0.3705 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24847 Z= 0.181 Angle : 0.618 10.917 33879 Z= 0.323 Chirality : 0.048 0.469 3913 Planarity : 0.004 0.056 4321 Dihedral : 5.900 57.314 3832 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.48 % Allowed : 14.23 % Favored : 82.28 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 2993 helix: 2.34 (0.20), residues: 648 sheet: 0.42 (0.19), residues: 671 loop : -0.79 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.005 0.001 HIS C 954 PHE 0.020 0.002 PHE B 342 TYR 0.019 0.002 TYR B1067 ARG 0.007 0.001 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 27) link_NAG-ASN : angle 2.70147 ( 81) hydrogen bonds : bond 0.04796 ( 959) hydrogen bonds : angle 5.47492 ( 2778) SS BOND : bond 0.00434 ( 37) SS BOND : angle 2.29063 ( 74) covalent geometry : bond 0.00428 (24783) covalent geometry : angle 0.59534 (33724) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 543 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7805 (t) REVERT: A 574 ASP cc_start: 0.7576 (t70) cc_final: 0.7196 (t0) REVERT: A 660 TYR cc_start: 0.8656 (m-80) cc_final: 0.8324 (m-80) REVERT: A 737 ASP cc_start: 0.7629 (t0) cc_final: 0.7292 (t0) REVERT: A 900 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8019 (mtt) REVERT: A 902 MET cc_start: 0.8568 (mmm) cc_final: 0.8336 (mmt) REVERT: A 933 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8315 (mtmm) REVERT: A 950 ASP cc_start: 0.7498 (m-30) cc_final: 0.7283 (m-30) REVERT: A 1041 ASP cc_start: 0.8065 (m-30) cc_final: 0.7218 (m-30) REVERT: A 1045 LYS cc_start: 0.8115 (mmtm) cc_final: 0.7242 (mmtm) REVERT: A 1091 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7862 (mtt-85) REVERT: B 117 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8081 (tt) REVERT: B 126 VAL cc_start: 0.7909 (OUTLIER) cc_final: 0.7623 (m) REVERT: B 140 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.6899 (p90) REVERT: B 512 VAL cc_start: 0.8187 (t) cc_final: 0.7931 (p) REVERT: B 558 LYS cc_start: 0.8279 (mmmt) cc_final: 0.7884 (mmmt) REVERT: B 567 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7909 (mtt180) REVERT: B 746 SER cc_start: 0.8495 (t) cc_final: 0.8144 (m) REVERT: B 820 ASP cc_start: 0.7844 (m-30) cc_final: 0.7501 (m-30) REVERT: B 868 GLU cc_start: 0.7770 (mp0) cc_final: 0.7494 (mp0) REVERT: B 988 GLU cc_start: 0.7564 (tm-30) cc_final: 0.6945 (tm-30) REVERT: B 994 ASP cc_start: 0.7571 (t70) cc_final: 0.7335 (t0) REVERT: B 1010 GLN cc_start: 0.7968 (tp40) cc_final: 0.7751 (tp40) REVERT: B 1014 ARG cc_start: 0.8271 (ttm110) cc_final: 0.7786 (mtm-85) REVERT: B 1031 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7754 (mt-10) REVERT: B 1072 GLU cc_start: 0.8372 (pm20) cc_final: 0.8171 (pm20) REVERT: C 100 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.8025 (mp) REVERT: C 113 LYS cc_start: 0.7693 (tmtt) cc_final: 0.7426 (tmtt) REVERT: C 129 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7527 (mtpp) REVERT: C 191 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6746 (tm-30) REVERT: C 203 ILE cc_start: 0.7302 (tt) cc_final: 0.6441 (tt) REVERT: C 353 TRP cc_start: 0.7344 (OUTLIER) cc_final: 0.6540 (p90) REVERT: C 356 LYS cc_start: 0.8426 (tppp) cc_final: 0.8151 (tppp) REVERT: C 583 GLU cc_start: 0.7614 (tp30) cc_final: 0.7377 (tp30) REVERT: C 703 ASN cc_start: 0.8389 (t0) cc_final: 0.8144 (t0) REVERT: C 745 ASP cc_start: 0.7455 (t0) cc_final: 0.7231 (m-30) REVERT: C 811 LYS cc_start: 0.7717 (ptpt) cc_final: 0.7382 (ptpp) REVERT: C 814 LYS cc_start: 0.7940 (mmtm) cc_final: 0.7733 (mppt) REVERT: C 825 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8433 (mtmm) REVERT: C 868 GLU cc_start: 0.7728 (mp0) cc_final: 0.7468 (mp0) REVERT: C 918 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: C 1010 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7664 (mp10) REVERT: C 1092 GLU cc_start: 0.7057 (pm20) cc_final: 0.6835 (pm20) REVERT: C 1138 TYR cc_start: 0.8032 (t80) cc_final: 0.7814 (t80) outliers start: 93 outliers final: 47 residues processed: 578 average time/residue: 1.2401 time to fit residues: 830.0889 Evaluate side-chains 595 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 538 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 129 optimal weight: 0.8980 chunk 253 optimal weight: 0.5980 chunk 246 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 181 optimal weight: 0.9980 chunk 144 optimal weight: 0.0000 chunk 278 optimal weight: 0.0070 chunk 170 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 239 optimal weight: 1.9990 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 540 ASN A 658 ASN A 762 GLN A 955 ASN B 317 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 907 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.164377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.137843 restraints weight = 34070.922| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.12 r_work: 0.3715 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 24847 Z= 0.143 Angle : 0.624 20.759 33879 Z= 0.318 Chirality : 0.052 1.236 3913 Planarity : 0.004 0.053 4321 Dihedral : 5.997 59.075 3832 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.52 % Allowed : 15.17 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 2993 helix: 2.40 (0.20), residues: 648 sheet: 0.36 (0.19), residues: 684 loop : -0.77 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.005 0.001 HIS C 954 PHE 0.021 0.001 PHE A 592 TYR 0.019 0.001 TYR B1067 ARG 0.008 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 27) link_NAG-ASN : angle 3.72994 ( 81) hydrogen bonds : bond 0.04452 ( 959) hydrogen bonds : angle 5.38115 ( 2778) SS BOND : bond 0.00455 ( 37) SS BOND : angle 2.18533 ( 74) covalent geometry : bond 0.00336 (24783) covalent geometry : angle 0.58918 (33724) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 536 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7803 (t) REVERT: A 355 ARG cc_start: 0.7474 (ttt90) cc_final: 0.5632 (ttt90) REVERT: A 574 ASP cc_start: 0.7605 (t70) cc_final: 0.7236 (t0) REVERT: A 660 TYR cc_start: 0.8619 (m-80) cc_final: 0.8187 (m-80) REVERT: A 705 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8426 (p) REVERT: A 737 ASP cc_start: 0.7524 (t0) cc_final: 0.7285 (t0) REVERT: A 900 MET cc_start: 0.8320 (mtm) cc_final: 0.8048 (mtt) REVERT: A 902 MET cc_start: 0.8587 (mmm) cc_final: 0.8376 (mmt) REVERT: A 933 LYS cc_start: 0.8498 (ttmm) cc_final: 0.8250 (mtmm) REVERT: A 1041 ASP cc_start: 0.8058 (m-30) cc_final: 0.7220 (m-30) REVERT: A 1045 LYS cc_start: 0.8129 (mmtm) cc_final: 0.7298 (mmtm) REVERT: B 117 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8074 (tt) REVERT: B 126 VAL cc_start: 0.7864 (t) cc_final: 0.7606 (m) REVERT: B 129 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7949 (ttmm) REVERT: B 140 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.6885 (p90) REVERT: B 512 VAL cc_start: 0.8161 (t) cc_final: 0.7907 (p) REVERT: B 553 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7572 (t) REVERT: B 558 LYS cc_start: 0.8260 (mmmt) cc_final: 0.7860 (mmmt) REVERT: B 567 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7930 (mtt180) REVERT: B 574 ASP cc_start: 0.7391 (t0) cc_final: 0.6944 (t0) REVERT: B 820 ASP cc_start: 0.7830 (m-30) cc_final: 0.7495 (m-30) REVERT: B 868 GLU cc_start: 0.7768 (mp0) cc_final: 0.7499 (mp0) REVERT: B 988 GLU cc_start: 0.7606 (tm-30) cc_final: 0.6970 (tm-30) REVERT: B 994 ASP cc_start: 0.7541 (t70) cc_final: 0.7301 (t0) REVERT: B 1010 GLN cc_start: 0.7958 (tp40) cc_final: 0.7723 (tp40) REVERT: B 1014 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7792 (mtm180) REVERT: B 1031 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7688 (mt-10) REVERT: C 100 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.8005 (mp) REVERT: C 113 LYS cc_start: 0.7690 (tmtt) cc_final: 0.7421 (tmtt) REVERT: C 191 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6752 (tm-30) REVERT: C 203 ILE cc_start: 0.7193 (tt) cc_final: 0.6288 (tt) REVERT: C 235 ILE cc_start: 0.8420 (mm) cc_final: 0.8120 (tp) REVERT: C 353 TRP cc_start: 0.7320 (OUTLIER) cc_final: 0.6478 (p90) REVERT: C 356 LYS cc_start: 0.8445 (tppp) cc_final: 0.8170 (tppp) REVERT: C 583 GLU cc_start: 0.7638 (tp30) cc_final: 0.7399 (tp30) REVERT: C 663 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6788 (p0) REVERT: C 703 ASN cc_start: 0.8414 (t0) cc_final: 0.8159 (t0) REVERT: C 808 ASP cc_start: 0.7804 (t0) cc_final: 0.7604 (t0) REVERT: C 811 LYS cc_start: 0.7725 (ptpt) cc_final: 0.7371 (ptpp) REVERT: C 814 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7755 (mppt) REVERT: C 819 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7798 (mt-10) REVERT: C 821 LEU cc_start: 0.8363 (tt) cc_final: 0.8160 (tp) REVERT: C 868 GLU cc_start: 0.7708 (mp0) cc_final: 0.7456 (mp0) REVERT: C 918 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: C 1005 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7977 (mt0) REVERT: C 1010 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7632 (mp10) REVERT: C 1092 GLU cc_start: 0.7063 (pm20) cc_final: 0.6837 (pm20) REVERT: C 1138 TYR cc_start: 0.8020 (t80) cc_final: 0.7791 (t80) outliers start: 94 outliers final: 49 residues processed: 577 average time/residue: 1.2920 time to fit residues: 860.8055 Evaluate side-chains 584 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 523 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 68 optimal weight: 1.9990 chunk 263 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 0.0670 chunk 46 optimal weight: 0.0010 chunk 57 optimal weight: 0.9980 chunk 302 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 265 optimal weight: 0.8980 overall best weight: 0.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 658 ASN A 955 ASN B 317 ASN B 751 ASN C 30 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 907 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.163817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.137311 restraints weight = 34095.825| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.12 r_work: 0.3709 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 24847 Z= 0.170 Angle : 0.648 21.176 33879 Z= 0.330 Chirality : 0.050 0.691 3913 Planarity : 0.004 0.055 4321 Dihedral : 6.070 57.723 3830 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.18 % Allowed : 15.77 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 2993 helix: 2.38 (0.20), residues: 648 sheet: 0.43 (0.19), residues: 674 loop : -0.79 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.005 0.001 HIS C 954 PHE 0.030 0.002 PHE A 133 TYR 0.019 0.001 TYR B1067 ARG 0.010 0.001 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00698 ( 27) link_NAG-ASN : angle 4.11145 ( 81) hydrogen bonds : bond 0.04620 ( 959) hydrogen bonds : angle 5.41490 ( 2778) SS BOND : bond 0.00477 ( 37) SS BOND : angle 2.36897 ( 74) covalent geometry : bond 0.00404 (24783) covalent geometry : angle 0.60737 (33724) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 543 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 THR cc_start: 0.8126 (m) cc_final: 0.7820 (t) REVERT: A 574 ASP cc_start: 0.7592 (t70) cc_final: 0.7217 (t0) REVERT: A 660 TYR cc_start: 0.8627 (m-80) cc_final: 0.8193 (m-80) REVERT: A 705 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8399 (t) REVERT: A 737 ASP cc_start: 0.7572 (t0) cc_final: 0.7298 (t0) REVERT: A 900 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8068 (mtt) REVERT: A 902 MET cc_start: 0.8610 (mmm) cc_final: 0.8386 (mmt) REVERT: A 933 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8268 (mtmm) REVERT: A 1041 ASP cc_start: 0.8060 (m-30) cc_final: 0.7227 (m-30) REVERT: A 1045 LYS cc_start: 0.8125 (mmtm) cc_final: 0.7289 (mmtm) REVERT: B 126 VAL cc_start: 0.7877 (t) cc_final: 0.7627 (m) REVERT: B 129 LYS cc_start: 0.8170 (mtmm) cc_final: 0.7945 (ttmm) REVERT: B 140 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6945 (p90) REVERT: B 553 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7549 (t) REVERT: B 558 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7861 (mmmt) REVERT: B 567 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7934 (mtt180) REVERT: B 574 ASP cc_start: 0.7425 (t0) cc_final: 0.6976 (t0) REVERT: B 820 ASP cc_start: 0.7837 (m-30) cc_final: 0.7496 (m-30) REVERT: B 868 GLU cc_start: 0.7775 (mp0) cc_final: 0.7501 (mp0) REVERT: B 988 GLU cc_start: 0.7593 (tm-30) cc_final: 0.6926 (tm-30) REVERT: B 1010 GLN cc_start: 0.7945 (tp40) cc_final: 0.7714 (tp40) REVERT: B 1014 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7776 (mtm180) REVERT: B 1031 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7704 (mt-10) REVERT: C 100 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.8037 (mp) REVERT: C 113 LYS cc_start: 0.7711 (tmtt) cc_final: 0.7437 (tmtt) REVERT: C 191 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6737 (tm-30) REVERT: C 203 ILE cc_start: 0.7235 (tt) cc_final: 0.6351 (tt) REVERT: C 235 ILE cc_start: 0.8415 (mm) cc_final: 0.8137 (tp) REVERT: C 353 TRP cc_start: 0.7353 (OUTLIER) cc_final: 0.6467 (p90) REVERT: C 356 LYS cc_start: 0.8498 (tppp) cc_final: 0.8225 (tppp) REVERT: C 388 ASN cc_start: 0.6389 (OUTLIER) cc_final: 0.6126 (t0) REVERT: C 583 GLU cc_start: 0.7637 (tp30) cc_final: 0.7411 (tp30) REVERT: C 619 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.6034 (mp0) REVERT: C 703 ASN cc_start: 0.8437 (t0) cc_final: 0.8168 (t0) REVERT: C 811 LYS cc_start: 0.7748 (ptpt) cc_final: 0.7385 (ptpp) REVERT: C 814 LYS cc_start: 0.7954 (mmtm) cc_final: 0.7743 (mppt) REVERT: C 819 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7807 (mt-10) REVERT: C 868 GLU cc_start: 0.7749 (mp0) cc_final: 0.7495 (mp0) REVERT: C 918 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: C 1010 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7624 (mp10) REVERT: C 1092 GLU cc_start: 0.7081 (pm20) cc_final: 0.6850 (pm20) REVERT: C 1138 TYR cc_start: 0.8069 (t80) cc_final: 0.7848 (t80) outliers start: 85 outliers final: 47 residues processed: 578 average time/residue: 1.3033 time to fit residues: 870.6552 Evaluate side-chains 587 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 529 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 34 optimal weight: 4.9990 chunk 149 optimal weight: 0.4980 chunk 208 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 128 optimal weight: 0.0470 chunk 181 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 658 ASN A 955 ASN B 317 ASN B 935 GLN B1071 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 787 GLN C 907 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.164085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.137593 restraints weight = 34078.246| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.12 r_work: 0.3702 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 24847 Z= 0.168 Angle : 0.635 20.763 33879 Z= 0.324 Chirality : 0.048 0.479 3913 Planarity : 0.004 0.055 4321 Dihedral : 5.849 58.526 3830 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.07 % Allowed : 16.78 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2993 helix: 2.39 (0.20), residues: 647 sheet: 0.42 (0.19), residues: 676 loop : -0.78 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 886 HIS 0.005 0.001 HIS C 954 PHE 0.025 0.002 PHE A 592 TYR 0.019 0.001 TYR B1067 ARG 0.013 0.001 ARG C 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 27) link_NAG-ASN : angle 4.05301 ( 81) hydrogen bonds : bond 0.04653 ( 959) hydrogen bonds : angle 5.40822 ( 2778) SS BOND : bond 0.00454 ( 37) SS BOND : angle 2.33389 ( 74) covalent geometry : bond 0.00400 (24783) covalent geometry : angle 0.59502 (33724) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 536 time to evaluate : 2.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 THR cc_start: 0.8126 (m) cc_final: 0.7837 (t) REVERT: A 565 PHE cc_start: 0.6952 (m-80) cc_final: 0.6732 (m-80) REVERT: A 574 ASP cc_start: 0.7606 (t70) cc_final: 0.7236 (t0) REVERT: A 660 TYR cc_start: 0.8649 (m-80) cc_final: 0.8208 (m-80) REVERT: A 705 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8440 (t) REVERT: A 737 ASP cc_start: 0.7560 (t0) cc_final: 0.7343 (t0) REVERT: A 900 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8070 (mtt) REVERT: A 902 MET cc_start: 0.8613 (mmm) cc_final: 0.8393 (mmt) REVERT: A 933 LYS cc_start: 0.8492 (ttmm) cc_final: 0.8254 (mtmm) REVERT: A 1041 ASP cc_start: 0.8061 (m-30) cc_final: 0.7247 (m-30) REVERT: A 1045 LYS cc_start: 0.8146 (mmtm) cc_final: 0.7322 (mmtm) REVERT: B 126 VAL cc_start: 0.7918 (OUTLIER) cc_final: 0.7660 (m) REVERT: B 129 LYS cc_start: 0.8189 (mtmm) cc_final: 0.7969 (ttmm) REVERT: B 140 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6931 (p90) REVERT: B 553 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7555 (t) REVERT: B 558 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7855 (mmmt) REVERT: B 567 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7914 (mtt180) REVERT: B 868 GLU cc_start: 0.7777 (mp0) cc_final: 0.7506 (mp0) REVERT: B 988 GLU cc_start: 0.7592 (tm-30) cc_final: 0.6912 (tm-30) REVERT: B 1010 GLN cc_start: 0.7967 (tp40) cc_final: 0.7758 (tp40) REVERT: B 1014 ARG cc_start: 0.8229 (ttm110) cc_final: 0.7760 (mtm-85) REVERT: B 1031 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7762 (mt-10) REVERT: C 100 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8052 (mp) REVERT: C 113 LYS cc_start: 0.7734 (tmtt) cc_final: 0.7450 (tmtt) REVERT: C 191 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6763 (tm-30) REVERT: C 203 ILE cc_start: 0.7275 (tt) cc_final: 0.6403 (tt) REVERT: C 235 ILE cc_start: 0.8431 (mm) cc_final: 0.8160 (tp) REVERT: C 353 TRP cc_start: 0.7382 (OUTLIER) cc_final: 0.6503 (p90) REVERT: C 356 LYS cc_start: 0.8447 (tppp) cc_final: 0.8166 (tppp) REVERT: C 388 ASN cc_start: 0.6465 (OUTLIER) cc_final: 0.6211 (t0) REVERT: C 513 LEU cc_start: 0.8111 (mt) cc_final: 0.7909 (mt) REVERT: C 583 GLU cc_start: 0.7640 (tp30) cc_final: 0.7422 (tp30) REVERT: C 703 ASN cc_start: 0.8440 (t0) cc_final: 0.8164 (t0) REVERT: C 811 LYS cc_start: 0.7755 (ptpt) cc_final: 0.7387 (ptpp) REVERT: C 819 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7763 (tt0) REVERT: C 868 GLU cc_start: 0.7744 (mp0) cc_final: 0.7497 (mp0) REVERT: C 918 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: C 1010 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: C 1092 GLU cc_start: 0.7084 (pm20) cc_final: 0.6861 (pm20) REVERT: C 1138 TYR cc_start: 0.8087 (t80) cc_final: 0.7870 (t80) outliers start: 82 outliers final: 48 residues processed: 569 average time/residue: 1.3042 time to fit residues: 855.9837 Evaluate side-chains 595 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 536 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 193 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 161 optimal weight: 0.5980 chunk 240 optimal weight: 6.9990 chunk 299 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 658 ASN A 955 ASN B 580 GLN B 935 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 787 GLN C 907 ASN C 954 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.163068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.136640 restraints weight = 34232.233| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.11 r_work: 0.3690 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 24847 Z= 0.215 Angle : 0.694 22.012 33879 Z= 0.349 Chirality : 0.050 0.587 3913 Planarity : 0.005 0.063 4321 Dihedral : 6.009 57.280 3830 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.96 % Allowed : 17.15 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 2993 helix: 2.28 (0.20), residues: 643 sheet: 0.40 (0.19), residues: 681 loop : -0.86 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 886 HIS 0.006 0.001 HIS C 954 PHE 0.031 0.002 PHE C 565 TYR 0.020 0.002 TYR B 266 ARG 0.014 0.001 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 27) link_NAG-ASN : angle 5.30993 ( 81) hydrogen bonds : bond 0.04970 ( 959) hydrogen bonds : angle 5.47754 ( 2778) SS BOND : bond 0.00514 ( 37) SS BOND : angle 2.48641 ( 74) covalent geometry : bond 0.00517 (24783) covalent geometry : angle 0.63433 (33724) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 532 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 THR cc_start: 0.8150 (m) cc_final: 0.7856 (t) REVERT: A 233 ILE cc_start: 0.8739 (pt) cc_final: 0.8530 (pt) REVERT: A 574 ASP cc_start: 0.7619 (t70) cc_final: 0.7243 (t0) REVERT: A 660 TYR cc_start: 0.8675 (m-80) cc_final: 0.8212 (m-80) REVERT: A 705 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8511 (t) REVERT: A 737 ASP cc_start: 0.7595 (t0) cc_final: 0.7379 (t0) REVERT: A 900 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8074 (mtt) REVERT: A 902 MET cc_start: 0.8618 (mmm) cc_final: 0.8397 (mmt) REVERT: A 933 LYS cc_start: 0.8509 (ttmm) cc_final: 0.8275 (mtmm) REVERT: A 950 ASP cc_start: 0.7523 (m-30) cc_final: 0.7283 (m-30) REVERT: A 1041 ASP cc_start: 0.8047 (m-30) cc_final: 0.7235 (m-30) REVERT: A 1045 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7366 (mmtm) REVERT: B 126 VAL cc_start: 0.7927 (OUTLIER) cc_final: 0.7662 (m) REVERT: B 129 LYS cc_start: 0.8180 (mtmm) cc_final: 0.7975 (ttmm) REVERT: B 140 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.6917 (p90) REVERT: B 553 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7553 (t) REVERT: B 567 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7931 (mtt180) REVERT: B 574 ASP cc_start: 0.7462 (t0) cc_final: 0.7047 (t0) REVERT: B 811 LYS cc_start: 0.7557 (ptpt) cc_final: 0.7307 (ptpp) REVERT: B 868 GLU cc_start: 0.7788 (mp0) cc_final: 0.7504 (mp0) REVERT: B 988 GLU cc_start: 0.7572 (tm-30) cc_final: 0.6891 (tm-30) REVERT: B 1014 ARG cc_start: 0.8260 (ttm110) cc_final: 0.7764 (mtm-85) REVERT: B 1031 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7825 (mt-10) REVERT: C 100 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8095 (mp) REVERT: C 113 LYS cc_start: 0.7796 (tmtt) cc_final: 0.7510 (tmtt) REVERT: C 191 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6770 (tm-30) REVERT: C 203 ILE cc_start: 0.7247 (tt) cc_final: 0.6483 (tt) REVERT: C 228 ASP cc_start: 0.8028 (t0) cc_final: 0.7812 (t0) REVERT: C 235 ILE cc_start: 0.8446 (mm) cc_final: 0.8216 (tp) REVERT: C 353 TRP cc_start: 0.7435 (OUTLIER) cc_final: 0.6805 (p90) REVERT: C 356 LYS cc_start: 0.8495 (tppp) cc_final: 0.8215 (tppp) REVERT: C 388 ASN cc_start: 0.6527 (OUTLIER) cc_final: 0.6282 (t0) REVERT: C 513 LEU cc_start: 0.8104 (mt) cc_final: 0.7899 (mt) REVERT: C 583 GLU cc_start: 0.7643 (tp30) cc_final: 0.7431 (tp30) REVERT: C 703 ASN cc_start: 0.8468 (t0) cc_final: 0.8184 (t0) REVERT: C 811 LYS cc_start: 0.7818 (ptpt) cc_final: 0.7380 (ptpp) REVERT: C 819 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7800 (mt-10) REVERT: C 868 GLU cc_start: 0.7752 (mp0) cc_final: 0.7491 (mp0) REVERT: C 918 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: C 1010 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: C 1092 GLU cc_start: 0.7143 (pm20) cc_final: 0.6916 (pm20) REVERT: C 1138 TYR cc_start: 0.8080 (t80) cc_final: 0.7848 (t80) outliers start: 79 outliers final: 50 residues processed: 565 average time/residue: 1.2987 time to fit residues: 850.8369 Evaluate side-chains 584 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 523 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 300 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 0.0770 chunk 187 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 180 optimal weight: 0.5980 chunk 269 optimal weight: 0.9990 chunk 293 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 296 optimal weight: 0.6980 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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 658 ASN A 762 GLN B 360 ASN B 394 ASN B 779 GLN B 935 GLN B1010 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 787 GLN C 907 ASN C 954 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.163746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.137315 restraints weight = 34047.575| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.12 r_work: 0.3701 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 24847 Z= 0.166 Angle : 0.661 18.234 33879 Z= 0.335 Chirality : 0.050 0.767 3913 Planarity : 0.005 0.069 4321 Dihedral : 5.939 57.962 3828 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.70 % Allowed : 17.83 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 2993 helix: 2.29 (0.20), residues: 643 sheet: 0.37 (0.19), residues: 680 loop : -0.83 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 886 HIS 0.010 0.001 HIS C 207 PHE 0.028 0.001 PHE A 592 TYR 0.021 0.001 TYR B 170 ARG 0.015 0.001 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00649 ( 27) link_NAG-ASN : angle 4.47302 ( 81) hydrogen bonds : bond 0.04661 ( 959) hydrogen bonds : angle 5.44816 ( 2778) SS BOND : bond 0.00429 ( 37) SS BOND : angle 2.22722 ( 74) covalent geometry : bond 0.00393 (24783) covalent geometry : angle 0.61681 (33724) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 538 time to evaluate : 2.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 THR cc_start: 0.8114 (m) cc_final: 0.7848 (t) REVERT: A 233 ILE cc_start: 0.8722 (pt) cc_final: 0.8515 (pt) REVERT: A 574 ASP cc_start: 0.7628 (t70) cc_final: 0.7249 (t0) REVERT: A 660 TYR cc_start: 0.8649 (m-80) cc_final: 0.8211 (m-80) REVERT: A 737 ASP cc_start: 0.7520 (t0) cc_final: 0.7308 (t0) REVERT: A 900 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8073 (mtt) REVERT: A 902 MET cc_start: 0.8609 (mmm) cc_final: 0.8344 (mmt) REVERT: A 933 LYS cc_start: 0.8486 (ttmm) cc_final: 0.8249 (mtmm) REVERT: A 950 ASP cc_start: 0.7504 (m-30) cc_final: 0.7262 (m-30) REVERT: A 1041 ASP cc_start: 0.8065 (m-30) cc_final: 0.7259 (m-30) REVERT: A 1045 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7366 (mmtm) REVERT: B 117 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8166 (tt) REVERT: B 126 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7659 (m) REVERT: B 140 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.6906 (p90) REVERT: B 177 MET cc_start: 0.7023 (mmm) cc_final: 0.6780 (mtp) REVERT: B 314 GLN cc_start: 0.7847 (tp40) cc_final: 0.7604 (tp40) REVERT: B 553 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7574 (t) REVERT: B 558 LYS cc_start: 0.8256 (mmmt) cc_final: 0.7870 (mmmt) REVERT: B 567 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7934 (mtt180) REVERT: B 820 ASP cc_start: 0.7732 (m-30) cc_final: 0.7406 (m-30) REVERT: B 868 GLU cc_start: 0.7764 (mp0) cc_final: 0.7490 (mp0) REVERT: B 988 GLU cc_start: 0.7542 (tm-30) cc_final: 0.6841 (tm-30) REVERT: B 1031 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7778 (mt-10) REVERT: C 100 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8072 (mp) REVERT: C 113 LYS cc_start: 0.7747 (tmtt) cc_final: 0.7447 (tmtt) REVERT: C 191 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6798 (tm-30) REVERT: C 203 ILE cc_start: 0.7319 (tt) cc_final: 0.6554 (tt) REVERT: C 228 ASP cc_start: 0.8026 (t0) cc_final: 0.7807 (t0) REVERT: C 235 ILE cc_start: 0.8437 (mm) cc_final: 0.8220 (tp) REVERT: C 353 TRP cc_start: 0.7410 (OUTLIER) cc_final: 0.6829 (p90) REVERT: C 356 LYS cc_start: 0.8485 (tppp) cc_final: 0.8200 (tppp) REVERT: C 388 ASN cc_start: 0.6491 (OUTLIER) cc_final: 0.6269 (t0) REVERT: C 553 THR cc_start: 0.6864 (OUTLIER) cc_final: 0.6622 (p) REVERT: C 583 GLU cc_start: 0.7629 (tp30) cc_final: 0.7422 (tp30) REVERT: C 660 TYR cc_start: 0.8757 (m-80) cc_final: 0.8550 (m-80) REVERT: C 703 ASN cc_start: 0.8462 (t0) cc_final: 0.8175 (t0) REVERT: C 811 LYS cc_start: 0.7815 (ptpt) cc_final: 0.7427 (ptpp) REVERT: C 819 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7746 (mt-10) REVERT: C 868 GLU cc_start: 0.7725 (mp0) cc_final: 0.7473 (mp0) REVERT: C 918 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: C 1010 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7662 (mp10) REVERT: C 1092 GLU cc_start: 0.7137 (pm20) cc_final: 0.6914 (pm20) REVERT: C 1138 TYR cc_start: 0.8080 (t80) cc_final: 0.7841 (t80) outliers start: 72 outliers final: 48 residues processed: 569 average time/residue: 1.3114 time to fit residues: 861.4648 Evaluate side-chains 589 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 529 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 221 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 chunk 222 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 285 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 268 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 216 optimal weight: 0.5980 chunk 302 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 658 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 779 GLN B 935 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 787 GLN C 907 ASN C 954 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.163864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.137485 restraints weight = 34049.683| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.12 r_work: 0.3699 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 24847 Z= 0.205 Angle : 0.799 59.138 33879 Z= 0.431 Chirality : 0.052 0.989 3913 Planarity : 0.005 0.071 4321 Dihedral : 5.953 58.434 3828 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.47 % Allowed : 18.54 % Favored : 78.99 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 2993 helix: 2.28 (0.20), residues: 643 sheet: 0.37 (0.19), residues: 680 loop : -0.83 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.009 0.001 HIS C 207 PHE 0.026 0.001 PHE B 342 TYR 0.029 0.001 TYR C 200 ARG 0.012 0.001 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00624 ( 27) link_NAG-ASN : angle 4.45476 ( 81) hydrogen bonds : bond 0.04677 ( 959) hydrogen bonds : angle 5.44741 ( 2778) SS BOND : bond 0.01260 ( 37) SS BOND : angle 2.76866 ( 74) covalent geometry : bond 0.00456 (24783) covalent geometry : angle 0.75975 (33724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24147.43 seconds wall clock time: 418 minutes 21.52 seconds (25101.52 seconds total)