Starting phenix.real_space_refine on Sun Sep 29 17:15:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb3_31513/09_2024/7fb3_31513.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb3_31513/09_2024/7fb3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb3_31513/09_2024/7fb3_31513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb3_31513/09_2024/7fb3_31513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb3_31513/09_2024/7fb3_31513.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb3_31513/09_2024/7fb3_31513.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 13.69, per 1000 atoms: 0.60 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: 5.34 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 3.09 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: 9.52 Time building geometry restraints manager: 6.27 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 52.510 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.990 ------------------------------------------------------------------------------- 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 23432 Z= 0.218 Angle : 0.653 12.952 31879 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 : 9.15 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.001 TRP C 886 HIS 0.004 0.001 HIS C1064 PHE 0.022 0.001 PHE C 906 TYR 0.018 0.001 TYR B 756 ARG 0.005 0.000 ARG A 102 *********************** 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 fitting. rotamer outliers: 6 poor density : 250 time to evaluate : 2.413 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: 0.6688 (p0) REVERT: A 118 LEU cc_start: 0.8060 (tt) cc_final: 0.7560 (mt) REVERT: A 129 LYS cc_start: 0.7702 (pttp) cc_final: 0.7155 (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: 0.8048 (t0) REVERT: B 1138 TYR cc_start: 0.7653 (t80) cc_final: 0.7442 (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: 0.8230 (mm-40) 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: 0.4040 time to fit residues: 156.9898 Evaluate side-chains 171 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 2.593 ------------------------------------------------------------------------------- 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 246 optimal weight: 0.5980 chunk 221 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 118 optimal weight: 30.0000 chunk 228 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 755 GLN C 901 GLN C 907 ASN C 920 GLN C 925 ASN C 954 GLN ** 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: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23432 Z= 0.227 Angle : 0.580 12.672 31879 Z= 0.300 Chirality : 0.044 0.193 3643 Planarity : 0.004 0.046 4139 Dihedral : 5.173 59.670 3131 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.90 % Allowed : 9.31 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.15), residues: 2892 helix: 0.94 (0.22), residues: 629 sheet: -2.27 (0.19), residues: 575 loop : -3.24 (0.13), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 436 HIS 0.004 0.001 HIS A1048 PHE 0.029 0.001 PHE B 329 TYR 0.020 0.001 TYR C 351 ARG 0.008 0.000 ARG A 509 *********************** 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 210 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 187 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8402 (tm-30) REVERT: A 92 PHE cc_start: 0.7971 (t80) cc_final: 0.7765 (t80) REVERT: A 104 TRP cc_start: 0.6621 (m-90) cc_final: 0.6400 (m-90) REVERT: A 118 LEU cc_start: 0.8045 (tt) cc_final: 0.7540 (mp) REVERT: A 129 LYS cc_start: 0.7419 (pttp) cc_final: 0.6334 (pttp) REVERT: A 190 ARG cc_start: 0.7684 (mtt180) cc_final: 0.7068 (mtt180) REVERT: A 192 PHE cc_start: 0.7364 (m-10) cc_final: 0.6960 (m-10) REVERT: A 226 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7157 (mp) REVERT: A 237 ARG cc_start: 0.7566 (ptp90) cc_final: 0.6994 (mtm110) REVERT: A 265 TYR cc_start: 0.5747 (p90) cc_final: 0.5241 (p90) REVERT: A 347 PHE cc_start: 0.7072 (m-80) cc_final: 0.6746 (m-80) REVERT: A 351 TYR cc_start: 0.7548 (p90) cc_final: 0.6866 (p90) REVERT: A 380 TYR cc_start: 0.8182 (m-80) cc_final: 0.7668 (m-80) REVERT: A 525 CYS cc_start: 0.6324 (OUTLIER) cc_final: 0.6093 (m) REVERT: A 904 TYR cc_start: 0.7780 (m-10) cc_final: 0.7097 (m-10) REVERT: B 32 PHE cc_start: 0.8589 (m-80) cc_final: 0.8145 (m-80) REVERT: B 100 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7766 (pt) REVERT: B 102 ARG cc_start: 0.7289 (mtt90) cc_final: 0.6994 (mtt180) REVERT: B 104 TRP cc_start: 0.8049 (m-90) cc_final: 0.7683 (m-90) REVERT: B 121 ASN cc_start: 0.7299 (m-40) cc_final: 0.6341 (t0) REVERT: B 177 MET cc_start: 0.1360 (mtp) cc_final: 0.0483 (mtp) REVERT: B 239 GLN cc_start: 0.7404 (tt0) cc_final: 0.6719 (tt0) REVERT: B 990 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7364 (mt-10) REVERT: B 1138 TYR cc_start: 0.7702 (t80) cc_final: 0.7480 (t80) REVERT: C 271 GLN cc_start: 0.8218 (tp-100) cc_final: 0.7997 (mm-40) REVERT: C 787 GLN cc_start: 0.8640 (mp10) cc_final: 0.8194 (mt0) REVERT: C 904 TYR cc_start: 0.7462 (m-10) cc_final: 0.7173 (m-10) outliers start: 23 outliers final: 8 residues processed: 207 average time/residue: 0.3494 time to fit residues: 114.1537 Evaluate side-chains 171 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 160 time to evaluate : 2.298 ------------------------------------------------------------------------------- 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 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 147 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 220 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 286 optimal weight: 0.5980 chunk 236 optimal weight: 0.6980 chunk 263 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 544 ASN B 955 ASN B1011 GLN B1135 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN C 448 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23432 Z= 0.293 Angle : 0.583 12.299 31879 Z= 0.301 Chirality : 0.045 0.193 3643 Planarity : 0.004 0.073 4139 Dihedral : 4.944 43.642 3129 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.83 % Allowed : 11.45 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.15), residues: 2892 helix: 1.40 (0.22), residues: 628 sheet: -2.00 (0.20), residues: 589 loop : -3.01 (0.13), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 886 HIS 0.003 0.001 HIS A1088 PHE 0.020 0.001 PHE C 906 TYR 0.022 0.001 TYR C 351 ARG 0.006 0.000 ARG C 408 *********************** 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 217 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 170 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8373 (tm-30) REVERT: A 92 PHE cc_start: 0.8055 (t80) cc_final: 0.7810 (t80) REVERT: A 118 LEU cc_start: 0.8061 (tt) cc_final: 0.7620 (mp) REVERT: A 129 LYS cc_start: 0.7416 (pttp) cc_final: 0.6712 (pttp) REVERT: A 190 ARG cc_start: 0.7841 (mtt180) cc_final: 0.7322 (mtt180) REVERT: A 213 VAL cc_start: 0.4049 (OUTLIER) cc_final: 0.3747 (t) REVERT: A 226 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7306 (mp) REVERT: A 237 ARG cc_start: 0.7594 (ptp90) cc_final: 0.7116 (mtm110) REVERT: A 265 TYR cc_start: 0.5759 (p90) cc_final: 0.5222 (p90) REVERT: A 269 TYR cc_start: 0.7415 (m-10) cc_final: 0.6955 (m-10) REVERT: A 347 PHE cc_start: 0.6909 (m-80) cc_final: 0.6492 (m-80) REVERT: A 351 TYR cc_start: 0.7540 (p90) cc_final: 0.6885 (p90) REVERT: A 380 TYR cc_start: 0.8165 (m-80) cc_final: 0.7715 (m-80) REVERT: A 388 ASN cc_start: 0.9060 (t0) cc_final: 0.8838 (t0) REVERT: A 392 PHE cc_start: 0.8303 (m-80) cc_final: 0.8073 (m-80) REVERT: A 592 PHE cc_start: 0.5649 (OUTLIER) cc_final: 0.4749 (t80) REVERT: A 904 TYR cc_start: 0.7823 (m-10) cc_final: 0.7042 (m-10) REVERT: A 988 GLU cc_start: 0.8261 (tp30) cc_final: 0.8059 (tp30) REVERT: B 32 PHE cc_start: 0.8473 (m-80) cc_final: 0.7834 (m-80) REVERT: B 100 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7773 (pt) REVERT: B 102 ARG cc_start: 0.7287 (mtt90) cc_final: 0.7011 (mtt90) REVERT: B 104 TRP cc_start: 0.8073 (m-90) cc_final: 0.7697 (m-90) REVERT: B 121 ASN cc_start: 0.7201 (m-40) cc_final: 0.6343 (t0) REVERT: B 239 GLN cc_start: 0.7433 (tt0) cc_final: 0.6949 (tt0) REVERT: B 619 GLU cc_start: 0.8062 (tt0) cc_final: 0.7855 (tm-30) REVERT: B 960 ASN cc_start: 0.8083 (m-40) cc_final: 0.7762 (t0) REVERT: B 990 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7341 (mt-10) REVERT: B 1138 TYR cc_start: 0.7718 (t80) cc_final: 0.7489 (t80) REVERT: C 271 GLN cc_start: 0.8270 (tp-100) cc_final: 0.8037 (mm-40) REVERT: C 448 ASN cc_start: 0.6172 (OUTLIER) cc_final: 0.5598 (m110) REVERT: C 525 CYS cc_start: 0.5092 (OUTLIER) cc_final: 0.4581 (m) REVERT: C 787 GLN cc_start: 0.8631 (mp10) cc_final: 0.8241 (mt0) REVERT: C 904 TYR cc_start: 0.7539 (m-10) cc_final: 0.7108 (m-10) outliers start: 47 outliers final: 28 residues processed: 211 average time/residue: 0.3203 time to fit residues: 110.2119 Evaluate side-chains 190 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 156 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 915 VAL Chi-restraints excluded: chain A residue 1104 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 1114 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 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 262 optimal weight: 1.9990 chunk 199 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 chunk 266 optimal weight: 2.9990 chunk 282 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 252 optimal weight: 0.6980 chunk 76 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 762 GLN B 99 ASN C 207 HIS C 450 ASN C 493 GLN C 907 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23432 Z= 0.152 Angle : 0.520 13.837 31879 Z= 0.269 Chirality : 0.043 0.194 3643 Planarity : 0.004 0.044 4139 Dihedral : 4.509 38.789 3128 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.10 % Allowed : 12.74 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.15), residues: 2892 helix: 1.97 (0.22), residues: 624 sheet: -1.69 (0.20), residues: 589 loop : -2.73 (0.13), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.001 0.000 HIS A 655 PHE 0.026 0.001 PHE A 194 TYR 0.022 0.001 TYR C 351 ARG 0.006 0.000 ARG C 403 *********************** 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 236 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 182 time to evaluate : 4.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8303 (tm-30) REVERT: A 118 LEU cc_start: 0.7939 (tt) cc_final: 0.7422 (mt) REVERT: A 129 LYS cc_start: 0.7581 (pttp) cc_final: 0.6805 (pttp) REVERT: A 190 ARG cc_start: 0.7836 (mtt180) cc_final: 0.7298 (mtt180) REVERT: A 192 PHE cc_start: 0.7164 (m-10) cc_final: 0.6889 (m-10) REVERT: A 213 VAL cc_start: 0.4309 (OUTLIER) cc_final: 0.4013 (t) REVERT: A 237 ARG cc_start: 0.7624 (ptp90) cc_final: 0.7078 (mtm110) REVERT: A 265 TYR cc_start: 0.5696 (p90) cc_final: 0.5239 (p90) REVERT: A 269 TYR cc_start: 0.7596 (m-10) cc_final: 0.7321 (m-10) REVERT: A 347 PHE cc_start: 0.7173 (m-80) cc_final: 0.6943 (m-80) REVERT: A 351 TYR cc_start: 0.7537 (p90) cc_final: 0.6866 (p90) REVERT: A 380 TYR cc_start: 0.8243 (m-80) cc_final: 0.7935 (m-80) REVERT: A 904 TYR cc_start: 0.7952 (m-10) cc_final: 0.7434 (m-10) REVERT: A 988 GLU cc_start: 0.8163 (tp30) cc_final: 0.7917 (tp30) REVERT: B 32 PHE cc_start: 0.8453 (m-80) cc_final: 0.7904 (m-80) REVERT: B 100 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7689 (pt) REVERT: B 102 ARG cc_start: 0.7201 (mtt90) cc_final: 0.6635 (mtt180) REVERT: B 121 ASN cc_start: 0.7279 (m-40) cc_final: 0.6373 (t0) REVERT: B 169 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7847 (mp0) REVERT: B 177 MET cc_start: 0.1998 (mtt) cc_final: 0.1766 (mtt) REVERT: B 239 GLN cc_start: 0.7420 (tt0) cc_final: 0.7135 (tt0) REVERT: B 988 GLU cc_start: 0.7733 (pm20) cc_final: 0.7494 (pm20) REVERT: B 990 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7330 (mt-10) REVERT: B 1138 TYR cc_start: 0.7650 (t80) cc_final: 0.7390 (t80) REVERT: C 271 GLN cc_start: 0.8242 (tp-100) cc_final: 0.8009 (mm-40) REVERT: C 493 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7272 (mm-40) REVERT: C 525 CYS cc_start: 0.5082 (OUTLIER) cc_final: 0.4829 (m) REVERT: C 787 GLN cc_start: 0.8627 (mp10) cc_final: 0.8403 (mt0) REVERT: C 904 TYR cc_start: 0.7425 (m-10) cc_final: 0.7140 (m-10) REVERT: C 1123 SER cc_start: 0.8889 (m) cc_final: 0.8495 (t) outliers start: 54 outliers final: 29 residues processed: 228 average time/residue: 0.3124 time to fit residues: 116.0459 Evaluate side-chains 192 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 159 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 213 VAL 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 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 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 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 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 493 GLN 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 907 ASN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 235 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 210 optimal weight: 0.9980 chunk 116 optimal weight: 30.0000 chunk 240 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 253 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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** B 49 HIS B 239 GLN C 207 HIS C 343 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 965 GLN C1074 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 23432 Z= 0.356 Angle : 0.606 12.875 31879 Z= 0.311 Chirality : 0.045 0.196 3643 Planarity : 0.004 0.086 4139 Dihedral : 4.750 38.377 3128 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.65 % Allowed : 14.18 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.15), residues: 2892 helix: 1.83 (0.22), residues: 628 sheet: -1.59 (0.20), residues: 581 loop : -2.73 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 886 HIS 0.005 0.001 HIS A1088 PHE 0.018 0.002 PHE B 782 TYR 0.021 0.002 TYR C 351 ARG 0.006 0.000 ARG C 408 *********************** 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 233 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 165 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8572 (tm-30) REVERT: A 118 LEU cc_start: 0.7974 (tt) cc_final: 0.7647 (mp) REVERT: A 119 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7409 (mp) REVERT: A 129 LYS cc_start: 0.7671 (pttp) cc_final: 0.6938 (pttp) REVERT: A 190 ARG cc_start: 0.7642 (mtt180) cc_final: 0.7087 (mtt180) REVERT: A 192 PHE cc_start: 0.7233 (m-10) cc_final: 0.6975 (m-10) REVERT: A 223 LEU cc_start: 0.7531 (mt) cc_final: 0.6848 (mt) REVERT: A 237 ARG cc_start: 0.7550 (ptp90) cc_final: 0.7025 (mtm110) REVERT: A 265 TYR cc_start: 0.5729 (p90) cc_final: 0.5288 (p90) REVERT: A 269 TYR cc_start: 0.7487 (m-10) cc_final: 0.7240 (m-10) REVERT: A 347 PHE cc_start: 0.7251 (m-80) cc_final: 0.7038 (m-80) REVERT: A 351 TYR cc_start: 0.7549 (p90) cc_final: 0.6884 (p90) REVERT: A 380 TYR cc_start: 0.8192 (m-80) cc_final: 0.7837 (m-80) REVERT: A 592 PHE cc_start: 0.5566 (OUTLIER) cc_final: 0.4855 (t80) REVERT: A 904 TYR cc_start: 0.7895 (m-10) cc_final: 0.7065 (m-10) REVERT: A 988 GLU cc_start: 0.8254 (tp30) cc_final: 0.7980 (tp30) REVERT: B 32 PHE cc_start: 0.8462 (m-80) cc_final: 0.8069 (m-80) REVERT: B 100 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7769 (pt) REVERT: B 102 ARG cc_start: 0.7167 (mtt90) cc_final: 0.6574 (mtt180) REVERT: B 121 ASN cc_start: 0.7253 (m-40) cc_final: 0.6418 (t0) REVERT: B 169 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7718 (mp0) REVERT: B 177 MET cc_start: 0.2296 (mtt) cc_final: 0.1458 (mtt) REVERT: B 239 GLN cc_start: 0.7472 (tt0) cc_final: 0.7264 (tt0) REVERT: B 990 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7450 (mt-10) REVERT: B 1138 TYR cc_start: 0.7742 (t80) cc_final: 0.7525 (t80) REVERT: C 515 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.6276 (p90) REVERT: C 537 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8431 (mtpp) REVERT: C 756 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.6867 (m-80) REVERT: C 787 GLN cc_start: 0.8646 (mp10) cc_final: 0.8419 (mt0) REVERT: C 904 TYR cc_start: 0.7522 (m-10) cc_final: 0.7226 (m-10) REVERT: C 1141 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7282 (pp) outliers start: 68 outliers final: 37 residues processed: 223 average time/residue: 0.3159 time to fit residues: 116.0685 Evaluate side-chains 196 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 153 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE 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 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 915 VAL Chi-restraints excluded: chain A residue 934 ILE 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 319 ARG Chi-restraints excluded: chain B residue 604 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 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 407 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 756 TYR Chi-restraints excluded: chain C residue 878 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 0.8980 chunk 254 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 282 optimal weight: 1.9990 chunk 234 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 207 HIS C 487 ASN C 907 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23432 Z= 0.166 Angle : 0.539 14.958 31879 Z= 0.275 Chirality : 0.043 0.184 3643 Planarity : 0.004 0.087 4139 Dihedral : 4.401 36.716 3127 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.26 % Allowed : 15.11 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.16), residues: 2892 helix: 2.26 (0.22), residues: 623 sheet: -1.50 (0.20), residues: 606 loop : -2.57 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 886 HIS 0.001 0.000 HIS A1088 PHE 0.035 0.001 PHE A 194 TYR 0.031 0.001 TYR C 505 ARG 0.005 0.000 ARG B 319 *********************** 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 227 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 169 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7952 (tt) cc_final: 0.7619 (mp) REVERT: A 119 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7534 (mp) REVERT: A 129 LYS cc_start: 0.7616 (pttp) cc_final: 0.6952 (pttp) REVERT: A 192 PHE cc_start: 0.6870 (m-10) cc_final: 0.6620 (m-10) REVERT: A 213 VAL cc_start: 0.4726 (OUTLIER) cc_final: 0.4409 (t) REVERT: A 237 ARG cc_start: 0.7659 (ptp90) cc_final: 0.7074 (mtm110) REVERT: A 265 TYR cc_start: 0.5729 (p90) cc_final: 0.5265 (p90) REVERT: A 269 TYR cc_start: 0.7697 (m-10) cc_final: 0.7407 (m-10) REVERT: A 351 TYR cc_start: 0.7534 (p90) cc_final: 0.6882 (p90) REVERT: A 360 ASN cc_start: 0.8144 (m110) cc_final: 0.7888 (t0) REVERT: A 380 TYR cc_start: 0.8258 (m-80) cc_final: 0.8030 (m-80) REVERT: A 592 PHE cc_start: 0.5609 (OUTLIER) cc_final: 0.4780 (t80) REVERT: A 904 TYR cc_start: 0.7885 (m-10) cc_final: 0.7367 (m-10) REVERT: A 988 GLU cc_start: 0.8175 (tp30) cc_final: 0.7917 (tp30) REVERT: B 32 PHE cc_start: 0.8435 (m-80) cc_final: 0.7964 (m-80) REVERT: B 100 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7705 (pt) REVERT: B 102 ARG cc_start: 0.7124 (mtt90) cc_final: 0.6531 (mtt180) REVERT: B 121 ASN cc_start: 0.7248 (m-40) cc_final: 0.6297 (t0) REVERT: B 169 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7903 (mp0) REVERT: B 177 MET cc_start: 0.1950 (mtt) cc_final: 0.1570 (mtt) REVERT: B 553 THR cc_start: 0.7401 (OUTLIER) cc_final: 0.7135 (m) REVERT: B 988 GLU cc_start: 0.7663 (pm20) cc_final: 0.7436 (pm20) REVERT: B 990 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7282 (mt-10) REVERT: B 1138 TYR cc_start: 0.7672 (t80) cc_final: 0.7438 (t80) REVERT: C 51 THR cc_start: 0.8129 (p) cc_final: 0.7856 (p) REVERT: C 756 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.6355 (m-80) REVERT: C 787 GLN cc_start: 0.8625 (mp10) cc_final: 0.8392 (mt0) REVERT: C 904 TYR cc_start: 0.7435 (m-10) cc_final: 0.7173 (m-10) REVERT: C 1141 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7319 (pp) outliers start: 58 outliers final: 38 residues processed: 220 average time/residue: 0.3206 time to fit residues: 116.4842 Evaluate side-chains 204 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 159 time to evaluate : 2.497 ------------------------------------------------------------------------------- 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 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 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 319 ARG 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 900 MET 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 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 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 756 TYR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU 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 272 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 157 optimal weight: 0.5980 chunk 281 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 30 ASN C 207 HIS C 907 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23432 Z= 0.289 Angle : 0.575 14.433 31879 Z= 0.295 Chirality : 0.044 0.200 3643 Planarity : 0.004 0.045 4139 Dihedral : 4.514 35.489 3127 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.34 % Allowed : 15.97 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.16), residues: 2892 helix: 2.11 (0.22), residues: 626 sheet: -1.44 (0.21), residues: 608 loop : -2.54 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 104 HIS 0.006 0.001 HIS A 207 PHE 0.047 0.001 PHE A 194 TYR 0.020 0.001 TYR C 351 ARG 0.003 0.000 ARG C 408 *********************** 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 222 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 162 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8008 (tt) cc_final: 0.7676 (mp) REVERT: A 129 LYS cc_start: 0.7601 (pttp) cc_final: 0.7016 (pttp) REVERT: A 190 ARG cc_start: 0.7524 (mtt180) cc_final: 0.6654 (mpt-90) REVERT: A 192 PHE cc_start: 0.6742 (m-10) cc_final: 0.6306 (m-10) REVERT: A 213 VAL cc_start: 0.4835 (OUTLIER) cc_final: 0.4518 (t) REVERT: A 226 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7073 (mp) REVERT: A 237 ARG cc_start: 0.7610 (ptp90) cc_final: 0.7034 (mtm110) REVERT: A 265 TYR cc_start: 0.5776 (p90) cc_final: 0.5313 (p90) REVERT: A 269 TYR cc_start: 0.7556 (m-10) cc_final: 0.7267 (m-10) REVERT: A 351 TYR cc_start: 0.7540 (p90) cc_final: 0.6840 (p90) REVERT: A 360 ASN cc_start: 0.8172 (m110) cc_final: 0.7924 (t0) REVERT: A 380 TYR cc_start: 0.8223 (m-80) cc_final: 0.7951 (m-80) REVERT: A 592 PHE cc_start: 0.5666 (OUTLIER) cc_final: 0.4918 (t80) REVERT: A 904 TYR cc_start: 0.7932 (m-10) cc_final: 0.7363 (m-10) REVERT: A 988 GLU cc_start: 0.8277 (tp30) cc_final: 0.8059 (tp30) REVERT: B 32 PHE cc_start: 0.8402 (m-80) cc_final: 0.8078 (m-80) REVERT: B 100 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7789 (pt) REVERT: B 102 ARG cc_start: 0.7161 (mtt90) cc_final: 0.6624 (mtt180) REVERT: B 121 ASN cc_start: 0.7364 (m-40) cc_final: 0.6401 (t0) REVERT: B 177 MET cc_start: 0.1992 (mtt) cc_final: 0.1618 (mtt) REVERT: B 553 THR cc_start: 0.7178 (OUTLIER) cc_final: 0.6941 (m) REVERT: B 990 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7384 (mt-10) REVERT: B 1138 TYR cc_start: 0.7691 (t80) cc_final: 0.7477 (t80) REVERT: C 515 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.6217 (p90) REVERT: C 537 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8457 (mtpp) REVERT: C 756 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: C 787 GLN cc_start: 0.8627 (mp10) cc_final: 0.8395 (mt0) REVERT: C 904 TYR cc_start: 0.7494 (m-10) cc_final: 0.7191 (m-10) REVERT: C 1141 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7348 (pp) outliers start: 60 outliers final: 39 residues processed: 215 average time/residue: 0.3436 time to fit residues: 122.5070 Evaluate side-chains 202 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 155 time to evaluate : 2.630 ------------------------------------------------------------------------------- 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 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 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 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 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 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 1001 LEU 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 174 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 55 optimal weight: 0.0270 chunk 54 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 191 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 221 optimal weight: 7.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23432 Z= 0.184 Angle : 0.547 16.525 31879 Z= 0.281 Chirality : 0.043 0.174 3643 Planarity : 0.004 0.045 4139 Dihedral : 4.391 34.272 3127 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.87 % Allowed : 16.87 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.16), residues: 2892 helix: 2.33 (0.22), residues: 621 sheet: -1.32 (0.21), residues: 607 loop : -2.43 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 104 HIS 0.005 0.000 HIS A 207 PHE 0.043 0.001 PHE A 194 TYR 0.044 0.001 TYR C 505 ARG 0.003 0.000 ARG C 408 *********************** 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 208 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 160 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.5971 (m-80) cc_final: 0.5653 (m-80) REVERT: A 118 LEU cc_start: 0.7976 (tt) cc_final: 0.7633 (mp) REVERT: A 129 LYS cc_start: 0.7604 (pttp) cc_final: 0.6963 (pttp) REVERT: A 190 ARG cc_start: 0.7488 (mtt180) cc_final: 0.6940 (mpt180) REVERT: A 192 PHE cc_start: 0.7031 (m-10) cc_final: 0.6682 (m-10) REVERT: A 213 VAL cc_start: 0.4876 (OUTLIER) cc_final: 0.4551 (t) REVERT: A 265 TYR cc_start: 0.5742 (p90) cc_final: 0.5327 (p90) REVERT: A 269 TYR cc_start: 0.7668 (m-10) cc_final: 0.7414 (m-10) REVERT: A 347 PHE cc_start: 0.7248 (m-80) cc_final: 0.6517 (m-80) REVERT: A 351 TYR cc_start: 0.7463 (p90) cc_final: 0.6818 (p90) REVERT: A 360 ASN cc_start: 0.7982 (m110) cc_final: 0.7746 (t0) REVERT: A 380 TYR cc_start: 0.8228 (m-80) cc_final: 0.7968 (m-80) REVERT: A 592 PHE cc_start: 0.5610 (OUTLIER) cc_final: 0.4805 (t80) REVERT: A 904 TYR cc_start: 0.7886 (m-10) cc_final: 0.7355 (m-10) REVERT: B 32 PHE cc_start: 0.8427 (m-80) cc_final: 0.7931 (m-80) REVERT: B 100 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7756 (pt) REVERT: B 102 ARG cc_start: 0.7114 (mtt90) cc_final: 0.6568 (mtt180) REVERT: B 121 ASN cc_start: 0.7291 (m-40) cc_final: 0.6363 (t0) REVERT: B 177 MET cc_start: 0.1877 (mtt) cc_final: 0.1537 (mtt) REVERT: B 239 GLN cc_start: 0.7592 (tt0) cc_final: 0.7337 (tt0) REVERT: B 553 THR cc_start: 0.7380 (OUTLIER) cc_final: 0.7107 (m) REVERT: B 990 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7245 (mt-10) REVERT: B 1138 TYR cc_start: 0.7670 (t80) cc_final: 0.7436 (t80) REVERT: C 51 THR cc_start: 0.8084 (p) cc_final: 0.7783 (p) REVERT: C 515 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.6292 (p90) REVERT: C 537 LYS cc_start: 0.8757 (mmtt) cc_final: 0.8435 (mtpp) REVERT: C 756 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.6345 (m-80) REVERT: C 787 GLN cc_start: 0.8622 (mp10) cc_final: 0.8391 (mt0) REVERT: C 904 TYR cc_start: 0.7437 (m-10) cc_final: 0.7186 (m-10) REVERT: C 1141 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7354 (pp) outliers start: 48 outliers final: 36 residues processed: 204 average time/residue: 0.3045 time to fit residues: 102.1924 Evaluate side-chains 194 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 151 time to evaluate : 2.288 ------------------------------------------------------------------------------- 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 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 553 THR Chi-restraints excluded: chain B residue 604 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 1122 VAL Chi-restraints excluded: chain C residue 120 VAL 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 756 TYR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 chunk 245 optimal weight: 8.9990 chunk 262 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 236 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 207 HIS C 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23432 Z= 0.203 Angle : 0.555 15.363 31879 Z= 0.286 Chirality : 0.044 0.189 3643 Planarity : 0.004 0.045 4139 Dihedral : 4.331 32.928 3127 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.99 % Allowed : 16.71 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.16), residues: 2892 helix: 2.36 (0.22), residues: 621 sheet: -1.23 (0.21), residues: 604 loop : -2.40 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 104 HIS 0.005 0.000 HIS A 207 PHE 0.033 0.001 PHE A 194 TYR 0.020 0.001 TYR C 351 ARG 0.003 0.000 ARG A 346 *********************** 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 209 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 158 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.5860 (m-80) cc_final: 0.5610 (m-80) REVERT: A 118 LEU cc_start: 0.7974 (tt) cc_final: 0.7628 (mp) REVERT: A 129 LYS cc_start: 0.7568 (pttp) cc_final: 0.6928 (pttp) REVERT: A 190 ARG cc_start: 0.7730 (mtt180) cc_final: 0.7505 (mpt180) REVERT: A 192 PHE cc_start: 0.6820 (m-10) cc_final: 0.6519 (m-10) REVERT: A 213 VAL cc_start: 0.4672 (OUTLIER) cc_final: 0.4314 (t) REVERT: A 237 ARG cc_start: 0.7589 (ptp90) cc_final: 0.7066 (mtm110) REVERT: A 265 TYR cc_start: 0.5747 (p90) cc_final: 0.5336 (p90) REVERT: A 269 TYR cc_start: 0.7632 (m-10) cc_final: 0.7363 (m-10) REVERT: A 351 TYR cc_start: 0.7447 (p90) cc_final: 0.6806 (p90) REVERT: A 360 ASN cc_start: 0.7964 (m110) cc_final: 0.7694 (t0) REVERT: A 380 TYR cc_start: 0.8196 (m-80) cc_final: 0.7976 (m-80) REVERT: A 592 PHE cc_start: 0.5611 (OUTLIER) cc_final: 0.4801 (t80) REVERT: A 904 TYR cc_start: 0.7898 (m-10) cc_final: 0.7352 (m-10) REVERT: B 32 PHE cc_start: 0.8422 (m-80) cc_final: 0.7937 (m-80) REVERT: B 100 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7812 (pt) REVERT: B 102 ARG cc_start: 0.7093 (mtt90) cc_final: 0.6570 (mtt180) REVERT: B 121 ASN cc_start: 0.7400 (m-40) cc_final: 0.6488 (t0) REVERT: B 177 MET cc_start: 0.1879 (mtt) cc_final: 0.1497 (mtt) REVERT: B 553 THR cc_start: 0.7379 (OUTLIER) cc_final: 0.7111 (m) REVERT: B 990 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7234 (mt-10) REVERT: B 1138 TYR cc_start: 0.7674 (t80) cc_final: 0.7450 (t80) REVERT: C 51 THR cc_start: 0.8036 (p) cc_final: 0.7748 (p) REVERT: C 515 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.6248 (p90) REVERT: C 537 LYS cc_start: 0.8787 (mmtt) cc_final: 0.8447 (mtpp) REVERT: C 756 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.6287 (m-80) REVERT: C 787 GLN cc_start: 0.8619 (mp10) cc_final: 0.8385 (mt0) REVERT: C 904 TYR cc_start: 0.7456 (m-10) cc_final: 0.7218 (m-10) REVERT: C 1141 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7447 (pp) outliers start: 51 outliers final: 38 residues processed: 203 average time/residue: 0.3002 time to fit residues: 101.1663 Evaluate side-chains 198 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 153 time to evaluate : 2.529 ------------------------------------------------------------------------------- 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 B residue 63 THR Chi-restraints excluded: chain B residue 100 ILE 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 553 THR Chi-restraints excluded: chain B residue 604 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 1122 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 756 TYR Chi-restraints excluded: chain C residue 878 LEU 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 1001 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 172 optimal weight: 0.1980 chunk 277 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 290 optimal weight: 2.9990 chunk 267 optimal weight: 0.0980 chunk 231 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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** A1142 GLN C 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23432 Z= 0.290 Angle : 0.587 17.855 31879 Z= 0.301 Chirality : 0.045 0.175 3643 Planarity : 0.004 0.045 4139 Dihedral : 4.463 32.200 3127 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.95 % Allowed : 17.02 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.16), residues: 2892 helix: 2.21 (0.22), residues: 621 sheet: -1.16 (0.21), residues: 600 loop : -2.41 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.003 TRP A 104 HIS 0.003 0.001 HIS A1088 PHE 0.041 0.001 PHE A 194 TYR 0.021 0.001 TYR C 351 ARG 0.005 0.000 ARG C 905 ********************** 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 204 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 154 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8034 (tt) cc_final: 0.7603 (mp) REVERT: A 129 LYS cc_start: 0.7567 (pttp) cc_final: 0.6820 (pttt) REVERT: A 190 ARG cc_start: 0.7788 (mtt180) cc_final: 0.7148 (mpt-90) REVERT: A 192 PHE cc_start: 0.6880 (m-10) cc_final: 0.6659 (m-10) REVERT: A 213 VAL cc_start: 0.4830 (OUTLIER) cc_final: 0.4478 (t) REVERT: A 237 ARG cc_start: 0.7510 (ptp90) cc_final: 0.7038 (mtm110) REVERT: A 265 TYR cc_start: 0.5762 (p90) cc_final: 0.5364 (p90) REVERT: A 269 TYR cc_start: 0.7597 (m-10) cc_final: 0.7318 (m-10) REVERT: A 351 TYR cc_start: 0.7454 (p90) cc_final: 0.6813 (p90) REVERT: A 360 ASN cc_start: 0.7988 (m110) cc_final: 0.7692 (t0) REVERT: A 380 TYR cc_start: 0.8245 (m-80) cc_final: 0.7914 (m-80) REVERT: A 592 PHE cc_start: 0.5650 (OUTLIER) cc_final: 0.4913 (t80) REVERT: A 904 TYR cc_start: 0.7923 (m-10) cc_final: 0.7356 (m-10) REVERT: B 32 PHE cc_start: 0.8439 (m-80) cc_final: 0.7949 (m-80) REVERT: B 100 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7844 (pt) REVERT: B 102 ARG cc_start: 0.7102 (mtt90) cc_final: 0.6597 (mtt180) REVERT: B 553 THR cc_start: 0.7417 (OUTLIER) cc_final: 0.7147 (m) REVERT: B 990 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7304 (mt-10) REVERT: B 1138 TYR cc_start: 0.7708 (t80) cc_final: 0.7473 (t80) REVERT: C 451 TYR cc_start: 0.4860 (m-80) cc_final: 0.4548 (m-80) REVERT: C 515 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.6299 (p90) REVERT: C 537 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8484 (mtpp) REVERT: C 756 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.6758 (m-80) REVERT: C 787 GLN cc_start: 0.8626 (mp10) cc_final: 0.8388 (mt0) REVERT: C 904 TYR cc_start: 0.7490 (m-10) cc_final: 0.7214 (m-10) REVERT: C 1141 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7370 (pp) outliers start: 50 outliers final: 40 residues processed: 198 average time/residue: 0.3281 time to fit residues: 107.4769 Evaluate side-chains 202 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 155 time to evaluate : 2.694 ------------------------------------------------------------------------------- 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 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 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 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 1122 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 756 TYR Chi-restraints excluded: chain C residue 878 LEU 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 1001 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 0.9990 chunk 246 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 213 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 232 optimal weight: 0.3980 chunk 97 optimal weight: 0.7980 chunk 238 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.149720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.088220 restraints weight = 36020.743| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.26 r_work: 0.3103 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23432 Z= 0.205 Angle : 0.556 17.363 31879 Z= 0.285 Chirality : 0.044 0.167 3643 Planarity : 0.004 0.044 4139 Dihedral : 4.375 31.383 3127 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.91 % Allowed : 17.22 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.16), residues: 2892 helix: 2.33 (0.22), residues: 621 sheet: -1.12 (0.21), residues: 603 loop : -2.35 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP A 104 HIS 0.005 0.000 HIS A 207 PHE 0.036 0.001 PHE A 194 TYR 0.021 0.001 TYR C 351 ARG 0.003 0.000 ARG C 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4412.76 seconds wall clock time: 79 minutes 55.33 seconds (4795.33 seconds total)