Starting phenix.real_space_refine on Thu Jun 26 22:18:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h6f_34501/06_2025/8h6f_34501.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h6f_34501/06_2025/8h6f_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_34501/06_2025/8h6f_34501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h6f_34501/06_2025/8h6f_34501.map" model { file = "/net/cci-nas-00/data/ceres_data/8h6f_34501/06_2025/8h6f_34501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h6f_34501/06_2025/8h6f_34501.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.075 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): 1.41s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 21 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 dihedrals: 24 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 18.81, per 1000 atoms: 0.61 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: 7.39 Conformation dependent library (CDL) restraints added in 4.3 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: 3.76 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: 11.18 Time building geometry restraints manager: 8.85 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: 16648 18.05 - 36.11: 2199 36.11 - 54.16: 511 54.16 - 72.22: 101 72.22 - 90.27: 37 Dihedral angle restraints: 19496 sinusoidal: 8137 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 19493 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 1149 or resid 1301 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 1149 or resid 1301 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 1149 or resid 1301 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: 5.200 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: 0.040 Extract box with map and model: 1.350 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 67.400 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 : 16.751 89.687 12021 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.87 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (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 TRP 0.021 0.001 TRP Y 218 HIS 0.007 0.001 HIS C 655 PHE 0.029 0.001 PHE C 192 TYR 0.016 0.001 TYR C 660 ARG 0.004 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00558 ( 29) link_NAG-ASN : angle 3.00103 ( 87) link_BETA1-4 : bond 0.00302 ( 5) link_BETA1-4 : angle 0.68064 ( 15) hydrogen bonds : bond 0.21254 ( 795) hydrogen bonds : angle 7.47181 ( 2223) SS BOND : bond 0.00205 ( 45) SS BOND : angle 1.51735 ( 90) covalent geometry : bond 0.00332 (31714) covalent geometry : angle 0.61715 (43170) Misc. bond : bond 0.60715 ( 1) *********************** 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 : 3.331 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: 0.3858 time to fit residues: 111.2003 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 : 3.159 ------------------------------------------------------------------------------- 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 326 optimal weight: 8.9990 chunk 293 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 197 optimal weight: 0.1980 chunk 156 optimal weight: 3.9990 chunk 303 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 chunk 351 optimal weight: 40.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4769 r_free = 0.4769 target = 0.250571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.204694 restraints weight = 36885.484| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 2.44 r_work: 0.4024 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.0671 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= 0.136 Angle : 0.601 11.649 43362 Z= 0.289 Chirality : 0.046 0.348 5034 Planarity : 0.004 0.063 5540 Dihedral : 5.852 59.330 4867 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.69 % Favored : 95.26 % Rotamer: Outliers : 2.60 % Allowed : 26.31 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 3842 helix: 1.38 (0.21), residues: 730 sheet: -0.25 (0.25), residues: 436 loop : -1.90 (0.11), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 104 HIS 0.007 0.001 HIS B 66 PHE 0.018 0.001 PHE B1121 TYR 0.021 0.001 TYR B1067 ARG 0.003 0.000 ARG B 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00795 ( 29) link_NAG-ASN : angle 3.21900 ( 87) link_BETA1-4 : bond 0.00736 ( 5) link_BETA1-4 : angle 1.44190 ( 15) hydrogen bonds : bond 0.05432 ( 795) hydrogen bonds : angle 5.51576 ( 2223) SS BOND : bond 0.00288 ( 45) SS BOND : angle 1.40108 ( 90) covalent geometry : bond 0.00320 (31714) covalent geometry : angle 0.58027 (43170) Misc. bond : bond 0.00200 ( 1) *********************** 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 251 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 161 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 190 ARG cc_start: 0.7881 (mtm180) cc_final: 0.7511 (mtm-85) REVERT: B 488 CYS cc_start: 0.0853 (OUTLIER) cc_final: 0.0068 (t) REVERT: B 983 ARG cc_start: 0.7392 (ttp-170) cc_final: 0.7128 (ttm170) REVERT: C 241 LEU cc_start: 0.2279 (OUTLIER) cc_final: 0.1937 (tp) REVERT: C 377 PHE cc_start: 0.0711 (OUTLIER) cc_final: -0.0843 (m-10) REVERT: C 995 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7841 (ptm160) REVERT: Z 142 MET cc_start: 0.3307 (OUTLIER) cc_final: 0.2480 (mtp) REVERT: Z 155 ASP cc_start: 0.3536 (OUTLIER) cc_final: 0.2010 (m-30) outliers start: 90 outliers final: 41 residues processed: 240 average time/residue: 0.4127 time to fit residues: 169.1950 Evaluate side-chains 194 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 3.248 ------------------------------------------------------------------------------- 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 66 HIS 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 649 CYS Chi-restraints excluded: chain B residue 723 THR 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 1040 VAL Chi-restraints excluded: chain B residue 1072 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 158 ARG Chi-restraints excluded: chain C residue 241 LEU 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 618 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 761 THR 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 142 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 325 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 334 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN 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 = 0.4738 r_free = 0.4738 target = 0.247312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.200392 restraints weight = 36980.800| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 2.55 r_work: 0.3956 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31794 Z= 0.165 Angle : 0.580 10.275 43362 Z= 0.285 Chirality : 0.046 0.372 5034 Planarity : 0.004 0.063 5540 Dihedral : 5.645 58.120 4862 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.13 % Favored : 94.85 % Rotamer: Outliers : 3.42 % Allowed : 26.19 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.13), residues: 3842 helix: 1.33 (0.21), residues: 729 sheet: -0.38 (0.25), residues: 435 loop : -1.89 (0.11), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 218 HIS 0.021 0.001 HIS B 66 PHE 0.020 0.001 PHE B1121 TYR 0.023 0.001 TYR B 265 ARG 0.003 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 29) link_NAG-ASN : angle 2.86262 ( 87) link_BETA1-4 : bond 0.00487 ( 5) link_BETA1-4 : angle 1.40622 ( 15) hydrogen bonds : bond 0.05895 ( 795) hydrogen bonds : angle 5.13653 ( 2223) SS BOND : bond 0.00307 ( 45) SS BOND : angle 1.43912 ( 90) covalent geometry : bond 0.00406 (31714) covalent geometry : angle 0.56222 (43170) Misc. bond : bond 0.00104 ( 1) *********************** 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 278 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 160 time to evaluate : 3.586 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: 0.3772 (mpp) cc_final: 0.3362 (tmm) REVERT: A 318 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.8033 (p90) REVERT: A 338 PHE cc_start: 0.4873 (OUTLIER) cc_final: 0.4620 (t80) REVERT: B 190 ARG cc_start: 0.7876 (mtm180) cc_final: 0.7515 (mtm-85) REVERT: B 488 CYS cc_start: 0.0885 (OUTLIER) cc_final: 0.0156 (t) REVERT: B 1029 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8060 (ttp) REVERT: B 1041 ASP cc_start: 0.7644 (t0) cc_final: 0.7437 (t0) REVERT: C 241 LEU cc_start: 0.2048 (OUTLIER) cc_final: 0.1634 (tp) REVERT: C 377 PHE cc_start: 0.0654 (OUTLIER) cc_final: -0.0826 (m-80) REVERT: Y 142 MET cc_start: 0.0044 (tpp) cc_final: -0.0413 (ttp) REVERT: Z 142 MET cc_start: 0.3348 (OUTLIER) cc_final: 0.2236 (mtp) REVERT: Z 231 TRP cc_start: 0.0887 (OUTLIER) cc_final: 0.0407 (t-100) outliers start: 118 outliers final: 71 residues processed: 265 average time/residue: 0.3754 time to fit residues: 170.4832 Evaluate side-chains 229 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 150 time to evaluate : 3.043 ------------------------------------------------------------------------------- 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 205 SER 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 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 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 785 VAL Chi-restraints excluded: chain B residue 878 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 1029 MET 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 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 307 THR 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 53 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 355 optimal weight: 4.9990 chunk 69 optimal weight: 0.4980 chunk 344 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 131 optimal weight: 5.9990 chunk 320 optimal weight: 0.0870 chunk 112 optimal weight: 4.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN B 907 ASN C 321 GLN C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.247864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.199210 restraints weight = 37400.684| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 2.66 r_work: 0.3887 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 31794 Z= 0.099 Angle : 0.522 10.101 43362 Z= 0.255 Chirality : 0.044 0.346 5034 Planarity : 0.004 0.070 5540 Dihedral : 5.300 57.791 4862 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 2.72 % Allowed : 26.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 3842 helix: 1.48 (0.21), residues: 737 sheet: -0.19 (0.25), residues: 441 loop : -1.79 (0.11), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.005 0.000 HIS C 655 PHE 0.021 0.001 PHE C 192 TYR 0.018 0.001 TYR B1067 ARG 0.010 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 29) link_NAG-ASN : angle 2.69223 ( 87) link_BETA1-4 : bond 0.00483 ( 5) link_BETA1-4 : angle 1.36704 ( 15) hydrogen bonds : bond 0.04358 ( 795) hydrogen bonds : angle 4.81180 ( 2223) SS BOND : bond 0.00223 ( 45) SS BOND : angle 1.09952 ( 90) covalent geometry : bond 0.00227 (31714) covalent geometry : angle 0.50594 (43170) Misc. bond : bond 0.00090 ( 1) *********************** 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 255 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 161 time to evaluate : 3.107 Fit side-chains 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: 0.3134 (tmm) REVERT: A 338 PHE cc_start: 0.4501 (OUTLIER) cc_final: 0.4191 (t80) REVERT: B 190 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7610 (mtm-85) REVERT: B 488 CYS cc_start: 0.0942 (OUTLIER) cc_final: 0.0056 (t) REVERT: B 1041 ASP cc_start: 0.7503 (t0) cc_final: 0.7285 (t0) REVERT: C 241 LEU cc_start: 0.2058 (OUTLIER) cc_final: 0.1713 (tp) REVERT: C 377 PHE cc_start: 0.0530 (OUTLIER) cc_final: -0.0952 (m-80) REVERT: Y 12 GLN cc_start: 0.1824 (OUTLIER) cc_final: 0.1235 (tp40) REVERT: Y 142 MET cc_start: -0.0290 (tpp) cc_final: -0.0606 (ttp) REVERT: Z 142 MET cc_start: 0.3248 (OUTLIER) cc_final: 0.1967 (mtp) REVERT: Z 231 TRP cc_start: 0.0774 (OUTLIER) cc_final: 0.0351 (t-100) outliers start: 94 outliers final: 54 residues processed: 242 average time/residue: 0.3752 time to fit residues: 155.8456 Evaluate side-chains 207 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 146 time to evaluate : 2.998 ------------------------------------------------------------------------------- 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 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 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 875 SER 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 1120 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 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 488 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 662 CYS 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 984 LEU Chi-restraints excluded: chain B residue 1051 SER 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 241 LEU 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 599 THR Chi-restraints excluded: chain C residue 780 GLU 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 186 ASP Chi-restraints excluded: chain X residue 189 LEU 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 231 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 138 optimal weight: 1.9990 chunk 303 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 142 optimal weight: 30.0000 chunk 199 optimal weight: 0.8980 chunk 355 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4761 r_free = 0.4761 target = 0.253587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.200047 restraints weight = 38171.577| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 2.67 r_work: 0.3885 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31794 Z= 0.112 Angle : 0.522 9.632 43362 Z= 0.257 Chirality : 0.044 0.342 5034 Planarity : 0.004 0.060 5540 Dihedral : 5.228 57.023 4862 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.48 % Favored : 95.50 % Rotamer: Outliers : 3.18 % Allowed : 26.05 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3842 helix: 1.53 (0.21), residues: 737 sheet: -0.29 (0.24), residues: 474 loop : -1.72 (0.11), residues: 2631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 104 HIS 0.004 0.001 HIS C 655 PHE 0.017 0.001 PHE C 92 TYR 0.018 0.001 TYR B1067 ARG 0.007 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 29) link_NAG-ASN : angle 2.61131 ( 87) link_BETA1-4 : bond 0.00437 ( 5) link_BETA1-4 : angle 1.44850 ( 15) hydrogen bonds : bond 0.04571 ( 795) hydrogen bonds : angle 4.67865 ( 2223) SS BOND : bond 0.00244 ( 45) SS BOND : angle 1.18211 ( 90) covalent geometry : bond 0.00267 (31714) covalent geometry : angle 0.50608 (43170) Misc. bond : bond 0.00112 ( 1) *********************** 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 269 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 159 time to evaluate : 3.124 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: 0.3791 (mpp) cc_final: 0.3105 (tmm) REVERT: A 298 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: A 338 PHE cc_start: 0.4456 (OUTLIER) cc_final: 0.4149 (t80) REVERT: B 488 CYS cc_start: 0.0979 (OUTLIER) cc_final: 0.0084 (t) REVERT: C 377 PHE cc_start: 0.0588 (OUTLIER) cc_final: -0.0871 (m-80) REVERT: Y 12 GLN cc_start: 0.1813 (OUTLIER) cc_final: 0.1171 (tp40) REVERT: Y 142 MET cc_start: -0.0286 (tpp) cc_final: -0.0507 (ttp) REVERT: Z 142 MET cc_start: 0.3224 (OUTLIER) cc_final: 0.1976 (mtp) REVERT: Z 155 ASP cc_start: 0.3536 (OUTLIER) cc_final: 0.1846 (m-30) REVERT: Z 231 TRP cc_start: 0.0790 (OUTLIER) cc_final: 0.0348 (t-100) outliers start: 110 outliers final: 77 residues processed: 255 average time/residue: 0.3657 time to fit residues: 160.4559 Evaluate side-chains 232 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 147 time to evaluate : 3.112 ------------------------------------------------------------------------------- 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 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 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 875 SER 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 1120 THR Chi-restraints excluded: chain B residue 66 HIS 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 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 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 785 VAL 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 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 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 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 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 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 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 155 ASP 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 340 optimal weight: 0.0020 chunk 262 optimal weight: 3.9990 chunk 365 optimal weight: 30.0000 chunk 257 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 281 optimal weight: 1.9990 chunk 333 optimal weight: 20.0000 chunk 264 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN B 907 ASN B1101 HIS C 321 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.248694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.202070 restraints weight = 37138.974| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 2.49 r_work: 0.3989 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31794 Z= 0.115 Angle : 0.522 9.593 43362 Z= 0.257 Chirality : 0.044 0.340 5034 Planarity : 0.004 0.059 5540 Dihedral : 5.255 57.513 4862 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 3.59 % Allowed : 25.33 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 3842 helix: 1.53 (0.21), residues: 738 sheet: -0.27 (0.24), residues: 473 loop : -1.70 (0.11), residues: 2631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 104 HIS 0.004 0.001 HIS C 655 PHE 0.023 0.001 PHE C 192 TYR 0.018 0.001 TYR B1067 ARG 0.006 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 29) link_NAG-ASN : angle 2.60161 ( 87) link_BETA1-4 : bond 0.00432 ( 5) link_BETA1-4 : angle 1.45257 ( 15) hydrogen bonds : bond 0.04609 ( 795) hydrogen bonds : angle 4.61282 ( 2223) SS BOND : bond 0.00274 ( 45) SS BOND : angle 1.22475 ( 90) covalent geometry : bond 0.00273 (31714) covalent geometry : angle 0.50583 (43170) Misc. bond : bond 0.00111 ( 1) *********************** 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 281 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 157 time to evaluate : 3.382 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: 0.6568 (OUTLIER) cc_final: 0.5805 (t80) REVERT: A 153 MET cc_start: 0.3875 (mpp) cc_final: 0.3231 (tmm) REVERT: A 298 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: A 318 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.8022 (p90) REVERT: A 338 PHE cc_start: 0.4581 (OUTLIER) cc_final: 0.4229 (t80) REVERT: A 1041 ASP cc_start: 0.7187 (t0) cc_final: 0.6975 (t0) REVERT: B 190 ARG cc_start: 0.7929 (mtm180) cc_final: 0.7584 (mtm-85) REVERT: B 488 CYS cc_start: 0.1128 (OUTLIER) cc_final: 0.0166 (t) REVERT: C 153 MET cc_start: 0.3330 (mmp) cc_final: 0.0641 (ttm) REVERT: C 377 PHE cc_start: 0.0761 (OUTLIER) cc_final: -0.0725 (m-80) REVERT: Y 12 GLN cc_start: 0.1920 (OUTLIER) cc_final: 0.1350 (tp40) REVERT: Z 142 MET cc_start: 0.3180 (OUTLIER) cc_final: 0.1939 (mtp) REVERT: Z 155 ASP cc_start: 0.3653 (OUTLIER) cc_final: 0.1901 (m-30) REVERT: Z 231 TRP cc_start: 0.0919 (OUTLIER) cc_final: 0.0484 (t-100) outliers start: 124 outliers final: 91 residues processed: 265 average time/residue: 0.3804 time to fit residues: 174.0037 Evaluate side-chains 248 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 147 time to evaluate : 3.301 ------------------------------------------------------------------------------- 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 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 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 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 1092 GLU 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 66 HIS 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 235 ILE Chi-restraints excluded: chain B residue 277 LEU 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 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 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 911 VAL 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 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 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 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 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 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 259 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 324 optimal weight: 30.0000 chunk 193 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 chunk 377 optimal weight: 8.9990 chunk 308 optimal weight: 1.9990 chunk 357 optimal weight: 0.0970 chunk 331 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN C 321 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.247952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.201814 restraints weight = 37145.512| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 2.48 r_work: 0.3942 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31794 Z= 0.140 Angle : 0.538 9.619 43362 Z= 0.266 Chirality : 0.045 0.342 5034 Planarity : 0.004 0.059 5540 Dihedral : 5.326 58.370 4862 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 3.47 % Allowed : 25.35 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3842 helix: 1.46 (0.21), residues: 739 sheet: -0.31 (0.24), residues: 473 loop : -1.69 (0.11), residues: 2630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.004 0.001 HIS C 655 PHE 0.023 0.001 PHE B 906 TYR 0.019 0.001 TYR B 265 ARG 0.006 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 29) link_NAG-ASN : angle 2.59141 ( 87) link_BETA1-4 : bond 0.00482 ( 5) link_BETA1-4 : angle 1.55891 ( 15) hydrogen bonds : bond 0.05157 ( 795) hydrogen bonds : angle 4.64221 ( 2223) SS BOND : bond 0.00297 ( 45) SS BOND : angle 1.39183 ( 90) covalent geometry : bond 0.00342 (31714) covalent geometry : angle 0.52153 (43170) Misc. bond : bond 0.00138 ( 1) *********************** 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 266 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 146 time to evaluate : 3.307 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: 0.6466 (OUTLIER) cc_final: 0.5562 (t80) REVERT: A 153 MET cc_start: 0.3850 (mpp) cc_final: 0.3144 (tmm) REVERT: A 298 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: A 318 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8059 (p90) REVERT: A 338 PHE cc_start: 0.4742 (OUTLIER) cc_final: 0.4359 (t80) REVERT: A 1041 ASP cc_start: 0.6944 (t0) cc_final: 0.6739 (t0) REVERT: B 190 ARG cc_start: 0.7906 (mtm180) cc_final: 0.7480 (mtm-85) REVERT: B 488 CYS cc_start: 0.0985 (OUTLIER) cc_final: -0.0007 (t) REVERT: C 153 MET cc_start: 0.3947 (mmp) cc_final: 0.0675 (ttm) REVERT: C 377 PHE cc_start: 0.0735 (OUTLIER) cc_final: -0.0747 (m-80) REVERT: Y 12 GLN cc_start: 0.2116 (OUTLIER) cc_final: 0.1544 (tp40) REVERT: Z 155 ASP cc_start: 0.3650 (OUTLIER) cc_final: 0.1832 (m-30) REVERT: Z 231 TRP cc_start: 0.0901 (OUTLIER) cc_final: 0.0464 (t-100) outliers start: 120 outliers final: 92 residues processed: 250 average time/residue: 0.3700 time to fit residues: 158.9580 Evaluate side-chains 243 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 142 time to evaluate : 3.087 ------------------------------------------------------------------------------- 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 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 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 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 1092 GLU 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 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU 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 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 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL 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 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 1076 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 90 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 261 optimal weight: 9.9990 chunk 262 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 367 optimal weight: 3.9990 chunk 345 optimal weight: 8.9990 chunk 363 optimal weight: 0.0030 chunk 357 optimal weight: 10.0000 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 321 GLN C 856 ASN C 901 GLN Z 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.245285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.199243 restraints weight = 37213.660| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 2.52 r_work: 0.3935 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 31794 Z= 0.184 Angle : 0.585 9.768 43362 Z= 0.291 Chirality : 0.046 0.324 5034 Planarity : 0.004 0.060 5540 Dihedral : 5.655 59.812 4862 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.92 % Favored : 95.05 % Rotamer: Outliers : 3.33 % Allowed : 25.67 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.13), residues: 3842 helix: 1.26 (0.20), residues: 739 sheet: -0.51 (0.24), residues: 462 loop : -1.73 (0.11), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.005 0.001 HIS C1064 PHE 0.024 0.002 PHE A1121 TYR 0.027 0.001 TYR B 265 ARG 0.006 0.000 ARG C1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 29) link_NAG-ASN : angle 2.67072 ( 87) link_BETA1-4 : bond 0.00379 ( 5) link_BETA1-4 : angle 1.60874 ( 15) hydrogen bonds : bond 0.06112 ( 795) hydrogen bonds : angle 4.77850 ( 2223) SS BOND : bond 0.00343 ( 45) SS BOND : angle 1.50826 ( 90) covalent geometry : bond 0.00459 (31714) covalent geometry : angle 0.56897 (43170) Misc. bond : bond 0.00179 ( 1) *********************** 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 256 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 141 time to evaluate : 3.335 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: 0.6525 (OUTLIER) cc_final: 0.5283 (t80) REVERT: A 153 MET cc_start: 0.4024 (mpp) cc_final: 0.3230 (tmm) REVERT: A 298 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: A 318 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.8126 (p90) REVERT: A 338 PHE cc_start: 0.4956 (OUTLIER) cc_final: 0.4625 (t80) REVERT: B 488 CYS cc_start: 0.0949 (OUTLIER) cc_final: -0.0029 (t) REVERT: C 153 MET cc_start: 0.4331 (mmp) cc_final: 0.0929 (ttm) REVERT: C 377 PHE cc_start: 0.0870 (OUTLIER) cc_final: -0.0565 (m-80) REVERT: Z 155 ASP cc_start: 0.3856 (OUTLIER) cc_final: 0.1653 (m-30) REVERT: Z 231 TRP cc_start: 0.1026 (OUTLIER) cc_final: 0.0570 (t-100) outliers start: 115 outliers final: 91 residues processed: 244 average time/residue: 0.3743 time to fit residues: 156.5657 Evaluate side-chains 236 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 137 time to evaluate : 3.541 ------------------------------------------------------------------------------- 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 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 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 1092 GLU 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 A residue 1133 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP 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 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 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 725 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU 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 937 SER Chi-restraints excluded: chain B residue 976 VAL 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 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 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 1076 THR 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 139 LEU Chi-restraints excluded: chain Z residue 66 VAL Chi-restraints excluded: chain Z residue 155 ASP 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 69 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 326 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 154 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 0.0060 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 321 GLN C 544 ASN ** Y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.247321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.200881 restraints weight = 36986.627| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 2.50 r_work: 0.3967 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31794 Z= 0.127 Angle : 0.535 9.626 43362 Z= 0.265 Chirality : 0.044 0.327 5034 Planarity : 0.004 0.058 5540 Dihedral : 5.491 59.734 4862 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.24 % Favored : 95.73 % Rotamer: Outliers : 3.01 % Allowed : 26.16 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.13), residues: 3842 helix: 1.38 (0.21), residues: 739 sheet: -0.42 (0.23), residues: 487 loop : -1.67 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.004 0.001 HIS C 655 PHE 0.016 0.001 PHE A1121 TYR 0.018 0.001 TYR B1067 ARG 0.007 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 29) link_NAG-ASN : angle 2.67540 ( 87) link_BETA1-4 : bond 0.00385 ( 5) link_BETA1-4 : angle 1.52928 ( 15) hydrogen bonds : bond 0.04935 ( 795) hydrogen bonds : angle 4.60190 ( 2223) SS BOND : bond 0.00264 ( 45) SS BOND : angle 1.28135 ( 90) covalent geometry : bond 0.00308 (31714) covalent geometry : angle 0.51832 (43170) Misc. bond : bond 0.00113 ( 1) *********************** 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 248 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 144 time to evaluate : 3.274 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: 0.4043 (mpp) cc_final: 0.3271 (tmm) REVERT: A 298 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: A 318 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.8100 (p90) REVERT: A 338 PHE cc_start: 0.4894 (OUTLIER) cc_final: 0.4515 (t80) REVERT: B 488 CYS cc_start: 0.0939 (OUTLIER) cc_final: -0.0016 (t) REVERT: C 153 MET cc_start: 0.4323 (mmp) cc_final: 0.1016 (ttm) REVERT: C 377 PHE cc_start: 0.0888 (OUTLIER) cc_final: -0.0589 (m-80) REVERT: C 740 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7606 (ttp) REVERT: Z 155 ASP cc_start: 0.3875 (OUTLIER) cc_final: 0.1748 (m-30) REVERT: Z 231 TRP cc_start: 0.1027 (OUTLIER) cc_final: 0.0585 (t-100) outliers start: 104 outliers final: 87 residues processed: 234 average time/residue: 0.3832 time to fit residues: 153.3580 Evaluate side-chains 231 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 136 time to evaluate : 3.298 ------------------------------------------------------------------------------- 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 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 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 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 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 1092 GLU 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 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 235 ILE 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 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 725 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL 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 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 377 PHE 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 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 866 THR 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 139 LEU Chi-restraints excluded: chain Z residue 66 VAL Chi-restraints excluded: chain Z residue 155 ASP 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 322 optimal weight: 9.9990 chunk 368 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 152 optimal weight: 0.0570 chunk 79 optimal weight: 1.9990 chunk 11 optimal weight: 0.0170 chunk 296 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 321 GLN C 901 GLN ** Y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 120 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.250578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.203083 restraints weight = 37167.992| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.55 r_work: 0.3932 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31794 Z= 0.101 Angle : 0.511 9.552 43362 Z= 0.253 Chirality : 0.044 0.329 5034 Planarity : 0.004 0.056 5540 Dihedral : 5.284 57.059 4862 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.01 % Favored : 95.97 % Rotamer: Outliers : 2.58 % Allowed : 26.63 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 3842 helix: 1.39 (0.21), residues: 749 sheet: -0.32 (0.24), residues: 486 loop : -1.59 (0.12), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.004 0.001 HIS C 655 PHE 0.017 0.001 PHE C 92 TYR 0.018 0.001 TYR B1067 ARG 0.007 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 29) link_NAG-ASN : angle 2.59473 ( 87) link_BETA1-4 : bond 0.00409 ( 5) link_BETA1-4 : angle 1.49360 ( 15) hydrogen bonds : bond 0.04200 ( 795) hydrogen bonds : angle 4.43042 ( 2223) SS BOND : bond 0.00229 ( 45) SS BOND : angle 1.07521 ( 90) covalent geometry : bond 0.00237 (31714) covalent geometry : angle 0.49573 (43170) Misc. bond : bond 0.00081 ( 1) ********************** 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 238 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 149 time to evaluate : 3.400 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: 0.3934 (mpp) cc_final: 0.3160 (tmm) REVERT: A 298 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: A 318 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.8086 (p90) REVERT: A 338 PHE cc_start: 0.4861 (OUTLIER) cc_final: 0.4490 (t80) REVERT: B 190 ARG cc_start: 0.7845 (mtp-110) cc_final: 0.7450 (mtm-85) REVERT: B 488 CYS cc_start: 0.0968 (OUTLIER) cc_final: -0.0049 (t) REVERT: C 153 MET cc_start: 0.4296 (mmp) cc_final: 0.1135 (ttt) REVERT: C 377 PHE cc_start: 0.0739 (OUTLIER) cc_final: -0.0658 (m-80) REVERT: X 71 LEU cc_start: 0.0934 (OUTLIER) cc_final: 0.0531 (mt) REVERT: Z 29 LYS cc_start: 0.0582 (tttt) cc_final: -0.0987 (tptp) REVERT: Z 231 TRP cc_start: 0.0966 (OUTLIER) cc_final: 0.0541 (t-100) outliers start: 89 outliers final: 78 residues processed: 226 average time/residue: 0.3929 time to fit residues: 151.9538 Evaluate side-chains 229 residues out of total 3455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 144 time to evaluate : 3.233 ------------------------------------------------------------------------------- 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 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 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 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 875 SER 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 1092 GLU 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 65 PHE Chi-restraints excluded: chain B residue 66 HIS 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 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 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 878 LEU 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 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1051 SER 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 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 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 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 907 ASN 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 44 ILE Chi-restraints excluded: chain X residue 71 LEU 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 139 LEU Chi-restraints excluded: chain Z residue 66 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 273 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 310 optimal weight: 0.6980 chunk 262 optimal weight: 6.9990 chunk 245 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 297 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 321 GLN ** X 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 120 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 = 0.250214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.203982 restraints weight = 37121.904| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 2.47 r_work: 0.3966 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 31794 Z= 0.150 Angle : 0.637 59.197 43362 Z= 0.350 Chirality : 0.045 0.406 5034 Planarity : 0.004 0.056 5540 Dihedral : 5.288 57.162 4862 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.06 % Favored : 95.91 % Rotamer: Outliers : 2.81 % Allowed : 26.54 % Favored : 70.65 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 3842 helix: 1.37 (0.21), residues: 749 sheet: -0.31 (0.24), residues: 486 loop : -1.59 (0.12), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.050 0.001 HIS X 140 PHE 0.018 0.001 PHE C 92 TYR 0.017 0.001 TYR B1067 ARG 0.004 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 29) link_NAG-ASN : angle 2.58412 ( 87) link_BETA1-4 : bond 0.00345 ( 5) link_BETA1-4 : angle 1.50666 ( 15) hydrogen bonds : bond 0.04386 ( 795) hydrogen bonds : angle 4.43235 ( 2223) SS BOND : bond 0.00233 ( 45) SS BOND : angle 1.07265 ( 90) covalent geometry : bond 0.00345 (31714) covalent geometry : angle 0.62563 (43170) Misc. bond : bond 0.00104 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14287.42 seconds wall clock time: 245 minutes 17.49 seconds (14717.49 seconds total)