Starting phenix.real_space_refine on Tue Aug 26 16:21:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yzc_39689/08_2025/8yzc_39689.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yzc_39689/08_2025/8yzc_39689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yzc_39689/08_2025/8yzc_39689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yzc_39689/08_2025/8yzc_39689.map" model { file = "/net/cci-nas-00/data/ceres_data/8yzc_39689/08_2025/8yzc_39689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yzc_39689/08_2025/8yzc_39689.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.047 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 195 5.16 5 C 24957 2.51 5 N 6450 2.21 5 O 7371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38973 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8121 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 54, 'TRANS': 978} Chain breaks: 8 Chain: "B" Number of atoms: 8121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8121 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 54, 'TRANS': 978} Chain breaks: 8 Chain: "C" Number of atoms: 8121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8121 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 54, 'TRANS': 978} Chain breaks: 8 Chain: "G" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "H" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "I" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Time building chain proxies: 9.56, per 1000 atoms: 0.25 Number of scatterers: 38973 At special positions: 0 Unit cell: (167.79, 166.6, 261.8, 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 195 16.00 O 7371 8.00 N 6450 7.00 C 24957 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 167 " 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 167 " 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 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 141 " distance=2.03 Simple disulfide: pdb=" SG CYS G 344 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 530 " - pdb=" SG CYS G 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 133 " - pdb=" SG CYS H 141 " distance=2.03 Simple disulfide: pdb=" SG CYS H 344 " - pdb=" SG CYS H 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 530 " - pdb=" SG CYS H 542 " distance=2.03 Simple disulfide: pdb=" SG CYS I 133 " - pdb=" SG CYS I 141 " distance=2.03 Simple disulfide: pdb=" SG CYS I 344 " - pdb=" SG CYS I 361 " distance=2.03 Simple disulfide: pdb=" SG CYS I 530 " - pdb=" SG CYS I 542 " 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: 3.42 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9216 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 54 sheets defined 40.3% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.652A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.899A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.877A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 616 through 626 removed outlier: 3.648A pdb=" N HIS A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.765A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.836A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.525A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 944 removed outlier: 3.675A pdb=" N ALA A 944 " --> pdb=" O THR A 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 941 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.612A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 958 " --> pdb=" O HIS A 954 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (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 981 removed outlier: 4.320A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.587A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1160 removed outlier: 3.724A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A1149 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A1150 " --> pdb=" O ASP A1146 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.516A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.858A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.881A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.157A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 616 through 626 removed outlier: 3.513A pdb=" N VAL B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS B 625 " --> pdb=" O SER B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.958A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 940 removed outlier: 3.596A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.583A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (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 981 removed outlier: 4.270A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1033 removed outlier: 3.670A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1160 removed outlier: 3.635A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B1149 " --> pdb=" O LEU B1145 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU B1150 " --> pdb=" O ASP B1146 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR B1155 " --> pdb=" O GLU B1151 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.609A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 342 removed outlier: 3.823A pdb=" N VAL C 341 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.698A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.760A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 371' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 616 through 626 removed outlier: 3.551A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 removed outlier: 3.785A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.714A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.591A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.506A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.639A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.597A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 980 removed outlier: 3.556A pdb=" N ASP C 979 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE C 980 " --> pdb=" O LEU C 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 980' Processing helix chain 'C' and resid 989 through 1033 removed outlier: 3.566A pdb=" N ILE C 993 " --> pdb=" O ALA C 989 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1160 removed outlier: 3.513A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU C1150 " --> pdb=" O ASP C1146 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C1155 " --> pdb=" O GLU C1151 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 53 removed outlier: 3.768A pdb=" N GLN G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP G 38 " --> pdb=" O HIS G 34 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 77 Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.192A pdb=" N MET G 82 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 79 through 83' Processing helix chain 'G' and resid 84 through 88 removed outlier: 3.752A pdb=" N GLU G 87 " --> pdb=" O PRO G 84 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE G 88 " --> pdb=" O LEU G 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 84 through 88' Processing helix chain 'G' and resid 90 through 101 Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.953A pdb=" N VAL G 107 " --> pdb=" O GLY G 104 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU G 108 " --> pdb=" O SER G 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 104 through 108' Processing helix chain 'G' and resid 109 through 129 Processing helix chain 'G' and resid 147 through 154 Processing helix chain 'G' and resid 157 through 172 removed outlier: 3.782A pdb=" N ARG G 161 " --> pdb=" O ASP G 157 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP G 168 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 194 Processing helix chain 'G' and resid 198 through 205 Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'G' and resid 220 through 252 removed outlier: 3.659A pdb=" N GLU G 232 " --> pdb=" O HIS G 228 " (cutoff:3.500A) Proline residue: G 235 - end of helix removed outlier: 3.669A pdb=" N LYS G 247 " --> pdb=" O TYR G 243 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 267 No H-bonds generated for 'chain 'G' and resid 265 through 267' Processing helix chain 'G' and resid 275 through 279 removed outlier: 3.506A pdb=" N LEU G 278 " --> pdb=" O TRP G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 301 Processing helix chain 'G' and resid 303 through 317 Processing helix chain 'G' and resid 324 through 330 removed outlier: 3.774A pdb=" N TRP G 328 " --> pdb=" O THR G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 385 removed outlier: 3.713A pdb=" N LEU G 370 " --> pdb=" O MET G 366 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS G 373 " --> pdb=" O PHE G 369 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR G 385 " --> pdb=" O TYR G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 393 removed outlier: 3.748A pdb=" N ARG G 393 " --> pdb=" O PHE G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 399 through 413 removed outlier: 3.650A pdb=" N MET G 408 " --> pdb=" O VAL G 404 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER G 411 " --> pdb=" O ILE G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 Processing helix chain 'G' and resid 431 through 447 removed outlier: 3.582A pdb=" N GLU G 435 " --> pdb=" O ASP G 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 466 Processing helix chain 'G' and resid 469 through 471 No H-bonds generated for 'chain 'G' and resid 469 through 471' Processing helix chain 'G' and resid 472 through 485 Processing helix chain 'G' and resid 498 through 502 Processing helix chain 'G' and resid 503 through 508 Processing helix chain 'G' and resid 512 through 533 removed outlier: 3.788A pdb=" N TYR G 516 " --> pdb=" O PHE G 512 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE G 523 " --> pdb=" O THR G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 547 through 559 removed outlier: 3.872A pdb=" N GLY G 551 " --> pdb=" O SER G 547 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET G 557 " --> pdb=" O LYS G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 565 through 575 removed outlier: 3.543A pdb=" N VAL G 573 " --> pdb=" O ALA G 569 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 600 Proline residue: G 590 - end of helix Processing helix chain 'H' and resid 20 through 53 removed outlier: 3.768A pdb=" N GLN H 24 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP H 38 " --> pdb=" O HIS H 34 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU H 39 " --> pdb=" O GLU H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 77 Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.187A pdb=" N MET H 82 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR H 83 " --> pdb=" O ALA H 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 79 through 83' Processing helix chain 'H' and resid 84 through 88 removed outlier: 3.751A pdb=" N GLU H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE H 88 " --> pdb=" O LEU H 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 84 through 88' Processing helix chain 'H' and resid 90 through 101 Processing helix chain 'H' and resid 104 through 108 removed outlier: 3.957A pdb=" N VAL H 107 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU H 108 " --> pdb=" O SER H 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 104 through 108' Processing helix chain 'H' and resid 109 through 129 Processing helix chain 'H' and resid 147 through 154 Processing helix chain 'H' and resid 157 through 172 removed outlier: 3.782A pdb=" N ARG H 161 " --> pdb=" O ASP H 157 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP H 168 " --> pdb=" O ALA H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 194 Processing helix chain 'H' and resid 198 through 205 Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 220 through 252 removed outlier: 3.664A pdb=" N GLU H 232 " --> pdb=" O HIS H 228 " (cutoff:3.500A) Proline residue: H 235 - end of helix removed outlier: 3.670A pdb=" N LYS H 247 " --> pdb=" O TYR H 243 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 267 No H-bonds generated for 'chain 'H' and resid 265 through 267' Processing helix chain 'H' and resid 275 through 279 removed outlier: 3.508A pdb=" N LEU H 278 " --> pdb=" O TRP H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 301 Processing helix chain 'H' and resid 303 through 317 Processing helix chain 'H' and resid 324 through 330 removed outlier: 3.775A pdb=" N TRP H 328 " --> pdb=" O THR H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 385 removed outlier: 3.699A pdb=" N LEU H 370 " --> pdb=" O MET H 366 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS H 373 " --> pdb=" O PHE H 369 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR H 385 " --> pdb=" O TYR H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 389 through 393 removed outlier: 3.755A pdb=" N ARG H 393 " --> pdb=" O PHE H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 399 through 413 removed outlier: 3.659A pdb=" N MET H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER H 411 " --> pdb=" O ILE H 407 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 421 Processing helix chain 'H' and resid 431 through 447 removed outlier: 3.579A pdb=" N GLU H 435 " --> pdb=" O ASP H 431 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 466 Processing helix chain 'H' and resid 469 through 471 No H-bonds generated for 'chain 'H' and resid 469 through 471' Processing helix chain 'H' and resid 472 through 485 Processing helix chain 'H' and resid 498 through 502 Processing helix chain 'H' and resid 503 through 508 Processing helix chain 'H' and resid 512 through 533 removed outlier: 3.786A pdb=" N TYR H 516 " --> pdb=" O PHE H 512 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE H 523 " --> pdb=" O THR H 519 " (cutoff:3.500A) Processing helix chain 'H' and resid 547 through 559 removed outlier: 3.872A pdb=" N GLY H 551 " --> pdb=" O SER H 547 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET H 557 " --> pdb=" O LYS H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 575 removed outlier: 3.544A pdb=" N VAL H 573 " --> pdb=" O ALA H 569 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 600 Proline residue: H 590 - end of helix Processing helix chain 'I' and resid 20 through 53 removed outlier: 3.782A pdb=" N GLN I 24 " --> pdb=" O THR I 20 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASP I 38 " --> pdb=" O HIS I 34 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU I 39 " --> pdb=" O GLU I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 77 Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.197A pdb=" N MET I 82 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 79 through 83' Processing helix chain 'I' and resid 84 through 88 removed outlier: 3.749A pdb=" N GLU I 87 " --> pdb=" O PRO I 84 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE I 88 " --> pdb=" O LEU I 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 84 through 88' Processing helix chain 'I' and resid 90 through 101 Processing helix chain 'I' and resid 104 through 108 removed outlier: 3.956A pdb=" N VAL I 107 " --> pdb=" O GLY I 104 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU I 108 " --> pdb=" O SER I 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 104 through 108' Processing helix chain 'I' and resid 109 through 129 Processing helix chain 'I' and resid 147 through 154 Processing helix chain 'I' and resid 157 through 172 removed outlier: 3.780A pdb=" N ARG I 161 " --> pdb=" O ASP I 157 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP I 168 " --> pdb=" O ALA I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 194 Processing helix chain 'I' and resid 198 through 205 Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'I' and resid 220 through 252 removed outlier: 3.651A pdb=" N GLU I 232 " --> pdb=" O HIS I 228 " (cutoff:3.500A) Proline residue: I 235 - end of helix removed outlier: 3.670A pdb=" N LYS I 247 " --> pdb=" O TYR I 243 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN I 250 " --> pdb=" O ALA I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 267 No H-bonds generated for 'chain 'I' and resid 265 through 267' Processing helix chain 'I' and resid 275 through 279 removed outlier: 3.506A pdb=" N LEU I 278 " --> pdb=" O TRP I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 301 Processing helix chain 'I' and resid 303 through 317 Processing helix chain 'I' and resid 324 through 330 removed outlier: 3.792A pdb=" N TRP I 328 " --> pdb=" O THR I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 366 through 385 removed outlier: 3.700A pdb=" N LEU I 370 " --> pdb=" O MET I 366 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS I 373 " --> pdb=" O PHE I 369 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR I 385 " --> pdb=" O TYR I 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 389 through 393 removed outlier: 3.727A pdb=" N ARG I 393 " --> pdb=" O PHE I 390 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 413 removed outlier: 3.652A pdb=" N MET I 408 " --> pdb=" O VAL I 404 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER I 411 " --> pdb=" O ILE I 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 421 Processing helix chain 'I' and resid 431 through 447 removed outlier: 3.583A pdb=" N GLU I 435 " --> pdb=" O ASP I 431 " (cutoff:3.500A) Processing helix chain 'I' and resid 449 through 466 Processing helix chain 'I' and resid 469 through 471 No H-bonds generated for 'chain 'I' and resid 469 through 471' Processing helix chain 'I' and resid 472 through 485 Processing helix chain 'I' and resid 498 through 502 Processing helix chain 'I' and resid 503 through 508 Processing helix chain 'I' and resid 512 through 533 removed outlier: 3.789A pdb=" N TYR I 516 " --> pdb=" O PHE I 512 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE I 523 " --> pdb=" O THR I 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 547 through 559 removed outlier: 3.871A pdb=" N GLY I 551 " --> pdb=" O SER I 547 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET I 557 " --> pdb=" O LYS I 553 " (cutoff:3.500A) Processing helix chain 'I' and resid 565 through 575 removed outlier: 3.543A pdb=" N VAL I 573 " --> pdb=" O ALA I 569 " (cutoff:3.500A) Processing helix chain 'I' and resid 581 through 600 Proline residue: I 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.523A pdb=" N ASP A 57 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68 removed outlier: 3.566A pdb=" N THR A 67 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 95 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 92 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 195 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 192 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 207 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 204 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 227 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER A 206 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 removed outlier: 4.149A pdb=" N GLY A 109 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP A 106 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 121 " --> pdb=" O TRP A 106 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 130 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 132 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE A 169 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.162A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.623A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.817A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.554A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.195A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.030A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.030A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.726A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.541A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 52 through 59 removed outlier: 7.545A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 67 through 68 removed outlier: 3.518A pdb=" N THR B 67 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA B 95 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL B 92 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE B 195 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 192 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 207 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N PHE B 202 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP B 228 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE B 204 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 224 " --> pdb=" O SER B 206 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 86 through 87 removed outlier: 3.906A pdb=" N GLY B 109 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP B 106 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 130 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 132 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE B 169 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.165A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.636A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.810A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 removed outlier: 3.564A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.222A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.896A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.896A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.569A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.562A pdb=" N ASP C 57 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 67 through 68 removed outlier: 3.576A pdb=" N THR C 67 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA C 95 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 92 " --> pdb=" O PHE C 195 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE C 195 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU C 192 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS C 207 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 204 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL C 227 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER C 206 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 86 through 87 removed outlier: 3.970A pdb=" N GLY C 109 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP C 106 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 130 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL C 132 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE C 169 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.161A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 355 through 358 removed outlier: 3.581A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA C 435 " --> pdb=" O ALA C 376 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.825A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.560A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.215A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.951A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.951A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.587A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 132 through 133 Processing sheet with id=AF2, first strand: chain 'G' and resid 262 through 263 removed outlier: 5.694A pdb=" N LEU G 262 " --> pdb=" O VAL G 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'G' and resid 347 through 350 removed outlier: 3.767A pdb=" N THR G 347 " --> pdb=" O LEU G 359 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU G 359 " --> pdb=" O THR G 347 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP G 349 " --> pdb=" O ARG G 357 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG G 357 " --> pdb=" O TRP G 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'H' and resid 132 through 133 Processing sheet with id=AF5, first strand: chain 'H' and resid 262 through 263 removed outlier: 5.692A pdb=" N LEU H 262 " --> pdb=" O VAL H 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'H' and resid 347 through 350 removed outlier: 3.728A pdb=" N THR H 347 " --> pdb=" O LEU H 359 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU H 359 " --> pdb=" O THR H 347 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP H 349 " --> pdb=" O ARG H 357 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG H 357 " --> pdb=" O TRP H 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'I' and resid 132 through 133 Processing sheet with id=AF8, first strand: chain 'I' and resid 262 through 263 removed outlier: 5.697A pdb=" N LEU I 262 " --> pdb=" O VAL I 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'I' and resid 347 through 350 removed outlier: 3.776A pdb=" N THR I 347 " --> pdb=" O LEU I 359 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU I 359 " --> pdb=" O THR I 347 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP I 349 " --> pdb=" O ARG I 357 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG I 357 " --> pdb=" O TRP I 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 1641 hydrogen bonds defined for protein. 4698 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: 10.17 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 12514 1.34 - 1.46: 9721 1.46 - 1.58: 17452 1.58 - 1.70: 0 1.70 - 1.82: 282 Bond restraints: 39969 Sorted by residual: bond pdb=" C PHE A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 1.332 1.351 -0.020 1.33e-02 5.65e+03 2.15e+00 bond pdb=" CB PHE C 374 " pdb=" CG PHE C 374 " ideal model delta sigma weight residual 1.502 1.523 -0.021 2.30e-02 1.89e+03 8.38e-01 bond pdb=" C ILE A 714 " pdb=" O ILE A 714 " ideal model delta sigma weight residual 1.232 1.240 -0.008 8.90e-03 1.26e+04 8.22e-01 bond pdb=" N CYS A 743 " pdb=" CA CYS A 743 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 6.92e-01 bond pdb=" C THR A 630 " pdb=" N PRO A 631 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.65e-01 ... (remaining 39964 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 53285 1.17 - 2.34: 770 2.34 - 3.51: 247 3.51 - 4.68: 42 4.68 - 5.85: 13 Bond angle restraints: 54357 Sorted by residual: angle pdb=" N ILE B 980 " pdb=" CA ILE B 980 " pdb=" C ILE B 980 " ideal model delta sigma weight residual 113.53 110.02 3.51 9.80e-01 1.04e+00 1.28e+01 angle pdb=" N ILE A 980 " pdb=" CA ILE A 980 " pdb=" C ILE A 980 " ideal model delta sigma weight residual 113.53 110.13 3.40 9.80e-01 1.04e+00 1.21e+01 angle pdb=" C SER C 349 " pdb=" N VAL C 350 " pdb=" CA VAL C 350 " ideal model delta sigma weight residual 120.53 124.69 -4.16 1.41e+00 5.03e-01 8.72e+00 angle pdb=" N PHE C 338 " pdb=" CA PHE C 338 " pdb=" C PHE C 338 " ideal model delta sigma weight residual 114.56 111.30 3.26 1.27e+00 6.20e-01 6.57e+00 angle pdb=" N PHE C 342 " pdb=" CA PHE C 342 " pdb=" C PHE C 342 " ideal model delta sigma weight residual 114.04 110.88 3.16 1.24e+00 6.50e-01 6.49e+00 ... (remaining 54352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 23099 17.87 - 35.74: 524 35.74 - 53.60: 69 53.60 - 71.47: 13 71.47 - 89.34: 7 Dihedral angle restraints: 23712 sinusoidal: 9408 harmonic: 14304 Sorted by residual: dihedral pdb=" CA ILE B 198 " pdb=" C ILE B 198 " pdb=" N ASP B 199 " pdb=" CA ASP B 199 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CB GLU H 495 " pdb=" CG GLU H 495 " pdb=" CD GLU H 495 " pdb=" OE1 GLU H 495 " ideal model delta sinusoidal sigma weight residual 0.00 87.20 -87.20 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU G 495 " pdb=" CG GLU G 495 " pdb=" CD GLU G 495 " pdb=" OE1 GLU G 495 " ideal model delta sinusoidal sigma weight residual 0.00 87.11 -87.11 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 23709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 3585 0.026 - 0.052: 1546 0.052 - 0.077: 402 0.077 - 0.103: 283 0.103 - 0.129: 160 Chirality restraints: 5976 Sorted by residual: chirality pdb=" CB ILE B 198 " pdb=" CA ILE B 198 " pdb=" CG1 ILE B 198 " pdb=" CG2 ILE B 198 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE G 468 " pdb=" N ILE G 468 " pdb=" C ILE G 468 " pdb=" CB ILE G 468 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE I 468 " pdb=" N ILE I 468 " pdb=" C ILE I 468 " pdb=" CB ILE I 468 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 5973 not shown) Planarity restraints: 7020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO A 330 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO C 330 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO C 373 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " -0.019 5.00e-02 4.00e+02 ... (remaining 7017 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1206 2.72 - 3.26: 36465 3.26 - 3.81: 58089 3.81 - 4.35: 70445 4.35 - 4.90: 124580 Nonbonded interactions: 290785 Sorted by model distance: nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.171 3.040 nonbonded pdb=" OG1 THR C 111 " pdb=" OD2 ASP C 113 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.196 3.040 nonbonded pdb=" OG1 THR A 111 " pdb=" OD2 ASP A 113 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR B 111 " pdb=" OD2 ASP B 113 " model vdw 2.203 3.040 ... (remaining 290780 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.160 Process input model: 39.440 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:7.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4874 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 : 0.002 0.040 40011 Z= 0.080 Angle : 0.404 5.845 54441 Z= 0.228 Chirality : 0.038 0.129 5976 Planarity : 0.003 0.053 7020 Dihedral : 7.453 89.342 14370 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.25 % Allowed : 3.80 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.11), residues: 4830 helix: 0.07 (0.12), residues: 1773 sheet: 0.13 (0.21), residues: 591 loop : -2.96 (0.10), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 457 TYR 0.006 0.000 TYR H 385 PHE 0.010 0.001 PHE C 36 TRP 0.005 0.000 TRP I 165 HIS 0.001 0.000 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00153 (39969) covalent geometry : angle 0.40419 (54357) SS BOND : bond 0.00085 ( 42) SS BOND : angle 0.47039 ( 84) hydrogen bonds : bond 0.19439 ( 1614) hydrogen bonds : angle 6.24223 ( 4698) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 314 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 123 MET cc_start: -0.1096 (mtm) cc_final: -0.1422 (ttt) REVERT: H 297 MET cc_start: -0.2136 (mtp) cc_final: -0.2375 (mtt) REVERT: H 323 MET cc_start: 0.0703 (mmt) cc_final: -0.0263 (tpt) REVERT: I 297 MET cc_start: -0.2866 (mtp) cc_final: -0.3852 (mpt) outliers start: 97 outliers final: 16 residues processed: 402 average time/residue: 0.7752 time to fit residues: 377.2065 Evaluate side-chains 161 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain H residue 131 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 50.0000 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.0370 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 6.9990 chunk 470 optimal weight: 20.0000 overall best weight: 2.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 123 ASN ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 321 GLN A 334 ASN A 474 GLN A 493 GLN A 607 GLN A 613 GLN A 628 GLN A 677 GLN A 787 GLN A 804 GLN A 872 GLN A 901 GLN A 913 GLN A 914 ASN A 957 GLN A1002 GLN A1071 GLN A1142 GLN B 89 ASN B 123 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 321 GLN B 370 ASN B 474 GLN B 493 GLN B 607 GLN B 613 GLN B 628 GLN B 677 GLN B 787 GLN B 804 GLN B 872 GLN B 901 GLN B 913 GLN B 914 ASN B 957 GLN B1002 GLN B1071 GLN B1142 GLN C 123 ASN C 174 GLN C 271 GLN C 321 GLN C 474 GLN C 493 GLN C 607 GLN C 613 GLN C 628 GLN C 677 GLN C 787 GLN C 804 GLN C 872 GLN C 901 GLN C 913 GLN C 914 ASN C 957 GLN C1002 GLN C1071 GLN C1142 GLN G 60 GLN G 89 GLN G 121 ASN G 149 ASN G 338 ASN G 340 GLN G 508 ASN G 524 GLN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN H 149 ASN H 338 ASN H 340 GLN H 524 GLN H 580 ASN ** H 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN ** I 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 ASN I 340 GLN I 524 GLN ** I 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.171052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.108661 restraints weight = 140664.175| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 7.08 r_work: 0.2945 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 40011 Z= 0.192 Angle : 0.572 15.329 54441 Z= 0.293 Chirality : 0.043 0.295 5976 Planarity : 0.004 0.046 7020 Dihedral : 3.496 41.308 5272 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.13 % Allowed : 7.92 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.12), residues: 4830 helix: 1.12 (0.13), residues: 1797 sheet: 0.32 (0.20), residues: 642 loop : -2.46 (0.11), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 115 TYR 0.027 0.001 TYR G 215 PHE 0.023 0.002 PHE B1095 TRP 0.009 0.001 TRP A 886 HIS 0.006 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00450 (39969) covalent geometry : angle 0.56751 (54357) SS BOND : bond 0.00200 ( 42) SS BOND : angle 2.00059 ( 84) hydrogen bonds : bond 0.04901 ( 1614) hydrogen bonds : angle 4.71640 ( 4698) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 157 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8310 (mtmm) REVERT: A 468 ILE cc_start: 0.6503 (OUTLIER) cc_final: 0.6268 (mm) REVERT: A 869 MET cc_start: 0.9351 (mtt) cc_final: 0.9114 (mtp) REVERT: A 1010 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8500 (mp10) REVERT: B 1010 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.8604 (mp10) REVERT: C 331 ASN cc_start: 0.3857 (OUTLIER) cc_final: 0.2919 (p0) REVERT: G 366 MET cc_start: 0.2898 (OUTLIER) cc_final: 0.2659 (tpt) REVERT: G 408 MET cc_start: 0.4667 (ptp) cc_final: 0.4077 (tmm) REVERT: G 579 MET cc_start: 0.6428 (mmm) cc_final: 0.5740 (mmt) REVERT: H 249 MET cc_start: 0.5671 (mtt) cc_final: 0.5438 (mpp) REVERT: H 549 GLU cc_start: 0.8413 (mp0) cc_final: 0.8048 (pp20) REVERT: H 579 MET cc_start: 0.5612 (mmm) cc_final: 0.5285 (mmm) REVERT: I 323 MET cc_start: 0.8726 (mmt) cc_final: 0.8427 (tpt) REVERT: I 408 MET cc_start: 0.6466 (pp-130) cc_final: 0.5935 (pp-130) REVERT: I 579 MET cc_start: 0.6752 (mmt) cc_final: 0.6313 (mmt) outliers start: 92 outliers final: 25 residues processed: 234 average time/residue: 0.7615 time to fit residues: 217.5841 Evaluate side-chains 158 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 1144 GLU Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 366 MET Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 131 LYS Chi-restraints excluded: chain I residue 582 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 384 optimal weight: 50.0000 chunk 442 optimal weight: 50.0000 chunk 419 optimal weight: 50.0000 chunk 370 optimal weight: 50.0000 chunk 72 optimal weight: 4.9990 chunk 458 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 429 optimal weight: 30.0000 chunk 266 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 955 ASN A1011 GLN B 65 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 935 GLN B 955 ASN B1088 HIS C 65 ASN C 89 ASN C 174 GLN C 388 ASN C 901 GLN C 913 GLN C 955 ASN C1010 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 GLN I 121 ASN I 149 ASN ** I 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.169144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.102777 restraints weight = 140308.968| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 8.28 r_work: 0.2852 rms_B_bonded: 6.85 restraints_weight: 2.0000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 40011 Z= 0.271 Angle : 0.612 14.126 54441 Z= 0.317 Chirality : 0.045 0.208 5976 Planarity : 0.004 0.051 7020 Dihedral : 3.952 47.552 5267 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.48 % Allowed : 8.52 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.12), residues: 4830 helix: 1.08 (0.12), residues: 1872 sheet: 0.38 (0.20), residues: 672 loop : -2.21 (0.12), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 48 TYR 0.020 0.001 TYR A1047 PHE 0.026 0.002 PHE A 906 TRP 0.020 0.001 TRP A 452 HIS 0.009 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00640 (39969) covalent geometry : angle 0.60903 (54357) SS BOND : bond 0.01059 ( 42) SS BOND : angle 1.66153 ( 84) hydrogen bonds : bond 0.05734 ( 1614) hydrogen bonds : angle 4.70742 ( 4698) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 139 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1010 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8478 (mp10) REVERT: B 45 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8292 (mtpt) REVERT: B 452 TRP cc_start: 0.8784 (m-90) cc_final: 0.8190 (t-100) REVERT: B 1010 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8478 (mp10) REVERT: B 1031 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.9015 (mt-10) REVERT: C 331 ASN cc_start: 0.5466 (OUTLIER) cc_final: 0.4152 (p0) REVERT: C 900 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8853 (mtm) REVERT: G 249 MET cc_start: 0.5982 (mtt) cc_final: 0.5747 (mmt) REVERT: G 383 MET cc_start: 0.7636 (mpt) cc_final: 0.7079 (mpt) REVERT: G 408 MET cc_start: 0.5070 (ptp) cc_final: 0.4461 (ppp) REVERT: H 383 MET cc_start: 0.7821 (mpt) cc_final: 0.7438 (mmp) REVERT: H 549 GLU cc_start: 0.8267 (mp0) cc_final: 0.7976 (pp20) REVERT: I 408 MET cc_start: 0.6941 (pp-130) cc_final: 0.6698 (pp-130) REVERT: I 579 MET cc_start: 0.7916 (mmt) cc_final: 0.7715 (mmt) outliers start: 107 outliers final: 39 residues processed: 234 average time/residue: 0.7207 time to fit residues: 207.6451 Evaluate side-chains 170 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 125 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain H residue 131 LYS Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain I residue 283 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 17 optimal weight: 9.9990 chunk 371 optimal weight: 50.0000 chunk 19 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 287 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 417 optimal weight: 50.0000 chunk 109 optimal weight: 4.9990 chunk 235 optimal weight: 20.0000 chunk 186 optimal weight: 0.9990 chunk 370 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B1011 GLN C 913 GLN C1011 GLN G 89 GLN G 121 ASN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN ** I 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.173252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.112257 restraints weight = 141131.350| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 5.60 r_work: 0.2946 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 40011 Z= 0.172 Angle : 0.544 12.209 54441 Z= 0.276 Chirality : 0.043 0.263 5976 Planarity : 0.004 0.058 7020 Dihedral : 3.801 48.175 5257 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.11 % Allowed : 9.59 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.12), residues: 4830 helix: 1.32 (0.12), residues: 1869 sheet: 0.42 (0.20), residues: 687 loop : -2.05 (0.12), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 559 TYR 0.016 0.001 TYR B 279 PHE 0.016 0.001 PHE H 308 TRP 0.009 0.001 TRP G 271 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00407 (39969) covalent geometry : angle 0.54219 (54357) SS BOND : bond 0.00317 ( 42) SS BOND : angle 1.31183 ( 84) hydrogen bonds : bond 0.04849 ( 1614) hydrogen bonds : angle 4.48116 ( 4698) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 130 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8427 (mtmm) REVERT: A 1010 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8498 (mp10) REVERT: B 45 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8039 (mtpp) REVERT: C 331 ASN cc_start: 0.3699 (OUTLIER) cc_final: 0.2753 (p0) REVERT: C 738 CYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7936 (t) REVERT: C 900 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8873 (mtm) REVERT: C 985 ASP cc_start: 0.6242 (OUTLIER) cc_final: 0.6040 (p0) REVERT: G 408 MET cc_start: 0.4457 (ptp) cc_final: 0.4127 (ppp) REVERT: H 549 GLU cc_start: 0.8476 (mp0) cc_final: 0.8132 (pp20) REVERT: I 249 MET cc_start: 0.4362 (mmt) cc_final: 0.4138 (mmt) REVERT: I 568 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7258 (pp) REVERT: I 579 MET cc_start: 0.6250 (mmt) cc_final: 0.5744 (mmt) outliers start: 91 outliers final: 45 residues processed: 202 average time/residue: 0.7087 time to fit residues: 177.5478 Evaluate side-chains 175 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 122 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain H residue 131 LYS Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 285 PHE Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 568 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 85 optimal weight: 0.6980 chunk 242 optimal weight: 7.9990 chunk 405 optimal weight: 50.0000 chunk 172 optimal weight: 3.9990 chunk 325 optimal weight: 10.0000 chunk 296 optimal weight: 1.9990 chunk 133 optimal weight: 50.0000 chunk 147 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 304 optimal weight: 0.0870 chunk 138 optimal weight: 50.0000 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN I 401 HIS ** I 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.171985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.109124 restraints weight = 144588.533| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 7.90 r_work: 0.2894 rms_B_bonded: 7.00 restraints_weight: 2.0000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40011 Z= 0.117 Angle : 0.513 11.141 54441 Z= 0.256 Chirality : 0.041 0.217 5976 Planarity : 0.004 0.063 7020 Dihedral : 3.701 48.001 5257 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.15 % Allowed : 9.84 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.12), residues: 4830 helix: 1.70 (0.12), residues: 1830 sheet: 0.42 (0.20), residues: 720 loop : -1.94 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 559 TYR 0.014 0.001 TYR C1067 PHE 0.026 0.001 PHE B 377 TRP 0.009 0.001 TRP I 271 HIS 0.003 0.000 HIS H 373 Details of bonding type rmsd covalent geometry : bond 0.00271 (39969) covalent geometry : angle 0.51177 (54357) SS BOND : bond 0.00290 ( 42) SS BOND : angle 1.14286 ( 84) hydrogen bonds : bond 0.04255 ( 1614) hydrogen bonds : angle 4.29498 ( 4698) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 128 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8312 (mtmm) REVERT: A 820 ASP cc_start: 0.9252 (OUTLIER) cc_final: 0.9026 (m-30) REVERT: A 980 ILE cc_start: 0.8097 (pt) cc_final: 0.7875 (pp) REVERT: B 45 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8129 (mtpp) REVERT: B 1031 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8699 (mt-10) REVERT: C 331 ASN cc_start: 0.4649 (OUTLIER) cc_final: 0.4093 (p0) REVERT: G 408 MET cc_start: 0.4448 (ptp) cc_final: 0.4125 (ppp) REVERT: H 408 MET cc_start: 0.5597 (pp-130) cc_final: 0.5369 (pp-130) REVERT: H 549 GLU cc_start: 0.8445 (mp0) cc_final: 0.8128 (pp20) REVERT: I 249 MET cc_start: 0.5168 (mmt) cc_final: 0.4954 (mmt) REVERT: I 408 MET cc_start: 0.6457 (pp-130) cc_final: 0.6222 (pp-130) REVERT: I 579 MET cc_start: 0.7410 (mmt) cc_final: 0.7144 (mmt) outliers start: 93 outliers final: 44 residues processed: 209 average time/residue: 0.5725 time to fit residues: 150.7910 Evaluate side-chains 171 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain H residue 131 LYS Chi-restraints excluded: chain H residue 270 MET Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 447 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 187 optimal weight: 0.0020 chunk 112 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 451 optimal weight: 9.9990 chunk 228 optimal weight: 5.9990 chunk 142 optimal weight: 40.0000 chunk 79 optimal weight: 3.9990 chunk 216 optimal weight: 20.0000 chunk 200 optimal weight: 0.8980 chunk 224 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN ** I 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.171589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.110214 restraints weight = 144881.679| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 8.36 r_work: 0.2846 rms_B_bonded: 5.27 restraints_weight: 2.0000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 40011 Z= 0.143 Angle : 0.533 13.844 54441 Z= 0.266 Chirality : 0.042 0.201 5976 Planarity : 0.004 0.060 7020 Dihedral : 3.727 47.684 5257 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.02 % Allowed : 10.28 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.12), residues: 4830 helix: 1.77 (0.12), residues: 1836 sheet: 0.58 (0.20), residues: 684 loop : -1.82 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 245 TYR 0.018 0.001 TYR I 202 PHE 0.020 0.001 PHE B 377 TRP 0.010 0.001 TRP I 271 HIS 0.005 0.001 HIS I 239 Details of bonding type rmsd covalent geometry : bond 0.00335 (39969) covalent geometry : angle 0.53142 (54357) SS BOND : bond 0.00327 ( 42) SS BOND : angle 1.27842 ( 84) hydrogen bonds : bond 0.04410 ( 1614) hydrogen bonds : angle 4.30257 ( 4698) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 132 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8344 (mtmm) REVERT: A 820 ASP cc_start: 0.9303 (OUTLIER) cc_final: 0.9042 (m-30) REVERT: B 45 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8083 (mtpp) REVERT: B 661 GLU cc_start: 0.9448 (tt0) cc_final: 0.9097 (tm-30) REVERT: B 1031 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8788 (mt-10) REVERT: C 331 ASN cc_start: 0.4086 (OUTLIER) cc_final: 0.3462 (p0) REVERT: C 985 ASP cc_start: 0.5947 (OUTLIER) cc_final: 0.5718 (OUTLIER) REVERT: G 152 MET cc_start: -0.3007 (OUTLIER) cc_final: -0.3207 (ptt) REVERT: G 408 MET cc_start: 0.4562 (ptp) cc_final: 0.4003 (ppp) REVERT: H 549 GLU cc_start: 0.8471 (mp0) cc_final: 0.8183 (pp20) REVERT: I 181 GLU cc_start: 0.7127 (tp30) cc_final: 0.6831 (mm-30) REVERT: I 249 MET cc_start: 0.5578 (mmt) cc_final: 0.5349 (mmt) REVERT: I 323 MET cc_start: 0.8832 (tpt) cc_final: 0.8617 (tpt) REVERT: I 579 MET cc_start: 0.7414 (mmt) cc_final: 0.7168 (mmt) outliers start: 87 outliers final: 53 residues processed: 200 average time/residue: 0.6112 time to fit residues: 153.1908 Evaluate side-chains 184 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 125 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain H residue 131 LYS Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 447 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 106 optimal weight: 4.9990 chunk 325 optimal weight: 20.0000 chunk 470 optimal weight: 40.0000 chunk 447 optimal weight: 30.0000 chunk 463 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 344 optimal weight: 40.0000 chunk 319 optimal weight: 7.9990 chunk 458 optimal weight: 50.0000 chunk 140 optimal weight: 30.0000 chunk 301 optimal weight: 3.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 913 GLN C1119 ASN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN ** I 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.169559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.105911 restraints weight = 143297.646| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 7.08 r_work: 0.2847 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 40011 Z= 0.312 Angle : 0.654 15.424 54441 Z= 0.334 Chirality : 0.046 0.210 5976 Planarity : 0.004 0.060 7020 Dihedral : 4.239 52.188 5257 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.04 % Allowed : 10.73 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.12), residues: 4830 helix: 1.61 (0.12), residues: 1839 sheet: 0.28 (0.20), residues: 708 loop : -1.84 (0.12), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 765 TYR 0.020 0.001 TYR B1047 PHE 0.022 0.002 PHE B1089 TRP 0.011 0.001 TRP H 473 HIS 0.010 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00738 (39969) covalent geometry : angle 0.65007 (54357) SS BOND : bond 0.00460 ( 42) SS BOND : angle 1.82691 ( 84) hydrogen bonds : bond 0.05911 ( 1614) hydrogen bonds : angle 4.66295 ( 4698) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 128 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 238 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8318 (t80) REVERT: B 1031 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8978 (mt-10) REVERT: C 331 ASN cc_start: 0.4613 (OUTLIER) cc_final: 0.4018 (p0) REVERT: C 900 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8874 (mtm) REVERT: G 332 MET cc_start: 0.1917 (ttt) cc_final: 0.1650 (ptt) REVERT: G 408 MET cc_start: 0.4724 (ptp) cc_final: 0.4459 (ppp) REVERT: H 549 GLU cc_start: 0.8505 (mp0) cc_final: 0.8197 (pp20) REVERT: H 568 LEU cc_start: 0.7829 (pt) cc_final: 0.7552 (tp) REVERT: I 181 GLU cc_start: 0.7006 (tp30) cc_final: 0.6777 (mm-30) REVERT: I 249 MET cc_start: 0.4637 (mmt) cc_final: 0.4390 (mmt) REVERT: I 270 MET cc_start: -0.2052 (mpt) cc_final: -0.2705 (mmt) REVERT: I 323 MET cc_start: 0.8066 (tpt) cc_final: 0.7673 (tpt) REVERT: I 579 MET cc_start: 0.6649 (mmt) cc_final: 0.6143 (mmt) outliers start: 88 outliers final: 54 residues processed: 201 average time/residue: 0.5774 time to fit residues: 145.6107 Evaluate side-chains 183 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 125 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain H residue 131 LYS Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 568 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 112 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 341 optimal weight: 30.0000 chunk 409 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 279 optimal weight: 0.8980 chunk 426 optimal weight: 8.9990 chunk 139 optimal weight: 50.0000 chunk 119 optimal weight: 5.9990 chunk 324 optimal weight: 50.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN ** H 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN I 149 ASN ** I 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.172105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.114692 restraints weight = 140782.127| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 5.08 r_work: 0.2921 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 40011 Z= 0.146 Angle : 0.558 14.110 54441 Z= 0.278 Chirality : 0.042 0.202 5976 Planarity : 0.004 0.066 7020 Dihedral : 3.985 51.726 5257 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.64 % Allowed : 11.33 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.12), residues: 4830 helix: 1.77 (0.12), residues: 1854 sheet: 0.39 (0.20), residues: 705 loop : -1.72 (0.13), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 983 TYR 0.017 0.001 TYR I 50 PHE 0.015 0.001 PHE A1121 TRP 0.012 0.001 TRP I 203 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00344 (39969) covalent geometry : angle 0.55653 (54357) SS BOND : bond 0.00299 ( 42) SS BOND : angle 1.28956 ( 84) hydrogen bonds : bond 0.04630 ( 1614) hydrogen bonds : angle 4.38371 ( 4698) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 131 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7623 (mtpt) REVERT: B 45 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8201 (mtpt) REVERT: B 661 GLU cc_start: 0.9409 (tt0) cc_final: 0.9069 (tm-30) REVERT: G 82 MET cc_start: 0.8304 (pmm) cc_final: 0.8047 (ppp) REVERT: G 190 MET cc_start: 0.3234 (pp-130) cc_final: 0.2798 (pp-130) REVERT: G 332 MET cc_start: 0.2110 (ttt) cc_final: 0.1840 (ptt) REVERT: G 408 MET cc_start: 0.4626 (ptp) cc_final: 0.4331 (ppp) REVERT: H 474 MET cc_start: -0.1068 (tpt) cc_final: -0.1269 (tpt) REVERT: H 549 GLU cc_start: 0.8550 (mp0) cc_final: 0.8197 (pp20) REVERT: H 568 LEU cc_start: 0.7670 (pt) cc_final: 0.7412 (tp) REVERT: I 249 MET cc_start: 0.5330 (mmt) cc_final: 0.5101 (mmt) REVERT: I 323 MET cc_start: 0.8120 (tpt) cc_final: 0.7791 (tpt) REVERT: I 579 MET cc_start: 0.7490 (mmt) cc_final: 0.7247 (mmt) outliers start: 71 outliers final: 52 residues processed: 191 average time/residue: 0.6988 time to fit residues: 166.4316 Evaluate side-chains 179 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 125 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain H residue 131 LYS Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 568 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 239 optimal weight: 20.0000 chunk 429 optimal weight: 20.0000 chunk 2 optimal weight: 0.8980 chunk 453 optimal weight: 40.0000 chunk 217 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 381 optimal weight: 5.9990 chunk 290 optimal weight: 0.0030 chunk 465 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 540 HIS ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.171459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.113317 restraints weight = 140446.355| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 4.23 r_work: 0.2963 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 40011 Z= 0.163 Angle : 0.577 18.377 54441 Z= 0.285 Chirality : 0.043 0.236 5976 Planarity : 0.004 0.064 7020 Dihedral : 3.942 51.322 5255 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.67 % Allowed : 11.21 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.12), residues: 4830 helix: 1.85 (0.12), residues: 1821 sheet: 0.40 (0.20), residues: 705 loop : -1.70 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 983 TYR 0.026 0.001 TYR G 199 PHE 0.030 0.001 PHE B 377 TRP 0.021 0.001 TRP I 473 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00386 (39969) covalent geometry : angle 0.57534 (54357) SS BOND : bond 0.00304 ( 42) SS BOND : angle 1.28630 ( 84) hydrogen bonds : bond 0.04704 ( 1614) hydrogen bonds : angle 4.38485 ( 4698) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 125 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8055 (mtpp) REVERT: B 661 GLU cc_start: 0.9297 (tt0) cc_final: 0.9027 (tm-30) REVERT: C 45 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.7743 (mtpt) REVERT: C 900 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8863 (mtm) REVERT: G 82 MET cc_start: 0.8210 (pmm) cc_final: 0.7944 (ppp) REVERT: G 332 MET cc_start: 0.1761 (ttt) cc_final: 0.1496 (ptt) REVERT: G 408 MET cc_start: 0.4741 (ptp) cc_final: 0.4474 (ppp) REVERT: H 332 MET cc_start: 0.1475 (ppp) cc_final: 0.0947 (pp-130) REVERT: H 549 GLU cc_start: 0.8521 (mp0) cc_final: 0.8138 (pp20) REVERT: H 568 LEU cc_start: 0.7604 (pt) cc_final: 0.7325 (tp) REVERT: I 323 MET cc_start: 0.7258 (tpt) cc_final: 0.6892 (tpt) REVERT: I 455 MET cc_start: 0.1352 (pp-130) cc_final: 0.0143 (ppp) REVERT: I 480 MET cc_start: 0.6830 (ptp) cc_final: 0.5942 (ppp) REVERT: I 579 MET cc_start: 0.6757 (mmt) cc_final: 0.6304 (mmt) outliers start: 72 outliers final: 55 residues processed: 188 average time/residue: 0.5330 time to fit residues: 125.7495 Evaluate side-chains 181 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 123 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain H residue 131 LYS Chi-restraints excluded: chain H residue 270 MET Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 568 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 39 optimal weight: 4.9990 chunk 449 optimal weight: 10.0000 chunk 389 optimal weight: 7.9990 chunk 302 optimal weight: 0.1980 chunk 260 optimal weight: 1.9990 chunk 407 optimal weight: 40.0000 chunk 210 optimal weight: 0.7980 chunk 184 optimal weight: 7.9990 chunk 470 optimal weight: 50.0000 chunk 349 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 540 HIS ** I 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.172035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.113992 restraints weight = 140256.988| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 4.62 r_work: 0.2921 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 40011 Z= 0.182 Angle : 0.591 18.658 54441 Z= 0.293 Chirality : 0.043 0.201 5976 Planarity : 0.004 0.109 7020 Dihedral : 4.017 52.734 5255 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.55 % Allowed : 11.37 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.12), residues: 4830 helix: 1.77 (0.12), residues: 1839 sheet: 0.34 (0.19), residues: 735 loop : -1.67 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 983 TYR 0.028 0.001 TYR I 202 PHE 0.025 0.001 PHE A 128 TRP 0.019 0.001 TRP I 473 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00433 (39969) covalent geometry : angle 0.58928 (54357) SS BOND : bond 0.00310 ( 42) SS BOND : angle 1.34264 ( 84) hydrogen bonds : bond 0.04843 ( 1614) hydrogen bonds : angle 4.44659 ( 4698) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 121 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8059 (mtpp) REVERT: B 661 GLU cc_start: 0.9391 (tt0) cc_final: 0.9061 (tm-30) REVERT: C 45 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.7702 (mtpt) REVERT: C 900 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8871 (mtm) REVERT: C 985 ASP cc_start: 0.5651 (OUTLIER) cc_final: 0.5424 (p0) REVERT: G 82 MET cc_start: 0.8252 (pmm) cc_final: 0.7925 (ppp) REVERT: G 332 MET cc_start: 0.2132 (ttt) cc_final: 0.1850 (ptt) REVERT: G 408 MET cc_start: 0.4812 (ptp) cc_final: 0.4563 (ppp) REVERT: H 332 MET cc_start: 0.1485 (ppp) cc_final: 0.0905 (pp-130) REVERT: H 549 GLU cc_start: 0.8445 (mp0) cc_final: 0.8089 (pp20) REVERT: H 568 LEU cc_start: 0.7622 (pt) cc_final: 0.7357 (tp) REVERT: I 323 MET cc_start: 0.7222 (tpt) cc_final: 0.6829 (tpt) REVERT: I 455 MET cc_start: 0.1369 (pp-130) cc_final: 0.0238 (ppp) REVERT: I 480 MET cc_start: 0.6528 (ptp) cc_final: 0.5681 (ttt) REVERT: I 579 MET cc_start: 0.6778 (mmt) cc_final: 0.6303 (mmt) outliers start: 67 outliers final: 53 residues processed: 177 average time/residue: 0.6827 time to fit residues: 150.1941 Evaluate side-chains 176 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 119 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain H residue 131 LYS Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 568 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.2667 > 50: distance: 39 - 62: 22.165 distance: 43 - 68: 9.907 distance: 48 - 54: 5.490 distance: 54 - 55: 10.154 distance: 55 - 56: 18.898 distance: 55 - 58: 10.283 distance: 56 - 57: 8.269 distance: 56 - 62: 9.142 distance: 57 - 82: 12.673 distance: 58 - 59: 18.154 distance: 59 - 60: 20.288 distance: 60 - 61: 5.169 distance: 62 - 63: 6.617 distance: 63 - 64: 6.671 distance: 63 - 66: 5.511 distance: 64 - 65: 8.869 distance: 64 - 68: 19.306 distance: 65 - 87: 16.622 distance: 66 - 67: 36.233 distance: 68 - 69: 10.070 distance: 69 - 70: 7.860 distance: 69 - 72: 9.185 distance: 70 - 71: 3.058 distance: 70 - 76: 4.448 distance: 72 - 73: 12.671 distance: 73 - 74: 8.095 distance: 73 - 75: 12.089 distance: 76 - 77: 12.896 distance: 77 - 78: 7.667 distance: 78 - 79: 7.836 distance: 78 - 82: 7.119 distance: 80 - 81: 10.624 distance: 82 - 83: 21.218 distance: 83 - 84: 10.792 distance: 83 - 86: 13.905 distance: 84 - 87: 5.175 distance: 87 - 88: 31.040 distance: 88 - 89: 27.823 distance: 88 - 91: 21.582 distance: 89 - 90: 19.635 distance: 89 - 92: 29.919 distance: 93 - 96: 5.440 distance: 94 - 95: 10.760 distance: 94 - 99: 18.791 distance: 95 - 125: 28.981 distance: 96 - 98: 22.651 distance: 99 - 100: 11.331 distance: 99 - 105: 26.021 distance: 100 - 101: 14.839 distance: 100 - 103: 23.738 distance: 101 - 102: 8.269 distance: 101 - 106: 10.516 distance: 102 - 133: 16.058 distance: 103 - 104: 12.461 distance: 104 - 105: 5.367 distance: 107 - 108: 8.948 distance: 107 - 110: 8.110 distance: 108 - 109: 12.242 distance: 108 - 115: 3.951 distance: 109 - 139: 12.764 distance: 110 - 111: 7.114 distance: 111 - 112: 8.441 distance: 112 - 113: 12.682 distance: 113 - 114: 12.485 distance: 115 - 116: 7.306 distance: 116 - 117: 4.686 distance: 116 - 119: 7.544 distance: 117 - 118: 10.396 distance: 117 - 125: 6.156 distance: 118 - 145: 16.630 distance: 119 - 120: 15.351 distance: 120 - 121: 18.175 distance: 120 - 122: 9.332 distance: 121 - 123: 11.360 distance: 122 - 124: 15.216 distance: 123 - 124: 9.852