Starting phenix.real_space_refine on Sun Jul 5 23:04:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h6f_34501/07_2026/8h6f_34501.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h6f_34501/07_2026/8h6f_34501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h6f_34501/07_2026/8h6f_34501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h6f_34501/07_2026/8h6f_34501.map" model { file = "/net/cci-nas-00/data/ceres_data/8h6f_34501/07_2026/8h6f_34501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h6f_34501/07_2026/8h6f_34501.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8h6f_34501/07_2026/8h6f_34501.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h6f_34501/07_2026/8h6f_34501.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.075 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 124 5.16 5 C 19796 2.51 5 N 5120 2.21 5 O 5977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31017 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8096 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 56, 'TRANS': 979} Chain breaks: 6 Chain: "B" Number of atoms: 8123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8123 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 56, 'TRANS': 981} Chain breaks: 6 Chain: "C" Number of atoms: 8106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8106 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 56, 'TRANS': 979} Chain breaks: 6 Chain: "X" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2072 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 244} Chain: "Y" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2072 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 244} Chain: "Z" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2072 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 244} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.71, per 1000 atoms: 0.22 Number of scatterers: 31017 At special positions: 0 Unit cell: (153.994, 185.13, 228.888, 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 124 16.00 O 5977 8.00 N 5120 7.00 C 19796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS X 220 " - pdb=" SG CYS X 253 " distance=2.03 Simple disulfide: pdb=" SG CYS X 222 " - pdb=" SG CYS X 265 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 220 " - pdb=" SG CYS Y 253 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 222 " - pdb=" SG CYS Y 265 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 220 " - pdb=" SG CYS Z 253 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 222 " - pdb=" SG CYS Z 265 " 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=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1134 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B1134 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 122 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 61 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B1098 " " NAG K 1 " - " ASN C1098 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.5 seconds 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7340 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 42 sheets defined 23.2% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.676A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 4.495A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 4.166A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 422' Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.936A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.749A pdb=" N ALA A 623 " --> pdb=" O GLU A 619 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 624' Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 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: 3.603A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.719A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.552A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 4.030A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.600A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.906A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.874A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 983 Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.673A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.878A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 341' Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.888A pdb=" N ALA B 372 " --> pdb=" O TYR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.879A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.902A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.845A pdb=" N VAL B 622 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 634 removed outlier: 3.672A pdb=" N TRP B 633 " --> pdb=" O THR B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.505A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 761 through 783 removed outlier: 3.911A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (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 886 through 890 removed outlier: 3.538A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.639A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.156A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.992A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.876A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1033 Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 172 through 176 removed outlier: 3.649A pdb=" N PHE C 175 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU C 176 " --> pdb=" O GLN C 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 176' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.042A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.798A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.628A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 423 Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.985A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 637 removed outlier: 4.092A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.592A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 removed outlier: 4.098A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.564A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.684A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 890' Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.576A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.970A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.510A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.039A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.753A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.856A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C1025 " --> pdb=" O SER C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1148 removed outlier: 4.507A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'X' and resid 17 through 27 removed outlier: 3.975A pdb=" N LEU X 27 " --> pdb=" O ILE X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 44 removed outlier: 3.708A pdb=" N SER X 43 " --> pdb=" O GLU X 40 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE X 44 " --> pdb=" O LEU X 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 40 through 44' Processing helix chain 'X' and resid 59 through 63 removed outlier: 3.833A pdb=" N TYR X 62 " --> pdb=" O GLY X 59 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 83 removed outlier: 3.628A pdb=" N ALA X 81 " --> pdb=" O ASP X 78 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS X 83 " --> pdb=" O SER X 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 104 through 108 removed outlier: 3.597A pdb=" N ASP X 107 " --> pdb=" O GLY X 104 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS X 108 " --> pdb=" O VAL X 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 104 through 108' Processing helix chain 'X' and resid 200 through 205 removed outlier: 4.678A pdb=" N ARG X 204 " --> pdb=" O GLY X 200 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU X 205 " --> pdb=" O VAL X 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 200 through 205' Processing helix chain 'X' and resid 225 through 235 Processing helix chain 'X' and resid 236 through 239 removed outlier: 3.792A pdb=" N VAL X 239 " --> pdb=" O SER X 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 236 through 239' Processing helix chain 'X' and resid 246 through 251 removed outlier: 3.675A pdb=" N SER X 250 " --> pdb=" O TRP X 246 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA X 251 " --> pdb=" O ALA X 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 246 through 251' Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 37 through 43 Processing helix chain 'Y' and resid 79 through 85 removed outlier: 3.544A pdb=" N LYS Y 83 " --> pdb=" O SER Y 80 " (cutoff:3.500A) Processing helix chain 'Y' and resid 225 through 235 removed outlier: 3.617A pdb=" N HIS Y 235 " --> pdb=" O TRP Y 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 27 Processing helix chain 'Z' and resid 37 through 44 removed outlier: 3.563A pdb=" N ILE Z 44 " --> pdb=" O GLU Z 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 83 removed outlier: 4.122A pdb=" N LEU Z 82 " --> pdb=" O ILE Z 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 201 through 205 removed outlier: 3.724A pdb=" N ARG Z 204 " --> pdb=" O VAL Z 201 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU Z 205 " --> pdb=" O PHE Z 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 201 through 205' Processing helix chain 'Z' and resid 223 through 235 removed outlier: 4.210A pdb=" N TYR Z 227 " --> pdb=" O PRO Z 223 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU Z 228 " --> pdb=" O GLY Z 224 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 3.757A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.073A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.756A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.682A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.905A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 327 removed outlier: 3.794A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 357 removed outlier: 4.271A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.947A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.881A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.709A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.739A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.876A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.288A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR B 266 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.643A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.963A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.542A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.806A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 355 through 357 removed outlier: 4.016A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 378 through 379 removed outlier: 4.128A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 542 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.217A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.591A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.612A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.612A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.517A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.823A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.161A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 49 removed outlier: 3.566A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 49 removed outlier: 3.566A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.620A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.919A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.632A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.243A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.779A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1097 812 hydrogen bonds defined for protein. 2223 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: 8.21 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9922 1.34 - 1.46: 6975 1.46 - 1.58: 14662 1.58 - 1.70: 0 1.70 - 1.82: 155 Bond restraints: 31714 Sorted by residual: bond pdb=" C ILE X 13 " pdb=" N PHE X 14 " ideal model delta sigma weight residual 1.331 1.376 -0.044 1.63e-02 3.76e+03 7.43e+00 bond pdb=" N SER C 155 " pdb=" CA SER C 155 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.18e-02 7.18e+03 7.42e+00 bond pdb=" CB ASN B 331 " pdb=" CG ASN B 331 " ideal model delta sigma weight residual 1.516 1.567 -0.051 2.50e-02 1.60e+03 4.21e+00 bond pdb=" CA ASP Y 164 " pdb=" CB ASP Y 164 " ideal model delta sigma weight residual 1.527 1.560 -0.033 1.75e-02 3.27e+03 3.66e+00 bond pdb=" N THR A1100 " pdb=" CA THR A1100 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.28e-02 6.10e+03 3.56e+00 ... (remaining 31709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 42366 1.96 - 3.92: 706 3.92 - 5.87: 70 5.87 - 7.83: 24 7.83 - 9.79: 4 Bond angle restraints: 43170 Sorted by residual: angle pdb=" N SER C 155 " pdb=" CA SER C 155 " pdb=" C SER C 155 " ideal model delta sigma weight residual 112.72 106.15 6.57 1.14e+00 7.69e-01 3.32e+01 angle pdb=" CA CYS A 166 " pdb=" CB CYS A 166 " pdb=" SG CYS A 166 " ideal model delta sigma weight residual 114.40 124.19 -9.79 2.30e+00 1.89e-01 1.81e+01 angle pdb=" N ARG X 72 " pdb=" CA ARG X 72 " pdb=" C ARG X 72 " ideal model delta sigma weight residual 111.55 106.38 5.17 1.37e+00 5.33e-01 1.43e+01 angle pdb=" CA GLN Y 12 " pdb=" CB GLN Y 12 " pdb=" CG GLN Y 12 " ideal model delta sigma weight residual 114.10 121.51 -7.41 2.00e+00 2.50e-01 1.37e+01 angle pdb=" N ILE Z 79 " pdb=" CA ILE Z 79 " pdb=" C ILE Z 79 " ideal model delta sigma weight residual 112.43 109.02 3.41 9.20e-01 1.18e+00 1.37e+01 ... (remaining 43165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 16001 18.05 - 36.11: 2156 36.11 - 54.16: 490 54.16 - 72.22: 98 72.22 - 90.27: 37 Dihedral angle restraints: 18782 sinusoidal: 7423 harmonic: 11359 Sorted by residual: dihedral pdb=" CB CYS X 222 " pdb=" SG CYS X 222 " pdb=" SG CYS X 265 " pdb=" CB CYS X 265 " ideal model delta sinusoidal sigma weight residual -86.00 -176.27 90.27 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 0.77 -86.77 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -5.96 -80.04 1 1.00e+01 1.00e-02 7.94e+01 ... (remaining 18779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 4997 0.145 - 0.291: 22 0.291 - 0.436: 11 0.436 - 0.581: 2 0.581 - 0.727: 2 Chirality restraints: 5034 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.10e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.53e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.46e+01 ... (remaining 5031 not shown) Planarity restraints: 5569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.347 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG H 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.095 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.531 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1302 " -0.348 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG C1302 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C1302 " -0.140 2.00e-02 2.50e+03 pdb=" N2 NAG C1302 " 0.532 2.00e-02 2.50e+03 pdb=" O7 NAG C1302 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1306 " -0.342 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG C1306 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1306 " -0.101 2.00e-02 2.50e+03 pdb=" N2 NAG C1306 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG C1306 " -0.164 2.00e-02 2.50e+03 ... (remaining 5566 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 757 2.70 - 3.25: 28578 3.25 - 3.80: 42715 3.80 - 4.35: 53114 4.35 - 4.90: 91733 Nonbonded interactions: 216897 Sorted by model distance: nonbonded pdb=" O THR A 108 " pdb=" OG1 THR A 236 " model vdw 2.148 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.204 3.040 nonbonded pdb=" OG SER A 438 " pdb=" O ASP A 442 " model vdw 2.212 3.040 nonbonded pdb=" NE2 GLN A 804 " pdb=" OE1 GLN A 935 " model vdw 2.220 3.120 nonbonded pdb=" O SER C 746 " pdb=" OG SER C 750 " model vdw 2.242 3.040 ... (remaining 216892 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 139 or resid 153 through 186 or resid 188 throu \ gh 243 or resid 263 through 675 or resid 691 through 1307)) selection = (chain 'B' and (resid 26 through 139 or resid 153 through 186 or resid 188 throu \ gh 243 or resid 263 through 675 or resid 691 through 1307)) selection = (chain 'C' and (resid 26 through 175 or resid 188 through 243 or resid 263 throu \ gh 675 or resid 691 through 1307)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 6.790 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: 0.750 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 31.090 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.005 0.607 31794 Z= 0.377 Angle : 0.634 9.790 43362 Z= 0.337 Chirality : 0.051 0.727 5034 Planarity : 0.016 0.299 5540 Dihedral : 17.044 89.687 11307 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.50 % Rotamer: Outliers : 0.26 % Allowed : 27.93 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.13), residues: 3842 helix: 1.34 (0.21), residues: 713 sheet: -0.42 (0.25), residues: 437 loop : -1.90 (0.11), residues: 2692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 995 TYR 0.016 0.001 TYR C 660 PHE 0.029 0.001 PHE C 192 TRP 0.021 0.001 TRP Y 218 HIS 0.007 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (31714) covalent geometry : angle 0.61715 / 0.33 (43170) SS BOND : bond 0.00205 / 0.12 ( 45) SS BOND : angle 1.51735 / 1.01 ( 90) hydrogen bonds : bond 0.21254 / 13.45 ( 795) hydrogen bonds : angle 7.47181 / 5.02 ( 2223) Misc. bond : bond 0.60715 / 40.48 ( 1) link_BETA1-4 : bond 0.00302 / 0.16 ( 5) link_BETA1-4 : angle 0.68064 / 0.42 ( 15) link_NAG-ASN : bond 0.00558 / 0.37 ( 29) link_NAG-ASN : angle 3.00103 / 2.08 ( 87) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1041 ASP cc_start: 0.6694 (t0) cc_final: 0.6384 (t0) REVERT: C 153 MET cc_start: 0.5157 (tpp) cc_final: 0.4920 (tpt) REVERT: X 63 LEU cc_start: -0.0087 (OUTLIER) cc_final: -0.0348 (mp) outliers start: 9 outliers final: 4 residues processed: 167 average time/residue: 0.1739 time to fit residues: 50.5074 Evaluate side-chains 157 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 152 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain X residue 63 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 0.0670 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 ASN A 710 ASN A1101 HIS B 66 HIS B 331 ASN B 360 ASN B 935 GLN C 321 GLN C 422 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.251611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.205972 restraints weight = 37187.234| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 2.49 r_work: 0.3920 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.0658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31794 Z= 0.117 Angle : 0.593 13.226 43362 Z= 0.283 Chirality : 0.045 0.370 5034 Planarity : 0.004 0.063 5540 Dihedral : 3.897 36.262 4153 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.40 % Favored : 95.55 % Rotamer: Outliers : 2.29 % Allowed : 26.37 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.13), residues: 3842 helix: 1.43 (0.21), residues: 732 sheet: -0.18 (0.26), residues: 435 loop : -1.88 (0.11), residues: 2675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.020 0.001 TYR B1067 PHE 0.016 0.001 PHE A 192 TRP 0.012 0.001 TRP B 104 HIS 0.007 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (31714) covalent geometry : angle 0.57200 / 0.28 (43170) SS BOND : bond 0.00266 / 0.17 ( 45) SS BOND : angle 1.32661 / 0.88 ( 90) hydrogen bonds : bond 0.05100 / 3.34 ( 795) hydrogen bonds : angle 5.50792 / 3.73 ( 2223) Misc. bond : bond 0.00408 / 0.27 ( 1) link_BETA1-4 : bond 0.00601 / 0.34 ( 5) link_BETA1-4 : angle 1.55924 / 1.03 ( 15) link_NAG-ASN : bond 0.00818 / 0.56 ( 29) link_NAG-ASN : angle 3.28071 / 2.25 ( 87) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 163 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 190 ARG cc_start: 0.7951 (mtm180) cc_final: 0.7534 (mtm-85) REVERT: B 488 CYS cc_start: 0.0929 (OUTLIER) cc_final: 0.0093 (t) REVERT: C 192 PHE cc_start: 0.7816 (m-80) cc_final: 0.7431 (m-80) REVERT: C 377 PHE cc_start: 0.0546 (OUTLIER) cc_final: -0.0978 (m-10) REVERT: C 995 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7818 (ptm160) REVERT: Z 142 MET cc_start: 0.3200 (OUTLIER) cc_final: 0.2408 (mtp) REVERT: Z 155 ASP cc_start: 0.3532 (OUTLIER) cc_final: 0.2019 (m-30) outliers start: 79 outliers final: 32 residues processed: 234 average time/residue: 0.1808 time to fit residues: 72.1571 Evaluate side-chains 185 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 186 ASP Chi-restraints excluded: chain X residue 189 LEU Chi-restraints excluded: chain Z residue 142 MET Chi-restraints excluded: chain Z residue 155 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 11 optimal weight: 20.0000 chunk 92 optimal weight: 0.0470 chunk 235 optimal weight: 40.0000 chunk 182 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 379 optimal weight: 20.0000 chunk 6 optimal weight: 0.0050 chunk 142 optimal weight: 10.0000 overall best weight: 1.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS B 949 GLN C 321 GLN C 580 GLN C 901 GLN C 907 ASN Z 61 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.247050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.200015 restraints weight = 37204.454| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 2.55 r_work: 0.3934 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31794 Z= 0.173 Angle : 0.597 10.772 43362 Z= 0.293 Chirality : 0.046 0.392 5034 Planarity : 0.004 0.063 5540 Dihedral : 4.040 31.013 4148 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.18 % Favored : 94.79 % Rotamer: Outliers : 3.47 % Allowed : 25.93 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.13), residues: 3842 helix: 1.27 (0.20), residues: 736 sheet: -0.41 (0.25), residues: 431 loop : -1.89 (0.11), residues: 2675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1039 TYR 0.028 0.001 TYR B 265 PHE 0.022 0.002 PHE A1121 TRP 0.008 0.001 TRP C 64 HIS 0.008 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.17 (31714) covalent geometry : angle 0.57922 / 0.29 (43170) SS BOND : bond 0.00335 / 0.22 ( 45) SS BOND : angle 1.46715 / 0.95 ( 90) hydrogen bonds : bond 0.06153 / 4.04 ( 795) hydrogen bonds : angle 5.11601 / 3.49 ( 2223) Misc. bond : bond 0.00182 / 0.12 ( 1) link_BETA1-4 : bond 0.00465 / 0.27 ( 5) link_BETA1-4 : angle 1.40656 / 0.88 ( 15) link_NAG-ASN : bond 0.00634 / 0.43 ( 29) link_NAG-ASN : angle 2.88515 / 1.99 ( 87) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 163 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3808 (mpp) cc_final: 0.3336 (tmm) REVERT: A 318 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.8058 (p90) REVERT: B 190 ARG cc_start: 0.7866 (mtm180) cc_final: 0.7506 (mtm-85) REVERT: B 488 CYS cc_start: 0.0908 (OUTLIER) cc_final: 0.0151 (t) REVERT: C 110 LEU cc_start: 0.3277 (OUTLIER) cc_final: 0.3026 (mt) REVERT: C 241 LEU cc_start: 0.1608 (OUTLIER) cc_final: 0.1131 (tp) REVERT: C 377 PHE cc_start: 0.0666 (OUTLIER) cc_final: -0.0822 (m-80) REVERT: Y 142 MET cc_start: -0.0156 (tpp) cc_final: -0.0501 (ttp) REVERT: Z 142 MET cc_start: 0.3296 (OUTLIER) cc_final: 0.2181 (mtp) REVERT: Z 231 TRP cc_start: 0.0901 (OUTLIER) cc_final: 0.0433 (t-100) outliers start: 120 outliers final: 72 residues processed: 270 average time/residue: 0.1731 time to fit residues: 80.4079 Evaluate side-chains 227 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 148 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 186 ASP Chi-restraints excluded: chain X residue 189 LEU Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Z residue 142 MET Chi-restraints excluded: chain Z residue 231 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 334 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 306 optimal weight: 0.8980 chunk 126 optimal weight: 0.0470 chunk 254 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 284 optimal weight: 0.5980 chunk 314 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN A 556 ASN A 907 ASN B 66 HIS B 907 ASN C 321 GLN C 907 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.246028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.198780 restraints weight = 37057.913| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 2.59 r_work: 0.3900 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31794 Z= 0.124 Angle : 0.546 10.515 43362 Z= 0.267 Chirality : 0.044 0.343 5034 Planarity : 0.004 0.067 5540 Dihedral : 3.878 31.954 4148 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 3.42 % Allowed : 25.96 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.13), residues: 3842 helix: 1.40 (0.21), residues: 736 sheet: -0.28 (0.25), residues: 443 loop : -1.81 (0.11), residues: 2663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 190 TYR 0.019 0.001 TYR B1067 PHE 0.019 0.001 PHE C 192 TRP 0.008 0.001 TRP B 104 HIS 0.007 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (31714) covalent geometry : angle 0.52960 / 0.26 (43170) SS BOND : bond 0.00317 / 0.17 ( 45) SS BOND : angle 1.26815 / 0.83 ( 90) hydrogen bonds : bond 0.04975 / 3.28 ( 795) hydrogen bonds : angle 4.86006 / 3.33 ( 2223) Misc. bond : bond 0.00115 / 0.08 ( 1) link_BETA1-4 : bond 0.00447 / 0.27 ( 5) link_BETA1-4 : angle 1.35770 / 0.88 ( 15) link_NAG-ASN : bond 0.00600 / 0.43 ( 29) link_NAG-ASN : angle 2.70481 / 1.90 ( 87) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 156 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3799 (mpp) cc_final: 0.3188 (tmm) REVERT: A 318 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.8002 (p90) REVERT: A 338 PHE cc_start: 0.4874 (OUTLIER) cc_final: 0.4627 (t80) REVERT: A 1041 ASP cc_start: 0.6967 (t0) cc_final: 0.6747 (t0) REVERT: B 190 ARG cc_start: 0.7884 (mtm180) cc_final: 0.7522 (mtm-85) REVERT: B 488 CYS cc_start: 0.0970 (OUTLIER) cc_final: 0.0103 (t) REVERT: B 1029 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8156 (ttp) REVERT: C 377 PHE cc_start: 0.0651 (OUTLIER) cc_final: -0.0853 (m-80) REVERT: Y 12 GLN cc_start: 0.1929 (OUTLIER) cc_final: 0.1306 (tp40) REVERT: Y 142 MET cc_start: -0.0271 (tpp) cc_final: -0.0553 (ttp) REVERT: Z 142 MET cc_start: 0.3279 (OUTLIER) cc_final: 0.1966 (mtp) REVERT: Z 169 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.6123 (mm-40) REVERT: Z 231 TRP cc_start: 0.0841 (OUTLIER) cc_final: 0.0393 (t-100) outliers start: 118 outliers final: 72 residues processed: 259 average time/residue: 0.1824 time to fit residues: 80.1201 Evaluate side-chains 225 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 144 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 186 ASP Chi-restraints excluded: chain X residue 189 LEU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 GLN Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Z residue 142 MET Chi-restraints excluded: chain Z residue 169 GLN Chi-restraints excluded: chain Z residue 231 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 197 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 185 optimal weight: 0.0370 chunk 287 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 364 optimal weight: 20.0000 chunk 224 optimal weight: 10.0000 chunk 253 optimal weight: 9.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS B 907 ASN C 321 GLN Y 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.245143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.199675 restraints weight = 36981.244| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 2.42 r_work: 0.3946 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 31794 Z= 0.229 Angle : 0.629 9.727 43362 Z= 0.312 Chirality : 0.048 0.345 5034 Planarity : 0.005 0.062 5540 Dihedral : 4.242 36.580 4148 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.70 % Favored : 94.27 % Rotamer: Outliers : 4.40 % Allowed : 25.41 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.13), residues: 3842 helix: 1.12 (0.20), residues: 739 sheet: -0.48 (0.25), residues: 446 loop : -1.90 (0.11), residues: 2657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 237 TYR 0.032 0.001 TYR B 265 PHE 0.027 0.002 PHE B1121 TRP 0.011 0.001 TRP C 64 HIS 0.008 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.23 (31714) covalent geometry : angle 0.61216 / 0.31 (43170) SS BOND : bond 0.00646 / 0.29 ( 45) SS BOND : angle 1.77863 / 1.11 ( 90) hydrogen bonds : bond 0.06733 / 4.45 ( 795) hydrogen bonds : angle 5.01882 / 3.45 ( 2223) Misc. bond : bond 0.00215 / 0.14 ( 1) link_BETA1-4 : bond 0.00423 / 0.23 ( 5) link_BETA1-4 : angle 1.48579 / 0.93 ( 15) link_NAG-ASN : bond 0.00603 / 0.41 ( 29) link_NAG-ASN : angle 2.74011 / 1.90 ( 87) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 156 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.6596 (OUTLIER) cc_final: 0.5455 (t80) REVERT: A 153 MET cc_start: 0.4012 (mpp) cc_final: 0.3331 (tmm) REVERT: A 318 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.8135 (p90) REVERT: A 338 PHE cc_start: 0.4976 (OUTLIER) cc_final: 0.4738 (t80) REVERT: A 1041 ASP cc_start: 0.7170 (t0) cc_final: 0.6967 (t0) REVERT: B 190 ARG cc_start: 0.7868 (mtm180) cc_final: 0.7556 (mtm-85) REVERT: B 488 CYS cc_start: 0.1026 (OUTLIER) cc_final: 0.0132 (t) REVERT: C 318 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.8240 (p90) REVERT: C 377 PHE cc_start: 0.0827 (OUTLIER) cc_final: -0.0597 (m-80) REVERT: Y 12 GLN cc_start: 0.1896 (OUTLIER) cc_final: 0.1366 (tp40) REVERT: Y 103 ASN cc_start: 0.4010 (OUTLIER) cc_final: 0.3800 (m110) REVERT: Y 142 MET cc_start: -0.0176 (tpp) cc_final: -0.0402 (ttp) REVERT: Z 142 MET cc_start: 0.3367 (OUTLIER) cc_final: 0.2026 (mtp) REVERT: Z 155 ASP cc_start: 0.3698 (OUTLIER) cc_final: 0.1778 (m-30) REVERT: Z 169 GLN cc_start: 0.6779 (OUTLIER) cc_final: 0.6077 (mm-40) REVERT: Z 231 TRP cc_start: 0.0963 (OUTLIER) cc_final: 0.0497 (t-100) outliers start: 152 outliers final: 109 residues processed: 290 average time/residue: 0.1748 time to fit residues: 87.4198 Evaluate side-chains 264 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 143 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 186 ASP Chi-restraints excluded: chain X residue 189 LEU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 GLN Chi-restraints excluded: chain Y residue 103 ASN Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Z residue 66 VAL Chi-restraints excluded: chain Z residue 142 MET Chi-restraints excluded: chain Z residue 155 ASP Chi-restraints excluded: chain Z residue 169 GLN Chi-restraints excluded: chain Z residue 197 VAL Chi-restraints excluded: chain Z residue 231 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 106 optimal weight: 2.9990 chunk 40 optimal weight: 30.0000 chunk 378 optimal weight: 9.9990 chunk 338 optimal weight: 6.9990 chunk 275 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 265 optimal weight: 0.9980 chunk 295 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 351 optimal weight: 40.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN A 907 ASN B 907 ASN C 321 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.250241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.203261 restraints weight = 37025.307| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 2.50 r_work: 0.3982 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3850 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31794 Z= 0.115 Angle : 0.538 9.591 43362 Z= 0.265 Chirality : 0.044 0.319 5034 Planarity : 0.004 0.058 5540 Dihedral : 3.968 36.748 4148 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.11 % Favored : 95.86 % Rotamer: Outliers : 3.33 % Allowed : 26.19 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.13), residues: 3842 helix: 1.40 (0.21), residues: 733 sheet: -0.43 (0.24), residues: 471 loop : -1.77 (0.11), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.018 0.001 TYR B1067 PHE 0.020 0.001 PHE B 65 TRP 0.012 0.001 TRP B 64 HIS 0.021 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (31714) covalent geometry : angle 0.52277 / 0.26 (43170) SS BOND : bond 0.00281 / 0.18 ( 45) SS BOND : angle 1.31565 / 0.84 ( 90) hydrogen bonds : bond 0.04897 / 3.24 ( 795) hydrogen bonds : angle 4.74353 / 3.26 ( 2223) Misc. bond : bond 0.00088 / 0.06 ( 1) link_BETA1-4 : bond 0.00465 / 0.28 ( 5) link_BETA1-4 : angle 1.29771 / 0.85 ( 15) link_NAG-ASN : bond 0.00584 / 0.41 ( 29) link_NAG-ASN : angle 2.58222 / 1.81 ( 87) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 148 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4019 (mpp) cc_final: 0.3242 (tmm) REVERT: A 194 PHE cc_start: 0.7733 (m-10) cc_final: 0.7495 (m-10) REVERT: A 318 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8235 (p90) REVERT: A 338 PHE cc_start: 0.4938 (OUTLIER) cc_final: 0.4649 (t80) REVERT: A 1041 ASP cc_start: 0.7695 (t0) cc_final: 0.7464 (t0) REVERT: B 190 ARG cc_start: 0.8052 (mtm180) cc_final: 0.7714 (mtm-85) REVERT: B 488 CYS cc_start: 0.1143 (OUTLIER) cc_final: 0.0178 (t) REVERT: B 907 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8845 (t0) REVERT: C 153 MET cc_start: 0.4320 (mmt) cc_final: 0.0787 (ttm) REVERT: C 377 PHE cc_start: 0.0791 (OUTLIER) cc_final: -0.0638 (m-80) REVERT: C 740 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7719 (ttp) REVERT: C 856 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7987 (t0) REVERT: Y 12 GLN cc_start: 0.2164 (OUTLIER) cc_final: 0.1597 (tp40) REVERT: Z 142 MET cc_start: 0.3074 (OUTLIER) cc_final: 0.1841 (mtp) REVERT: Z 155 ASP cc_start: 0.3684 (OUTLIER) cc_final: 0.1796 (m-30) REVERT: Z 169 GLN cc_start: 0.6710 (OUTLIER) cc_final: 0.5876 (mm-40) REVERT: Z 231 TRP cc_start: 0.0891 (OUTLIER) cc_final: 0.0459 (t-100) outliers start: 115 outliers final: 77 residues processed: 247 average time/residue: 0.1733 time to fit residues: 73.9881 Evaluate side-chains 228 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 139 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 186 ASP Chi-restraints excluded: chain X residue 189 LEU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 GLN Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Z residue 66 VAL Chi-restraints excluded: chain Z residue 142 MET Chi-restraints excluded: chain Z residue 155 ASP Chi-restraints excluded: chain Z residue 169 GLN Chi-restraints excluded: chain Z residue 197 VAL Chi-restraints excluded: chain Z residue 231 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 360 optimal weight: 40.0000 chunk 267 optimal weight: 6.9990 chunk 306 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 335 optimal weight: 6.9990 chunk 44 optimal weight: 0.0060 chunk 98 optimal weight: 1.9990 chunk 329 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 112 optimal weight: 0.2980 overall best weight: 1.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 907 ASN B 907 ASN C 321 GLN Y 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.251466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.197889 restraints weight = 38243.063| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 2.74 r_work: 0.3862 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31794 Z= 0.132 Angle : 0.543 9.596 43362 Z= 0.267 Chirality : 0.045 0.316 5034 Planarity : 0.004 0.058 5540 Dihedral : 3.912 37.525 4148 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 3.50 % Allowed : 26.31 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.13), residues: 3842 helix: 1.40 (0.21), residues: 733 sheet: -0.39 (0.24), residues: 469 loop : -1.73 (0.11), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 237 TYR 0.018 0.001 TYR B1067 PHE 0.024 0.001 PHE C 192 TRP 0.008 0.001 TRP A 104 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (31714) covalent geometry : angle 0.52824 / 0.26 (43170) SS BOND : bond 0.00265 / 0.16 ( 45) SS BOND : angle 1.32821 / 0.85 ( 90) hydrogen bonds : bond 0.05093 / 3.36 ( 795) hydrogen bonds : angle 4.64778 / 3.20 ( 2223) Misc. bond : bond 0.00118 / 0.08 ( 1) link_BETA1-4 : bond 0.00342 / 0.19 ( 5) link_BETA1-4 : angle 1.30358 / 0.84 ( 15) link_NAG-ASN : bond 0.00562 / 0.40 ( 29) link_NAG-ASN : angle 2.55570 / 1.78 ( 87) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 142 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5594 (OUTLIER) cc_final: 0.4830 (t-90) REVERT: A 86 PHE cc_start: 0.6467 (OUTLIER) cc_final: 0.5355 (t80) REVERT: A 153 MET cc_start: 0.3926 (mpp) cc_final: 0.3158 (tmm) REVERT: A 318 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8138 (p90) REVERT: A 338 PHE cc_start: 0.4873 (OUTLIER) cc_final: 0.4520 (t80) REVERT: A 1041 ASP cc_start: 0.7376 (t0) cc_final: 0.7146 (t0) REVERT: B 190 ARG cc_start: 0.7940 (mtm180) cc_final: 0.7577 (mtm-85) REVERT: B 488 CYS cc_start: 0.1036 (OUTLIER) cc_final: 0.0043 (t) REVERT: B 615 VAL cc_start: 0.8755 (OUTLIER) cc_final: 0.8536 (p) REVERT: B 1041 ASP cc_start: 0.7508 (t0) cc_final: 0.7301 (t0) REVERT: C 153 MET cc_start: 0.4404 (mmt) cc_final: 0.0832 (ttm) REVERT: C 377 PHE cc_start: 0.0709 (OUTLIER) cc_final: -0.0696 (m-80) REVERT: C 740 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7587 (ttp) REVERT: Y 12 GLN cc_start: 0.2314 (OUTLIER) cc_final: 0.1698 (tp40) REVERT: Z 155 ASP cc_start: 0.3651 (OUTLIER) cc_final: 0.1769 (m-30) REVERT: Z 169 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.5787 (mm-40) REVERT: Z 231 TRP cc_start: 0.0862 (OUTLIER) cc_final: 0.0437 (t-100) outliers start: 121 outliers final: 93 residues processed: 248 average time/residue: 0.1714 time to fit residues: 72.8585 Evaluate side-chains 241 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 136 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 186 ASP Chi-restraints excluded: chain X residue 189 LEU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 GLN Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Z residue 66 VAL Chi-restraints excluded: chain Z residue 155 ASP Chi-restraints excluded: chain Z residue 169 GLN Chi-restraints excluded: chain Z residue 197 VAL Chi-restraints excluded: chain Z residue 231 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 0.2980 chunk 42 optimal weight: 7.9990 chunk 317 optimal weight: 40.0000 chunk 32 optimal weight: 0.3980 chunk 254 optimal weight: 0.6980 chunk 202 optimal weight: 0.9980 chunk 226 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 262 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 321 GLN C 856 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.247706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.200559 restraints weight = 37168.699| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 2.48 r_work: 0.3948 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31794 Z= 0.121 Angle : 0.533 9.592 43362 Z= 0.263 Chirality : 0.044 0.320 5034 Planarity : 0.004 0.065 5540 Dihedral : 3.852 38.037 4148 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 3.42 % Allowed : 26.43 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.13), residues: 3842 helix: 1.46 (0.21), residues: 728 sheet: -0.40 (0.24), residues: 476 loop : -1.68 (0.11), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.018 0.001 TYR B1067 PHE 0.027 0.001 PHE C 192 TRP 0.007 0.001 TRP C 64 HIS 0.009 0.001 HIS X 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (31714) covalent geometry : angle 0.51814 / 0.26 (43170) SS BOND : bond 0.00256 / 0.16 ( 45) SS BOND : angle 1.22899 / 0.79 ( 90) hydrogen bonds : bond 0.04794 / 3.16 ( 795) hydrogen bonds : angle 4.56620 / 3.15 ( 2223) Misc. bond : bond 0.00101 / 0.07 ( 1) link_BETA1-4 : bond 0.00396 / 0.23 ( 5) link_BETA1-4 : angle 1.27624 / 0.83 ( 15) link_NAG-ASN : bond 0.00570 / 0.40 ( 29) link_NAG-ASN : angle 2.51150 / 1.75 ( 87) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 144 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5503 (OUTLIER) cc_final: 0.4741 (t-90) REVERT: A 86 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.5297 (t80) REVERT: A 153 MET cc_start: 0.3942 (mpp) cc_final: 0.3189 (tmm) REVERT: A 194 PHE cc_start: 0.7625 (m-10) cc_final: 0.7286 (m-10) REVERT: A 318 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8101 (p90) REVERT: A 338 PHE cc_start: 0.4867 (OUTLIER) cc_final: 0.4549 (t80) REVERT: A 796 ASP cc_start: 0.7400 (p0) cc_final: 0.7138 (p0) REVERT: B 190 ARG cc_start: 0.7875 (mtm180) cc_final: 0.7537 (mtm-85) REVERT: B 488 CYS cc_start: 0.0979 (OUTLIER) cc_final: -0.0003 (t) REVERT: C 153 MET cc_start: 0.4628 (mmt) cc_final: 0.1058 (ttm) REVERT: C 377 PHE cc_start: 0.0848 (OUTLIER) cc_final: -0.0572 (m-80) REVERT: C 740 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7482 (ttp) REVERT: Y 12 GLN cc_start: 0.2269 (OUTLIER) cc_final: 0.1626 (tp40) REVERT: Z 29 LYS cc_start: 0.0764 (tttt) cc_final: -0.0902 (tptp) REVERT: Z 155 ASP cc_start: 0.3672 (OUTLIER) cc_final: 0.1758 (m-30) REVERT: Z 169 GLN cc_start: 0.6723 (OUTLIER) cc_final: 0.5766 (mm-40) REVERT: Z 231 TRP cc_start: 0.0943 (OUTLIER) cc_final: 0.0505 (t-100) outliers start: 118 outliers final: 97 residues processed: 245 average time/residue: 0.1624 time to fit residues: 68.0650 Evaluate side-chains 249 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 141 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 186 ASP Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 GLN Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Z residue 66 VAL Chi-restraints excluded: chain Z residue 155 ASP Chi-restraints excluded: chain Z residue 169 GLN Chi-restraints excluded: chain Z residue 197 VAL Chi-restraints excluded: chain Z residue 231 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 194 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 330 optimal weight: 10.0000 chunk 151 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 321 GLN C 544 ASN C 856 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.247116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.200115 restraints weight = 37125.328| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 2.53 r_work: 0.3969 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31794 Z= 0.134 Angle : 0.541 9.569 43362 Z= 0.267 Chirality : 0.045 0.322 5034 Planarity : 0.004 0.070 5540 Dihedral : 3.851 38.740 4148 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 3.59 % Allowed : 26.28 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.13), residues: 3842 helix: 1.45 (0.21), residues: 728 sheet: -0.39 (0.24), residues: 478 loop : -1.68 (0.11), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.018 0.001 TYR B1067 PHE 0.029 0.001 PHE C 192 TRP 0.008 0.001 TRP C 64 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.13 (31714) covalent geometry : angle 0.52656 / 0.26 (43170) SS BOND : bond 0.00269 / 0.17 ( 45) SS BOND : angle 1.26085 / 0.81 ( 90) hydrogen bonds : bond 0.04988 / 3.29 ( 795) hydrogen bonds : angle 4.55541 / 3.14 ( 2223) Misc. bond : bond 0.00118 / 0.08 ( 1) link_BETA1-4 : bond 0.00344 / 0.20 ( 5) link_BETA1-4 : angle 1.29856 / 0.83 ( 15) link_NAG-ASN : bond 0.00556 / 0.39 ( 29) link_NAG-ASN : angle 2.50125 / 1.74 ( 87) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 146 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5448 (OUTLIER) cc_final: 0.4659 (t-90) REVERT: A 86 PHE cc_start: 0.6495 (OUTLIER) cc_final: 0.5317 (t80) REVERT: A 153 MET cc_start: 0.3995 (mpp) cc_final: 0.3251 (tmm) REVERT: A 318 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.8091 (p90) REVERT: A 338 PHE cc_start: 0.4912 (OUTLIER) cc_final: 0.4607 (t80) REVERT: A 796 ASP cc_start: 0.7413 (p0) cc_final: 0.7151 (p0) REVERT: B 190 ARG cc_start: 0.7841 (mtm180) cc_final: 0.7522 (mtm-85) REVERT: B 488 CYS cc_start: 0.0968 (OUTLIER) cc_final: -0.0002 (t) REVERT: B 615 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8521 (p) REVERT: C 153 MET cc_start: 0.4637 (mmt) cc_final: 0.1194 (ttp) REVERT: C 377 PHE cc_start: 0.0898 (OUTLIER) cc_final: -0.0519 (m-80) REVERT: C 740 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7551 (ttp) REVERT: Y 12 GLN cc_start: 0.2368 (OUTLIER) cc_final: 0.1688 (tp40) REVERT: Z 29 LYS cc_start: 0.0718 (tttt) cc_final: -0.0974 (tptp) REVERT: Z 155 ASP cc_start: 0.3803 (OUTLIER) cc_final: 0.1675 (m-30) REVERT: Z 169 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.5734 (mm-40) REVERT: Z 231 TRP cc_start: 0.1029 (OUTLIER) cc_final: 0.0580 (t-100) outliers start: 124 outliers final: 104 residues processed: 252 average time/residue: 0.1734 time to fit residues: 75.1355 Evaluate side-chains 259 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 143 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 186 ASP Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 GLN Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Z residue 66 VAL Chi-restraints excluded: chain Z residue 155 ASP Chi-restraints excluded: chain Z residue 169 GLN Chi-restraints excluded: chain Z residue 197 VAL Chi-restraints excluded: chain Z residue 231 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 244 optimal weight: 0.0270 chunk 3 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 345 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 319 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.245563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.198156 restraints weight = 37257.185| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 2.59 r_work: 0.3886 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31794 Z= 0.117 Angle : 0.526 9.538 43362 Z= 0.260 Chirality : 0.044 0.321 5034 Planarity : 0.004 0.072 5540 Dihedral : 3.783 39.258 4148 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.71 % Rotamer: Outliers : 3.27 % Allowed : 26.60 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.13), residues: 3842 helix: 1.45 (0.21), residues: 734 sheet: -0.36 (0.24), residues: 480 loop : -1.66 (0.12), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.018 0.001 TYR B1067 PHE 0.031 0.001 PHE C 192 TRP 0.007 0.001 TRP C 64 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (31714) covalent geometry : angle 0.51204 / 0.26 (43170) SS BOND : bond 0.00254 / 0.15 ( 45) SS BOND : angle 1.18118 / 0.76 ( 90) hydrogen bonds : bond 0.04668 / 3.08 ( 795) hydrogen bonds : angle 4.48872 / 3.10 ( 2223) Misc. bond : bond 0.00098 / 0.07 ( 1) link_BETA1-4 : bond 0.00420 / 0.25 ( 5) link_BETA1-4 : angle 1.26972 / 0.82 ( 15) link_NAG-ASN : bond 0.00557 / 0.39 ( 29) link_NAG-ASN : angle 2.47963 / 1.73 ( 87) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 146 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5535 (OUTLIER) cc_final: 0.4762 (t-90) REVERT: A 86 PHE cc_start: 0.6375 (OUTLIER) cc_final: 0.5268 (t80) REVERT: A 153 MET cc_start: 0.3896 (mpp) cc_final: 0.3118 (tmm) REVERT: A 318 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.8086 (p90) REVERT: A 338 PHE cc_start: 0.4867 (OUTLIER) cc_final: 0.4494 (t80) REVERT: A 796 ASP cc_start: 0.7306 (p0) cc_final: 0.7050 (p0) REVERT: A 1041 ASP cc_start: 0.6931 (t0) cc_final: 0.6686 (t0) REVERT: B 190 ARG cc_start: 0.7879 (mtm180) cc_final: 0.7541 (mtm-85) REVERT: B 488 CYS cc_start: 0.0974 (OUTLIER) cc_final: -0.0017 (t) REVERT: B 615 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8558 (p) REVERT: C 153 MET cc_start: 0.4816 (mmt) cc_final: 0.1169 (ttp) REVERT: C 377 PHE cc_start: 0.0856 (OUTLIER) cc_final: -0.0586 (m-80) REVERT: C 740 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7554 (ttp) REVERT: X 142 MET cc_start: 0.2734 (tpp) cc_final: 0.2449 (tpt) REVERT: Y 12 GLN cc_start: 0.2162 (OUTLIER) cc_final: 0.1682 (tp40) REVERT: Z 155 ASP cc_start: 0.3838 (OUTLIER) cc_final: 0.1711 (m-30) REVERT: Z 231 TRP cc_start: 0.0935 (OUTLIER) cc_final: 0.0506 (t-100) outliers start: 113 outliers final: 99 residues processed: 244 average time/residue: 0.1780 time to fit residues: 74.4369 Evaluate side-chains 250 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 140 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 186 ASP Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 GLN Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Z residue 66 VAL Chi-restraints excluded: chain Z residue 155 ASP Chi-restraints excluded: chain Z residue 197 VAL Chi-restraints excluded: chain Z residue 231 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 62 optimal weight: 0.6980 chunk 349 optimal weight: 30.0000 chunk 358 optimal weight: 0.4980 chunk 272 optimal weight: 0.1980 chunk 284 optimal weight: 0.5980 chunk 250 optimal weight: 4.9990 chunk 273 optimal weight: 0.8980 chunk 369 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 321 GLN C 901 GLN Y 120 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.251928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.198675 restraints weight = 38453.816| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 2.80 r_work: 0.3622 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31794 Z= 0.097 Angle : 0.509 9.516 43362 Z= 0.251 Chirality : 0.044 0.321 5034 Planarity : 0.004 0.090 5540 Dihedral : 3.659 39.330 4148 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 2.95 % Allowed : 26.80 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.13), residues: 3842 helix: 1.50 (0.21), residues: 739 sheet: -0.28 (0.24), residues: 479 loop : -1.61 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 237 TYR 0.017 0.001 TYR B1067 PHE 0.030 0.001 PHE C 192 TRP 0.008 0.001 TRP B 104 HIS 0.005 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (31714) covalent geometry : angle 0.49557 / 0.25 (43170) SS BOND : bond 0.00230 / 0.14 ( 45) SS BOND : angle 1.05902 / 0.68 ( 90) hydrogen bonds : bond 0.04110 / 2.71 ( 795) hydrogen bonds : angle 4.38501 / 3.03 ( 2223) Misc. bond : bond 0.00067 / 0.04 ( 1) link_BETA1-4 : bond 0.00389 / 0.23 ( 5) link_BETA1-4 : angle 1.24064 / 0.80 ( 15) link_NAG-ASN : bond 0.00558 / 0.39 ( 29) link_NAG-ASN : angle 2.43767 / 1.70 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7496.59 seconds wall clock time: 129 minutes 16.24 seconds (7756.24 seconds total)