Starting phenix.real_space_refine on Thu Mar 5 14:14:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fb3_31513/03_2026/7fb3_31513.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fb3_31513/03_2026/7fb3_31513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fb3_31513/03_2026/7fb3_31513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fb3_31513/03_2026/7fb3_31513.map" model { file = "/net/cci-nas-00/data/ceres_data/7fb3_31513/03_2026/7fb3_31513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fb3_31513/03_2026/7fb3_31513.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.100 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 105 5.16 5 C 14636 2.51 5 N 3812 2.21 5 O 4367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22920 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1045, 8175 Classifications: {'peptide': 1045} Link IDs: {'PTRANS': 52, 'TRANS': 992} Chain breaks: 6 Chain: "B" Number of atoms: 6606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 849, 6606 Classifications: {'peptide': 849} Link IDs: {'PTRANS': 42, 'TRANS': 806} Chain breaks: 7 Chain: "C" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8139 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 53, 'TRANS': 988} Chain breaks: 6 Time building chain proxies: 5.13, per 1000 atoms: 0.22 Number of scatterers: 22920 At special positions: 0 Unit cell: (141.44, 131.92, 176.8, 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 105 16.00 O 4367 8.00 N 3812 7.00 C 14636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 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=2.04 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 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=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 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 Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 809.7 milliseconds 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5506 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 50 sheets defined 24.4% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.524A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.669A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.675A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.368A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 removed outlier: 3.601A pdb=" N TYR A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 502 through 505' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.608A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.704A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.524A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.877A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 748 through 753 Processing helix chain 'B' and resid 754 through 756 No H-bonds generated for 'chain 'B' and resid 754 through 756' Processing helix chain 'B' and resid 757 through 782 removed outlier: 3.676A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.517A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.550A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 941 through 944 removed outlier: 4.030A pdb=" N ALA B 944 " --> pdb=" O THR B 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 941 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.118A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 6.009A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.364A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.681A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.218A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.879A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 852 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.699A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.616A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.309A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.958A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.460A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.249A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 51 removed outlier: 3.821A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.606A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.572A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 94 Processing sheet with id=AA6, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA7, first strand: chain 'A' and resid 195 through 197 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 317 removed outlier: 4.616A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.620A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.747A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.416A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.226A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.566A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.313A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.495A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 3.538A pdb=" N VAL A1104 " --> pdb=" O GLN A1113 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.854A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.854A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY B 268 " --> pdb=" O TYR B 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.627A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.742A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.318A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 538 through 543 Processing sheet with id=AD1, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.560A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.731A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.990A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.473A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1080 through 1082 removed outlier: 3.679A pdb=" N VAL B1133 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD8, first strand: chain 'C' and resid 29 through 30 removed outlier: 4.026A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 52 through 55 removed outlier: 7.653A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.938A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.753A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 191 through 197 removed outlier: 3.744A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.315A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 376 through 380 Processing sheet with id=AE6, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.544A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 566 through 567 removed outlier: 4.167A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 664 through 665 Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 722 removed outlier: 6.594A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 712 through 722 removed outlier: 6.594A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF4, first strand: chain 'C' and resid 1086 through 1090 removed outlier: 5.736A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1094 through 1097 800 hydrogen bonds defined for protein. 2163 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.34 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7433 1.35 - 1.47: 5861 1.47 - 1.60: 10004 1.60 - 1.72: 0 1.72 - 1.85: 134 Bond restraints: 23432 Sorted by residual: bond pdb=" C GLN A 173 " pdb=" N PRO A 174 " ideal model delta sigma weight residual 1.330 1.360 -0.030 1.19e-02 7.06e+03 6.38e+00 bond pdb=" C VAL B 620 " pdb=" N PRO B 621 " ideal model delta sigma weight residual 1.331 1.343 -0.012 7.90e-03 1.60e+04 2.18e+00 bond pdb=" CA ILE C1115 " pdb=" CB ILE C1115 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.47e+00 bond pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " ideal model delta sigma weight residual 1.808 1.846 -0.038 3.30e-02 9.18e+02 1.34e+00 bond pdb=" CA ILE C 909 " pdb=" C ILE C 909 " ideal model delta sigma weight residual 1.530 1.517 0.013 1.12e-02 7.97e+03 1.34e+00 ... (remaining 23427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 31585 2.59 - 5.18: 275 5.18 - 7.77: 15 7.77 - 10.36: 3 10.36 - 12.95: 1 Bond angle restraints: 31879 Sorted by residual: angle pdb=" C ARG B 328 " pdb=" N PHE B 329 " pdb=" CA PHE B 329 " ideal model delta sigma weight residual 121.80 134.75 -12.95 2.44e+00 1.68e-01 2.82e+01 angle pdb=" N ASN A 603 " pdb=" CA ASN A 603 " pdb=" C ASN A 603 " ideal model delta sigma weight residual 114.56 108.08 6.48 1.27e+00 6.20e-01 2.60e+01 angle pdb=" C HIS A 207 " pdb=" N THR A 208 " pdb=" CA THR A 208 " ideal model delta sigma weight residual 120.49 127.64 -7.15 1.42e+00 4.96e-01 2.54e+01 angle pdb=" N VAL B 213 " pdb=" CA VAL B 213 " pdb=" C VAL B 213 " ideal model delta sigma weight residual 113.20 109.13 4.07 9.60e-01 1.09e+00 1.79e+01 angle pdb=" N THR A 618 " pdb=" CA THR A 618 " pdb=" C THR A 618 " ideal model delta sigma weight residual 112.93 108.35 4.58 1.12e+00 7.97e-01 1.67e+01 ... (remaining 31874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 12605 17.97 - 35.94: 1137 35.94 - 53.92: 193 53.92 - 71.89: 38 71.89 - 89.86: 28 Dihedral angle restraints: 14001 sinusoidal: 5462 harmonic: 8539 Sorted by residual: dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N PHE A 79 " pdb=" CA PHE A 79 " ideal model delta harmonic sigma weight residual 180.00 136.54 43.46 0 5.00e+00 4.00e-02 7.55e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 170.03 -77.03 1 1.00e+01 1.00e-02 7.44e+01 dihedral pdb=" CA CYS A 617 " pdb=" C CYS A 617 " pdb=" N THR A 618 " pdb=" CA THR A 618 " ideal model delta harmonic sigma weight residual 180.00 142.98 37.02 0 5.00e+00 4.00e-02 5.48e+01 ... (remaining 13998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2487 0.040 - 0.080: 819 0.080 - 0.119: 292 0.119 - 0.159: 41 0.159 - 0.199: 4 Chirality restraints: 3643 Sorted by residual: chirality pdb=" CA PHE B 329 " pdb=" N PHE B 329 " pdb=" C PHE B 329 " pdb=" CB PHE B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.90e-01 chirality pdb=" CA ILE B 119 " pdb=" N ILE B 119 " pdb=" C ILE B 119 " pdb=" CB ILE B 119 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.45e-01 chirality pdb=" CA CYS A 617 " pdb=" N CYS A 617 " pdb=" C CYS A 617 " pdb=" CB CYS A 617 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 3640 not shown) Planarity restraints: 4139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 861 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO C 862 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 862 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 862 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1078 " 0.033 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO B1079 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B1079 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B1079 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1078 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO A1079 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A1079 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1079 " 0.028 5.00e-02 4.00e+02 ... (remaining 4136 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 458 2.67 - 3.23: 22273 3.23 - 3.79: 33823 3.79 - 4.34: 46793 4.34 - 4.90: 77738 Nonbonded interactions: 181085 Sorted by model distance: nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.114 3.040 nonbonded pdb=" N LEU C 24 " pdb=" O THR C 76 " model vdw 2.159 3.120 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.174 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.193 3.040 nonbonded pdb=" OE1 GLN C 965 " pdb=" OG SER C1003 " model vdw 2.221 3.040 ... (remaining 181080 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 24 through 144 or resid 153 through 245 or resid 261 throu \ gh 827 or resid 851 through 1146)) selection = (chain 'C' and (resid 24 through 620 or resid 641 through 1146)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.920 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.003 0.038 23466 Z= 0.166 Angle : 0.655 12.952 31947 Z= 0.380 Chirality : 0.044 0.199 3643 Planarity : 0.004 0.063 4139 Dihedral : 14.252 89.860 8393 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.23 % Allowed : 4.17 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.11 (0.13), residues: 2892 helix: -0.71 (0.20), residues: 639 sheet: -2.85 (0.18), residues: 559 loop : -3.70 (0.12), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 102 TYR 0.018 0.001 TYR B 756 PHE 0.022 0.001 PHE C 906 TRP 0.018 0.001 TRP C 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00335 (23432) covalent geometry : angle 0.65271 (31879) SS BOND : bond 0.00345 ( 34) SS BOND : angle 1.26837 ( 68) hydrogen bonds : bond 0.13922 ( 782) hydrogen bonds : angle 7.20560 ( 2163) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 250 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8477 (tm-30) REVERT: A 81 ASN cc_start: 0.7278 (p0) cc_final: 0.6689 (p0) REVERT: A 118 LEU cc_start: 0.8060 (tt) cc_final: 0.7559 (mt) REVERT: A 129 LYS cc_start: 0.7702 (pttp) cc_final: 0.7156 (pttp) REVERT: A 190 ARG cc_start: 0.7870 (mtt180) cc_final: 0.6944 (mtt180) REVERT: A 192 PHE cc_start: 0.7382 (m-10) cc_final: 0.6864 (m-10) REVERT: A 265 TYR cc_start: 0.5649 (p90) cc_final: 0.5100 (p90) REVERT: A 269 TYR cc_start: 0.7314 (m-10) cc_final: 0.7078 (m-10) REVERT: A 347 PHE cc_start: 0.7037 (m-80) cc_final: 0.6783 (m-80) REVERT: A 351 TYR cc_start: 0.7629 (p90) cc_final: 0.6954 (p90) REVERT: A 380 TYR cc_start: 0.8004 (m-80) cc_final: 0.7550 (m-80) REVERT: A 867 ASP cc_start: 0.6901 (t0) cc_final: 0.6638 (t0) REVERT: A 904 TYR cc_start: 0.7887 (m-10) cc_final: 0.7256 (m-10) REVERT: A 976 VAL cc_start: 0.8835 (t) cc_final: 0.8576 (m) REVERT: B 32 PHE cc_start: 0.8609 (m-80) cc_final: 0.7948 (m-80) REVERT: B 121 ASN cc_start: 0.7119 (m110) cc_final: 0.6385 (t0) REVERT: B 177 MET cc_start: 0.1412 (mtp) cc_final: 0.0773 (mtp) REVERT: B 239 GLN cc_start: 0.7221 (tt0) cc_final: 0.6380 (tt0) REVERT: B 619 GLU cc_start: 0.7958 (tt0) cc_final: 0.7732 (mt-10) REVERT: B 994 ASP cc_start: 0.8290 (t70) cc_final: 0.8047 (t0) REVERT: B 1138 TYR cc_start: 0.7653 (t80) cc_final: 0.7443 (t80) REVERT: C 265 TYR cc_start: 0.5690 (p90) cc_final: 0.5479 (p90) REVERT: C 271 GLN cc_start: 0.8478 (tp-100) cc_final: 0.8229 (mm-40) REVERT: C 453 TYR cc_start: 0.7156 (p90) cc_final: 0.6901 (p90) REVERT: C 787 GLN cc_start: 0.8669 (mp10) cc_final: 0.8251 (mt0) REVERT: C 902 MET cc_start: 0.8315 (tpt) cc_final: 0.7764 (tpt) REVERT: C 904 TYR cc_start: 0.7484 (m-10) cc_final: 0.7085 (m-10) REVERT: C 1142 GLN cc_start: 0.7272 (tp40) cc_final: 0.7033 (tp40) outliers start: 6 outliers final: 4 residues processed: 255 average time/residue: 0.1684 time to fit residues: 65.6851 Evaluate side-chains 171 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 167 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.0670 chunk 155 optimal weight: 0.0010 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.1528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 282 ASN A 321 GLN A 360 ASN A 388 ASN A 439 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN A 474 GLN A 544 ASN A 690 GLN A 751 ASN A 787 GLN A 872 GLN A 919 ASN A 954 GLN A 957 GLN A 969 ASN A1023 ASN A1054 GLN A1064 HIS B 30 ASN B 121 ASN B 188 ASN B 218 GLN B 239 GLN B 331 ASN B 607 GLN B 658 ASN B 751 ASN B 919 ASN B 925 ASN B 954 GLN B 965 GLN B1023 ASN B1064 HIS B1071 GLN B1074 ASN C 99 ASN C 122 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 450 ASN C 460 ASN C 481 ASN C 487 ASN C 519 HIS C 755 GLN C 901 GLN C 907 ASN C 920 GLN C 925 ASN C 954 GLN C 955 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1023 ASN C1054 GLN C1058 HIS C1064 HIS C1083 HIS C1134 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.155080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.095561 restraints weight = 35569.999| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.13 r_work: 0.3106 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23466 Z= 0.141 Angle : 0.574 12.660 31947 Z= 0.297 Chirality : 0.044 0.192 3643 Planarity : 0.004 0.046 4139 Dihedral : 5.157 59.711 3131 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.90 % Allowed : 8.88 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.15), residues: 2892 helix: 0.92 (0.22), residues: 625 sheet: -2.27 (0.19), residues: 575 loop : -3.23 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 509 TYR 0.019 0.001 TYR C 351 PHE 0.029 0.001 PHE B 329 TRP 0.025 0.002 TRP A 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00329 (23432) covalent geometry : angle 0.57198 (31879) SS BOND : bond 0.00279 ( 34) SS BOND : angle 1.17965 ( 68) hydrogen bonds : bond 0.04854 ( 782) hydrogen bonds : angle 5.33247 ( 2163) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8543 (tm-30) REVERT: A 92 PHE cc_start: 0.8104 (t80) cc_final: 0.7857 (t80) REVERT: A 118 LEU cc_start: 0.8006 (tt) cc_final: 0.7537 (mp) REVERT: A 129 LYS cc_start: 0.7086 (pttp) cc_final: 0.6439 (pttp) REVERT: A 190 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7233 (mtt180) REVERT: A 192 PHE cc_start: 0.7472 (m-10) cc_final: 0.7089 (m-10) REVERT: A 226 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7034 (mp) REVERT: A 237 ARG cc_start: 0.7563 (ptp90) cc_final: 0.6939 (mtm110) REVERT: A 265 TYR cc_start: 0.5717 (p90) cc_final: 0.5232 (p90) REVERT: A 347 PHE cc_start: 0.6863 (m-80) cc_final: 0.6496 (m-80) REVERT: A 351 TYR cc_start: 0.7449 (p90) cc_final: 0.6808 (p90) REVERT: A 360 ASN cc_start: 0.8725 (m-40) cc_final: 0.7994 (t0) REVERT: A 380 TYR cc_start: 0.8188 (m-80) cc_final: 0.7699 (m-80) REVERT: A 904 TYR cc_start: 0.7953 (m-10) cc_final: 0.7242 (m-10) REVERT: B 32 PHE cc_start: 0.8792 (m-80) cc_final: 0.7994 (m-80) REVERT: B 100 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7819 (pt) REVERT: B 102 ARG cc_start: 0.7472 (mtt90) cc_final: 0.7046 (mtt180) REVERT: B 121 ASN cc_start: 0.7322 (m-40) cc_final: 0.6213 (t0) REVERT: B 239 GLN cc_start: 0.7311 (tt0) cc_final: 0.6645 (tt0) REVERT: B 990 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7564 (mt-10) REVERT: B 1138 TYR cc_start: 0.8155 (t80) cc_final: 0.7806 (t80) REVERT: C 51 THR cc_start: 0.7815 (p) cc_final: 0.7522 (p) REVERT: C 613 GLN cc_start: 0.7911 (mt0) cc_final: 0.7662 (mt0) REVERT: C 787 GLN cc_start: 0.8888 (mp10) cc_final: 0.8376 (mt0) REVERT: C 902 MET cc_start: 0.8776 (tpt) cc_final: 0.8011 (tpt) REVERT: C 904 TYR cc_start: 0.7826 (m-10) cc_final: 0.7410 (m-10) REVERT: C 1142 GLN cc_start: 0.7083 (tp40) cc_final: 0.6856 (tp40) outliers start: 23 outliers final: 8 residues processed: 203 average time/residue: 0.1535 time to fit residues: 49.7694 Evaluate side-chains 168 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 204 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 269 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 268 optimal weight: 1.9990 chunk 258 optimal weight: 0.0040 chunk 167 optimal weight: 1.9990 overall best weight: 1.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B1135 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN C 343 ASN C 448 ASN C 907 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.149556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.087753 restraints weight = 36283.645| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.27 r_work: 0.3100 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23466 Z= 0.147 Angle : 0.555 12.140 31947 Z= 0.287 Chirality : 0.044 0.190 3643 Planarity : 0.004 0.069 4139 Dihedral : 4.826 45.908 3129 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.91 % Allowed : 11.06 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.15), residues: 2892 helix: 1.54 (0.22), residues: 628 sheet: -1.98 (0.20), residues: 570 loop : -2.93 (0.13), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 408 TYR 0.023 0.001 TYR C 265 PHE 0.019 0.001 PHE A 643 TRP 0.014 0.001 TRP C 886 HIS 0.002 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00343 (23432) covalent geometry : angle 0.55338 (31879) SS BOND : bond 0.00253 ( 34) SS BOND : angle 1.11679 ( 68) hydrogen bonds : bond 0.04640 ( 782) hydrogen bonds : angle 4.95864 ( 2163) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8512 (tm-30) REVERT: A 118 LEU cc_start: 0.7947 (tt) cc_final: 0.7512 (mp) REVERT: A 129 LYS cc_start: 0.7094 (pttp) cc_final: 0.6589 (pttp) REVERT: A 213 VAL cc_start: 0.4239 (OUTLIER) cc_final: 0.3984 (t) REVERT: A 226 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7123 (mp) REVERT: A 237 ARG cc_start: 0.7515 (ptp90) cc_final: 0.6830 (mtm110) REVERT: A 265 TYR cc_start: 0.5638 (p90) cc_final: 0.5133 (p90) REVERT: A 269 TYR cc_start: 0.7617 (m-10) cc_final: 0.7253 (m-10) REVERT: A 294 ASP cc_start: 0.7590 (m-30) cc_final: 0.7385 (m-30) REVERT: A 347 PHE cc_start: 0.6613 (m-80) cc_final: 0.6307 (m-80) REVERT: A 351 TYR cc_start: 0.7412 (p90) cc_final: 0.6792 (p90) REVERT: A 380 TYR cc_start: 0.8180 (m-80) cc_final: 0.7712 (m-80) REVERT: A 392 PHE cc_start: 0.8346 (m-80) cc_final: 0.8019 (m-80) REVERT: A 525 CYS cc_start: 0.6596 (OUTLIER) cc_final: 0.6357 (m) REVERT: A 904 TYR cc_start: 0.8015 (m-10) cc_final: 0.7378 (m-10) REVERT: A 988 GLU cc_start: 0.8313 (tp30) cc_final: 0.8022 (tp30) REVERT: B 32 PHE cc_start: 0.8708 (m-80) cc_final: 0.7915 (m-80) REVERT: B 100 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7842 (pt) REVERT: B 102 ARG cc_start: 0.7417 (mtt90) cc_final: 0.7008 (mtt90) REVERT: B 121 ASN cc_start: 0.7190 (m-40) cc_final: 0.6222 (t0) REVERT: B 169 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7699 (mp0) REVERT: B 239 GLN cc_start: 0.7248 (tt0) cc_final: 0.6770 (tt0) REVERT: B 960 ASN cc_start: 0.8260 (m-40) cc_final: 0.7732 (t0) REVERT: B 990 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7566 (mt-10) REVERT: B 1138 TYR cc_start: 0.8101 (t80) cc_final: 0.7728 (t80) REVERT: C 51 THR cc_start: 0.8126 (p) cc_final: 0.7885 (p) REVERT: C 448 ASN cc_start: 0.6133 (OUTLIER) cc_final: 0.5630 (m110) REVERT: C 525 CYS cc_start: 0.5189 (OUTLIER) cc_final: 0.4654 (m) REVERT: C 613 GLN cc_start: 0.8042 (mt0) cc_final: 0.7771 (mt0) REVERT: C 726 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8951 (mm) REVERT: C 787 GLN cc_start: 0.8837 (mp10) cc_final: 0.8239 (mt0) REVERT: C 1141 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6479 (pp) REVERT: C 1142 GLN cc_start: 0.7072 (tp40) cc_final: 0.6769 (mm-40) outliers start: 49 outliers final: 26 residues processed: 214 average time/residue: 0.1418 time to fit residues: 49.7303 Evaluate side-chains 195 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 84 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 144 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 264 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 99 ASN C 207 HIS C 450 ASN C 907 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.149543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.089656 restraints weight = 35411.365| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.11 r_work: 0.3113 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23466 Z= 0.124 Angle : 0.529 13.576 31947 Z= 0.273 Chirality : 0.043 0.192 3643 Planarity : 0.004 0.046 4139 Dihedral : 4.581 38.903 3129 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.03 % Allowed : 12.27 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.15), residues: 2892 helix: 1.95 (0.22), residues: 624 sheet: -1.67 (0.20), residues: 593 loop : -2.73 (0.13), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.023 0.001 TYR C 265 PHE 0.028 0.001 PHE A 194 TRP 0.013 0.001 TRP C 886 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00286 (23432) covalent geometry : angle 0.52732 (31879) SS BOND : bond 0.00226 ( 34) SS BOND : angle 1.03226 ( 68) hydrogen bonds : bond 0.04322 ( 782) hydrogen bonds : angle 4.70399 ( 2163) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 179 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8468 (tm-30) REVERT: A 118 LEU cc_start: 0.7867 (tt) cc_final: 0.7583 (mt) REVERT: A 119 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.7078 (mp) REVERT: A 129 LYS cc_start: 0.7322 (pttp) cc_final: 0.6968 (pttp) REVERT: A 213 VAL cc_start: 0.4023 (OUTLIER) cc_final: 0.3736 (t) REVERT: A 226 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.6967 (mp) REVERT: A 237 ARG cc_start: 0.7526 (ptp90) cc_final: 0.6926 (mtm110) REVERT: A 265 TYR cc_start: 0.5569 (p90) cc_final: 0.5151 (p90) REVERT: A 269 TYR cc_start: 0.7673 (m-10) cc_final: 0.7381 (m-10) REVERT: A 347 PHE cc_start: 0.6634 (m-80) cc_final: 0.6314 (m-80) REVERT: A 351 TYR cc_start: 0.7394 (p90) cc_final: 0.6758 (p90) REVERT: A 380 TYR cc_start: 0.8164 (m-80) cc_final: 0.7776 (m-80) REVERT: A 392 PHE cc_start: 0.8442 (m-80) cc_final: 0.8115 (m-80) REVERT: A 592 PHE cc_start: 0.5924 (OUTLIER) cc_final: 0.4965 (t80) REVERT: A 904 TYR cc_start: 0.8084 (m-10) cc_final: 0.7520 (m-10) REVERT: A 988 GLU cc_start: 0.8341 (tp30) cc_final: 0.8007 (tp30) REVERT: B 32 PHE cc_start: 0.8685 (m-80) cc_final: 0.7967 (m-80) REVERT: B 100 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7825 (pt) REVERT: B 102 ARG cc_start: 0.7384 (mtt90) cc_final: 0.6798 (mtt180) REVERT: B 121 ASN cc_start: 0.7115 (m-40) cc_final: 0.6353 (t0) REVERT: B 169 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7602 (mp0) REVERT: B 239 GLN cc_start: 0.7256 (tt0) cc_final: 0.6905 (tt0) REVERT: B 960 ASN cc_start: 0.8173 (m-40) cc_final: 0.7805 (t0) REVERT: B 988 GLU cc_start: 0.7688 (pm20) cc_final: 0.7427 (pm20) REVERT: B 990 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7489 (mt-10) REVERT: B 1138 TYR cc_start: 0.8134 (t80) cc_final: 0.7761 (t80) REVERT: C 525 CYS cc_start: 0.5154 (OUTLIER) cc_final: 0.4854 (m) REVERT: C 726 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8934 (mm) REVERT: C 787 GLN cc_start: 0.8819 (mp10) cc_final: 0.8414 (mt0) REVERT: C 1141 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6817 (pp) REVERT: C 1142 GLN cc_start: 0.7043 (tp40) cc_final: 0.6710 (mm-40) outliers start: 52 outliers final: 27 residues processed: 225 average time/residue: 0.1425 time to fit residues: 52.7587 Evaluate side-chains 194 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 199 optimal weight: 30.0000 chunk 124 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 209 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 chunk 274 optimal weight: 3.9990 chunk 278 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 360 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 30 ASN B 49 HIS B 239 GLN B 955 ASN B1005 GLN B1011 GLN C 49 HIS C 218 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 907 ASN C 965 GLN C1002 GLN C1074 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.144247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.083687 restraints weight = 35802.827| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.12 r_work: 0.3023 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 23466 Z= 0.354 Angle : 0.707 13.331 31947 Z= 0.363 Chirality : 0.049 0.215 3643 Planarity : 0.005 0.058 4139 Dihedral : 5.126 38.999 3128 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 2.77 % Allowed : 13.95 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.15), residues: 2892 helix: 1.50 (0.22), residues: 618 sheet: -1.79 (0.20), residues: 586 loop : -2.81 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 408 TYR 0.025 0.002 TYR C 756 PHE 0.027 0.002 PHE A 800 TRP 0.021 0.002 TRP C 886 HIS 0.006 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00852 (23432) covalent geometry : angle 0.70347 (31879) SS BOND : bond 0.00408 ( 34) SS BOND : angle 1.62639 ( 68) hydrogen bonds : bond 0.06319 ( 782) hydrogen bonds : angle 5.23154 ( 2163) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 163 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8772 (tm-30) REVERT: A 118 LEU cc_start: 0.8060 (tt) cc_final: 0.7589 (mp) REVERT: A 129 LYS cc_start: 0.7154 (pttp) cc_final: 0.6404 (pttp) REVERT: A 223 LEU cc_start: 0.7833 (mt) cc_final: 0.7390 (mt) REVERT: A 226 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7295 (mp) REVERT: A 237 ARG cc_start: 0.7603 (ptp90) cc_final: 0.7070 (mtm110) REVERT: A 265 TYR cc_start: 0.5751 (p90) cc_final: 0.5322 (p90) REVERT: A 347 PHE cc_start: 0.6906 (m-80) cc_final: 0.6587 (m-80) REVERT: A 351 TYR cc_start: 0.7429 (p90) cc_final: 0.6896 (p90) REVERT: A 380 TYR cc_start: 0.8175 (m-80) cc_final: 0.7598 (m-80) REVERT: A 592 PHE cc_start: 0.6157 (OUTLIER) cc_final: 0.5494 (t80) REVERT: A 904 TYR cc_start: 0.8054 (m-10) cc_final: 0.7260 (m-10) REVERT: A 988 GLU cc_start: 0.8508 (tp30) cc_final: 0.8120 (tp30) REVERT: B 32 PHE cc_start: 0.8658 (m-80) cc_final: 0.8157 (m-80) REVERT: B 100 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7917 (pt) REVERT: B 102 ARG cc_start: 0.7406 (mtt90) cc_final: 0.6837 (mtt180) REVERT: B 121 ASN cc_start: 0.7353 (m-40) cc_final: 0.6321 (t0) REVERT: B 239 GLN cc_start: 0.7419 (tt0) cc_final: 0.7212 (tt0) REVERT: B 990 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7775 (mt-10) REVERT: B 1138 TYR cc_start: 0.8277 (t80) cc_final: 0.7999 (t80) REVERT: C 515 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.6119 (p90) REVERT: C 756 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.7615 (m-80) REVERT: C 904 TYR cc_start: 0.7861 (m-10) cc_final: 0.7410 (m-10) REVERT: C 1141 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6771 (pp) REVERT: C 1142 GLN cc_start: 0.7033 (tp40) cc_final: 0.6700 (mm-40) outliers start: 71 outliers final: 45 residues processed: 224 average time/residue: 0.1301 time to fit residues: 48.6884 Evaluate side-chains 202 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 151 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 30.0000 chunk 161 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 225 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1142 GLN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 907 ASN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.148192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.087958 restraints weight = 35352.353| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.12 r_work: 0.3101 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23466 Z= 0.136 Angle : 0.558 14.924 31947 Z= 0.285 Chirality : 0.044 0.175 3643 Planarity : 0.004 0.056 4139 Dihedral : 4.633 37.659 3127 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.61 % Allowed : 15.47 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.15), residues: 2892 helix: 1.94 (0.22), residues: 635 sheet: -1.56 (0.20), residues: 593 loop : -2.66 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 408 TYR 0.021 0.001 TYR C 351 PHE 0.020 0.001 PHE A 643 TRP 0.016 0.001 TRP C 886 HIS 0.005 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00316 (23432) covalent geometry : angle 0.55609 (31879) SS BOND : bond 0.00257 ( 34) SS BOND : angle 1.09869 ( 68) hydrogen bonds : bond 0.04671 ( 782) hydrogen bonds : angle 4.71514 ( 2163) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 164 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8018 (tt) cc_final: 0.7596 (mp) REVERT: A 129 LYS cc_start: 0.7323 (pttp) cc_final: 0.6865 (pttp) REVERT: A 190 ARG cc_start: 0.7682 (mtt180) cc_final: 0.7011 (mpt-90) REVERT: A 213 VAL cc_start: 0.4559 (OUTLIER) cc_final: 0.4251 (t) REVERT: A 226 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7185 (mp) REVERT: A 237 ARG cc_start: 0.7619 (ptp90) cc_final: 0.7007 (mtm110) REVERT: A 265 TYR cc_start: 0.5702 (p90) cc_final: 0.5293 (p90) REVERT: A 269 TYR cc_start: 0.7555 (m-10) cc_final: 0.7101 (m-10) REVERT: A 347 PHE cc_start: 0.7025 (m-80) cc_final: 0.6706 (m-80) REVERT: A 351 TYR cc_start: 0.7509 (p90) cc_final: 0.6861 (p90) REVERT: A 380 TYR cc_start: 0.8195 (m-80) cc_final: 0.7828 (m-80) REVERT: A 592 PHE cc_start: 0.5990 (OUTLIER) cc_final: 0.5296 (t80) REVERT: A 904 TYR cc_start: 0.8076 (m-10) cc_final: 0.7458 (m-10) REVERT: A 988 GLU cc_start: 0.8427 (tp30) cc_final: 0.8119 (tp30) REVERT: B 32 PHE cc_start: 0.8658 (m-80) cc_final: 0.7976 (m-80) REVERT: B 100 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7881 (pt) REVERT: B 102 ARG cc_start: 0.7330 (mtt90) cc_final: 0.6703 (mtt180) REVERT: B 121 ASN cc_start: 0.7345 (m-40) cc_final: 0.6306 (t0) REVERT: B 169 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7820 (mp0) REVERT: B 239 GLN cc_start: 0.7447 (tt0) cc_final: 0.7245 (tt0) REVERT: B 553 THR cc_start: 0.6876 (OUTLIER) cc_final: 0.6647 (m) REVERT: B 592 PHE cc_start: 0.7613 (m-10) cc_final: 0.7402 (m-10) REVERT: B 780 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7910 (mm-30) REVERT: B 960 ASN cc_start: 0.8166 (m-40) cc_final: 0.7726 (t0) REVERT: B 990 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7647 (mt-10) REVERT: B 1138 TYR cc_start: 0.8107 (t80) cc_final: 0.7771 (t80) REVERT: C 726 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8921 (mm) REVERT: C 756 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.6749 (m-80) REVERT: C 787 GLN cc_start: 0.8870 (mp10) cc_final: 0.8478 (mt0) REVERT: C 904 TYR cc_start: 0.7880 (m-10) cc_final: 0.7404 (m-10) REVERT: C 1141 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6841 (pp) REVERT: C 1142 GLN cc_start: 0.6970 (tp40) cc_final: 0.6634 (mm-40) outliers start: 67 outliers final: 43 residues processed: 223 average time/residue: 0.1409 time to fit residues: 51.6294 Evaluate side-chains 211 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 160 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 5 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 285 optimal weight: 0.7980 chunk 282 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 422 ASN C 907 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.146277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.084227 restraints weight = 36163.696| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.26 r_work: 0.3046 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 23466 Z= 0.264 Angle : 0.636 16.604 31947 Z= 0.325 Chirality : 0.046 0.180 3643 Planarity : 0.004 0.057 4139 Dihedral : 4.872 36.671 3127 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 2.49 % Allowed : 16.13 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.15), residues: 2892 helix: 1.72 (0.22), residues: 636 sheet: -1.63 (0.20), residues: 600 loop : -2.67 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 408 TYR 0.021 0.002 TYR C 351 PHE 0.020 0.002 PHE A 800 TRP 0.032 0.002 TRP A 104 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00635 (23432) covalent geometry : angle 0.63375 (31879) SS BOND : bond 0.00316 ( 34) SS BOND : angle 1.36722 ( 68) hydrogen bonds : bond 0.05580 ( 782) hydrogen bonds : angle 4.97590 ( 2163) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 163 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8040 (tt) cc_final: 0.7606 (mp) REVERT: A 129 LYS cc_start: 0.7343 (pttp) cc_final: 0.6751 (pttt) REVERT: A 190 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7015 (mmt180) REVERT: A 213 VAL cc_start: 0.4399 (OUTLIER) cc_final: 0.4067 (t) REVERT: A 226 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7120 (mp) REVERT: A 237 ARG cc_start: 0.7602 (ptp90) cc_final: 0.6999 (mtm110) REVERT: A 265 TYR cc_start: 0.5758 (p90) cc_final: 0.5345 (p90) REVERT: A 347 PHE cc_start: 0.7046 (m-80) cc_final: 0.6673 (m-80) REVERT: A 351 TYR cc_start: 0.7519 (p90) cc_final: 0.6933 (p90) REVERT: A 360 ASN cc_start: 0.8515 (m110) cc_final: 0.8040 (t0) REVERT: A 380 TYR cc_start: 0.8258 (m-80) cc_final: 0.7769 (m-80) REVERT: A 592 PHE cc_start: 0.6086 (OUTLIER) cc_final: 0.5524 (t80) REVERT: A 904 TYR cc_start: 0.8129 (m-10) cc_final: 0.7464 (m-10) REVERT: A 988 GLU cc_start: 0.8518 (tp30) cc_final: 0.8203 (tp30) REVERT: B 32 PHE cc_start: 0.8704 (m-80) cc_final: 0.7993 (m-80) REVERT: B 100 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7919 (pt) REVERT: B 102 ARG cc_start: 0.7356 (mtt90) cc_final: 0.6754 (mtt180) REVERT: B 121 ASN cc_start: 0.7542 (m-40) cc_final: 0.6408 (t0) REVERT: B 169 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7752 (mp0) REVERT: B 592 PHE cc_start: 0.7889 (m-10) cc_final: 0.7512 (m-10) REVERT: B 988 GLU cc_start: 0.7657 (pm20) cc_final: 0.7399 (pm20) REVERT: B 990 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7772 (mt-10) REVERT: B 1138 TYR cc_start: 0.8221 (t80) cc_final: 0.7911 (t80) REVERT: C 51 THR cc_start: 0.8194 (p) cc_final: 0.7870 (p) REVERT: C 515 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.6077 (p90) REVERT: C 537 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8352 (mtpp) REVERT: C 726 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8899 (mm) REVERT: C 756 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7319 (m-80) REVERT: C 787 GLN cc_start: 0.8931 (mp10) cc_final: 0.8530 (mt0) REVERT: C 904 TYR cc_start: 0.7840 (m-10) cc_final: 0.7414 (m-10) REVERT: C 1141 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6944 (pp) REVERT: C 1142 GLN cc_start: 0.6948 (tp40) cc_final: 0.6611 (mm-40) outliers start: 64 outliers final: 47 residues processed: 218 average time/residue: 0.1395 time to fit residues: 50.2556 Evaluate side-chains 216 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 161 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 28 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 148 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.150317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.088679 restraints weight = 35777.652| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.27 r_work: 0.3107 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23466 Z= 0.111 Angle : 0.540 17.100 31947 Z= 0.277 Chirality : 0.043 0.173 3643 Planarity : 0.004 0.057 4139 Dihedral : 4.462 35.138 3127 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.14 % Allowed : 16.67 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.16), residues: 2892 helix: 2.18 (0.22), residues: 632 sheet: -1.44 (0.21), residues: 612 loop : -2.53 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 466 TYR 0.019 0.001 TYR C 351 PHE 0.021 0.001 PHE A 92 TRP 0.048 0.002 TRP A 104 HIS 0.003 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00254 (23432) covalent geometry : angle 0.53900 (31879) SS BOND : bond 0.00224 ( 34) SS BOND : angle 0.99355 ( 68) hydrogen bonds : bond 0.04225 ( 782) hydrogen bonds : angle 4.55737 ( 2163) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 172 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7950 (tt) cc_final: 0.7498 (mp) REVERT: A 129 LYS cc_start: 0.7210 (pttp) cc_final: 0.6702 (pttp) REVERT: A 190 ARG cc_start: 0.7764 (mtt180) cc_final: 0.7004 (mmt180) REVERT: A 213 VAL cc_start: 0.4364 (OUTLIER) cc_final: 0.4025 (t) REVERT: A 226 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.6833 (mp) REVERT: A 237 ARG cc_start: 0.7544 (ptp90) cc_final: 0.7007 (mtm110) REVERT: A 265 TYR cc_start: 0.5620 (p90) cc_final: 0.5197 (p90) REVERT: A 269 TYR cc_start: 0.7645 (m-10) cc_final: 0.7158 (m-10) REVERT: A 347 PHE cc_start: 0.7037 (m-80) cc_final: 0.6704 (m-80) REVERT: A 351 TYR cc_start: 0.7409 (p90) cc_final: 0.6801 (p90) REVERT: A 360 ASN cc_start: 0.8492 (m110) cc_final: 0.7979 (t0) REVERT: A 380 TYR cc_start: 0.8178 (m-80) cc_final: 0.7858 (m-80) REVERT: A 592 PHE cc_start: 0.5984 (OUTLIER) cc_final: 0.5252 (t80) REVERT: A 904 TYR cc_start: 0.8068 (m-10) cc_final: 0.7486 (m-10) REVERT: A 988 GLU cc_start: 0.8457 (tp30) cc_final: 0.8214 (tp30) REVERT: B 32 PHE cc_start: 0.8597 (m-80) cc_final: 0.7938 (m-80) REVERT: B 100 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7862 (pt) REVERT: B 102 ARG cc_start: 0.7226 (mtt90) cc_final: 0.6603 (mtt180) REVERT: B 121 ASN cc_start: 0.7407 (m-40) cc_final: 0.6366 (t0) REVERT: B 592 PHE cc_start: 0.7451 (m-10) cc_final: 0.7236 (m-10) REVERT: B 614 ASP cc_start: 0.8009 (t0) cc_final: 0.7717 (t0) REVERT: B 751 ASN cc_start: 0.9043 (m-40) cc_final: 0.8710 (t0) REVERT: B 780 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7793 (mm-30) REVERT: B 960 ASN cc_start: 0.8114 (m-40) cc_final: 0.7669 (t0) REVERT: B 988 GLU cc_start: 0.7585 (pm20) cc_final: 0.7313 (pm20) REVERT: B 990 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7546 (mt-10) REVERT: B 1138 TYR cc_start: 0.8025 (t80) cc_final: 0.7660 (t80) REVERT: C 53 ASP cc_start: 0.7492 (t0) cc_final: 0.7198 (t70) REVERT: C 726 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8912 (mm) REVERT: C 756 TYR cc_start: 0.7818 (OUTLIER) cc_final: 0.6275 (m-80) REVERT: C 787 GLN cc_start: 0.8853 (mp10) cc_final: 0.8448 (mt0) REVERT: C 904 TYR cc_start: 0.7817 (m-10) cc_final: 0.7413 (m-10) outliers start: 55 outliers final: 38 residues processed: 219 average time/residue: 0.1380 time to fit residues: 50.0662 Evaluate side-chains 203 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 142 optimal weight: 0.0670 chunk 53 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 174 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 81 optimal weight: 0.5980 chunk 116 optimal weight: 20.0000 chunk 203 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN C 122 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.149670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.087970 restraints weight = 35953.013| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.27 r_work: 0.3097 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23466 Z= 0.135 Angle : 0.559 15.822 31947 Z= 0.286 Chirality : 0.044 0.175 3643 Planarity : 0.004 0.054 4139 Dihedral : 4.435 34.084 3127 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.10 % Allowed : 16.83 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.16), residues: 2892 helix: 2.31 (0.22), residues: 622 sheet: -1.31 (0.21), residues: 606 loop : -2.46 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 466 TYR 0.022 0.001 TYR C 351 PHE 0.021 0.001 PHE C 201 TRP 0.075 0.002 TRP A 104 HIS 0.003 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00318 (23432) covalent geometry : angle 0.55418 (31879) SS BOND : bond 0.00456 ( 34) SS BOND : angle 1.68230 ( 68) hydrogen bonds : bond 0.04357 ( 782) hydrogen bonds : angle 4.55105 ( 2163) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 160 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8256 (t80) cc_final: 0.7754 (t80) REVERT: A 118 LEU cc_start: 0.7949 (tt) cc_final: 0.7446 (mp) REVERT: A 129 LYS cc_start: 0.7196 (pttp) cc_final: 0.6614 (pttp) REVERT: A 213 VAL cc_start: 0.4418 (OUTLIER) cc_final: 0.4081 (t) REVERT: A 226 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.6837 (mp) REVERT: A 237 ARG cc_start: 0.7525 (ptp90) cc_final: 0.6953 (mtm110) REVERT: A 265 TYR cc_start: 0.5604 (p90) cc_final: 0.5202 (p90) REVERT: A 269 TYR cc_start: 0.7619 (m-10) cc_final: 0.7125 (m-10) REVERT: A 347 PHE cc_start: 0.7201 (m-80) cc_final: 0.6917 (m-80) REVERT: A 351 TYR cc_start: 0.7416 (p90) cc_final: 0.6811 (p90) REVERT: A 360 ASN cc_start: 0.8469 (m110) cc_final: 0.8034 (t0) REVERT: A 380 TYR cc_start: 0.8185 (m-80) cc_final: 0.7820 (m-80) REVERT: A 592 PHE cc_start: 0.6026 (OUTLIER) cc_final: 0.5298 (t80) REVERT: A 904 TYR cc_start: 0.8083 (m-10) cc_final: 0.7471 (m-10) REVERT: A 988 GLU cc_start: 0.8461 (tp30) cc_final: 0.8213 (tp30) REVERT: B 32 PHE cc_start: 0.8661 (m-80) cc_final: 0.8017 (m-80) REVERT: B 100 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7867 (pt) REVERT: B 102 ARG cc_start: 0.7231 (mtt90) cc_final: 0.6595 (mtt180) REVERT: B 121 ASN cc_start: 0.7387 (m-40) cc_final: 0.6394 (t0) REVERT: B 239 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6498 (tm-30) REVERT: B 592 PHE cc_start: 0.7530 (m-10) cc_final: 0.7315 (m-10) REVERT: B 614 ASP cc_start: 0.8028 (t0) cc_final: 0.7728 (t0) REVERT: B 751 ASN cc_start: 0.9039 (m-40) cc_final: 0.8714 (t0) REVERT: B 990 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7397 (mt-10) REVERT: B 1138 TYR cc_start: 0.8090 (t80) cc_final: 0.7745 (t80) REVERT: C 53 ASP cc_start: 0.7555 (t0) cc_final: 0.7352 (t70) REVERT: C 177 MET cc_start: 0.0669 (ptm) cc_final: -0.4673 (mmt) REVERT: C 515 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.6040 (p90) REVERT: C 516 GLU cc_start: 0.7204 (pm20) cc_final: 0.6695 (pm20) REVERT: C 726 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8915 (mm) REVERT: C 787 GLN cc_start: 0.8841 (mp10) cc_final: 0.8440 (mt0) REVERT: C 904 TYR cc_start: 0.7778 (m-10) cc_final: 0.7475 (m-10) outliers start: 54 outliers final: 38 residues processed: 208 average time/residue: 0.1382 time to fit residues: 47.8713 Evaluate side-chains 205 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 182 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 273 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 242 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 212 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN C 125 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.150502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.089128 restraints weight = 35940.171| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.26 r_work: 0.3115 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23466 Z= 0.117 Angle : 0.552 16.130 31947 Z= 0.282 Chirality : 0.043 0.194 3643 Planarity : 0.004 0.059 4139 Dihedral : 4.333 33.074 3127 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.87 % Allowed : 17.22 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.16), residues: 2892 helix: 2.37 (0.22), residues: 622 sheet: -1.22 (0.21), residues: 608 loop : -2.40 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 466 TYR 0.021 0.001 TYR C 351 PHE 0.022 0.001 PHE C 906 TRP 0.086 0.002 TRP A 104 HIS 0.003 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00271 (23432) covalent geometry : angle 0.54736 (31879) SS BOND : bond 0.00438 ( 34) SS BOND : angle 1.60120 ( 68) hydrogen bonds : bond 0.04173 ( 782) hydrogen bonds : angle 4.47021 ( 2163) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7880 (tt) cc_final: 0.7485 (mp) REVERT: A 129 LYS cc_start: 0.7182 (pttp) cc_final: 0.6680 (pttp) REVERT: A 190 ARG cc_start: 0.7268 (mtt180) cc_final: 0.6982 (mpt-90) REVERT: A 213 VAL cc_start: 0.4381 (OUTLIER) cc_final: 0.4025 (t) REVERT: A 237 ARG cc_start: 0.7526 (ptp90) cc_final: 0.6951 (mtm110) REVERT: A 265 TYR cc_start: 0.5608 (p90) cc_final: 0.5211 (p90) REVERT: A 269 TYR cc_start: 0.7670 (m-10) cc_final: 0.7228 (m-10) REVERT: A 347 PHE cc_start: 0.7224 (m-80) cc_final: 0.6933 (m-80) REVERT: A 351 TYR cc_start: 0.7420 (p90) cc_final: 0.6825 (p90) REVERT: A 360 ASN cc_start: 0.8355 (m110) cc_final: 0.7923 (t0) REVERT: A 380 TYR cc_start: 0.8194 (m-80) cc_final: 0.7894 (m-80) REVERT: A 592 PHE cc_start: 0.5983 (OUTLIER) cc_final: 0.5258 (t80) REVERT: A 904 TYR cc_start: 0.8071 (m-10) cc_final: 0.7474 (m-10) REVERT: A 988 GLU cc_start: 0.8398 (tp30) cc_final: 0.8141 (tp30) REVERT: B 32 PHE cc_start: 0.8657 (m-80) cc_final: 0.8036 (m-80) REVERT: B 100 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7855 (pt) REVERT: B 102 ARG cc_start: 0.7212 (mtt90) cc_final: 0.6604 (mtt180) REVERT: B 121 ASN cc_start: 0.7394 (m-40) cc_final: 0.6404 (t0) REVERT: B 239 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6516 (tm-30) REVERT: B 614 ASP cc_start: 0.8040 (t0) cc_final: 0.7690 (t0) REVERT: B 751 ASN cc_start: 0.9035 (m-40) cc_final: 0.8723 (t0) REVERT: B 990 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7352 (mt-10) REVERT: B 1138 TYR cc_start: 0.8073 (t80) cc_final: 0.7713 (t80) REVERT: C 53 ASP cc_start: 0.7549 (t0) cc_final: 0.7311 (t70) REVERT: C 125 ASN cc_start: 0.4199 (OUTLIER) cc_final: 0.3157 (m-40) REVERT: C 177 MET cc_start: 0.0568 (ptm) cc_final: -0.4303 (mmt) REVERT: C 537 LYS cc_start: 0.8664 (mmtt) cc_final: 0.8264 (mtpp) REVERT: C 726 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8892 (mm) REVERT: C 756 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.5849 (m-80) REVERT: C 787 GLN cc_start: 0.8755 (mp10) cc_final: 0.8356 (mt0) REVERT: C 904 TYR cc_start: 0.7831 (m-10) cc_final: 0.7449 (m-10) outliers start: 48 outliers final: 39 residues processed: 208 average time/residue: 0.1383 time to fit residues: 47.5732 Evaluate side-chains 207 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 275 optimal weight: 0.3980 chunk 209 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 225 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B1119 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.149601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.089753 restraints weight = 35284.450| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.12 r_work: 0.3114 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 23466 Z= 0.179 Angle : 0.747 59.200 31947 Z= 0.416 Chirality : 0.046 0.475 3643 Planarity : 0.004 0.059 4139 Dihedral : 4.335 33.099 3127 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.99 % Allowed : 17.26 % Favored : 80.76 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.16), residues: 2892 helix: 2.35 (0.22), residues: 622 sheet: -1.21 (0.21), residues: 608 loop : -2.40 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 466 TYR 0.018 0.001 TYR C 351 PHE 0.020 0.001 PHE C 906 TRP 0.079 0.002 TRP A 104 HIS 0.003 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00377 (23432) covalent geometry : angle 0.71599 (31879) SS BOND : bond 0.01877 ( 34) SS BOND : angle 4.68420 ( 68) hydrogen bonds : bond 0.04230 ( 782) hydrogen bonds : angle 4.46932 ( 2163) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6201.05 seconds wall clock time: 106 minutes 27.34 seconds (6387.34 seconds total)