Starting phenix.real_space_refine on Sun Jun 22 15:55:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zy1_60552/06_2025/8zy1_60552.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zy1_60552/06_2025/8zy1_60552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zy1_60552/06_2025/8zy1_60552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zy1_60552/06_2025/8zy1_60552.map" model { file = "/net/cci-nas-00/data/ceres_data/8zy1_60552/06_2025/8zy1_60552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zy1_60552/06_2025/8zy1_60552.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 138 5.16 5 C 16539 2.51 5 N 4236 2.21 5 O 5112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26025 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8367 Classifications: {'peptide': 1076} Link IDs: {'PTRANS': 49, 'TRANS': 1026} Chain breaks: 4 Chain: "B" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8367 Classifications: {'peptide': 1076} Link IDs: {'PTRANS': 49, 'TRANS': 1026} Chain breaks: 4 Chain: "C" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8367 Classifications: {'peptide': 1076} Link IDs: {'PTRANS': 49, 'TRANS': 1026} Chain breaks: 4 Chain: "D" 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: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "G" 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "J" 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 202 Unusual residues: {'EIC': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 222 Unusual residues: {'EIC': 2, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 16.11, per 1000 atoms: 0.62 Number of scatterers: 26025 At special positions: 0 Unit cell: (134.32, 143.664, 171.696, 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 138 16.00 O 5112 8.00 N 4236 7.00 C 16539 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 140 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 164 " distance=2.02 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 371 " - pdb=" SG CYS A 424 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 512 " distance=2.03 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 638 " distance=2.03 Simple disulfide: pdb=" SG CYS A 651 " - pdb=" SG CYS A 660 " distance=2.03 Simple disulfide: pdb=" SG CYS A 724 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 729 " - pdb=" SG CYS A 735 " distance=2.02 Simple disulfide: pdb=" SG CYS A 826 " - pdb=" SG CYS A 837 " distance=2.03 Simple disulfide: pdb=" SG CYS A1018 " - pdb=" SG CYS A1029 " distance=2.03 Simple disulfide: pdb=" SG CYS A1068 " - pdb=" SG CYS A1112 " distance=2.04 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 140 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 371 " - pdb=" SG CYS B 424 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 512 " distance=2.03 Simple disulfide: pdb=" SG CYS B 468 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 604 " - pdb=" SG CYS B 638 " distance=2.03 Simple disulfide: pdb=" SG CYS B 651 " - pdb=" SG CYS B 660 " distance=2.03 Simple disulfide: pdb=" SG CYS B 724 " - pdb=" SG CYS B 746 " distance=2.02 Simple disulfide: pdb=" SG CYS B 729 " - pdb=" SG CYS B 735 " distance=2.03 Simple disulfide: pdb=" SG CYS B 826 " - pdb=" SG CYS B 837 " distance=2.03 Simple disulfide: pdb=" SG CYS B1018 " - pdb=" SG CYS B1029 " distance=2.03 Simple disulfide: pdb=" SG CYS B1068 " - pdb=" SG CYS B1112 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 140 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 164 " distance=2.04 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 371 " - pdb=" SG CYS C 424 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 512 " distance=2.03 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 525 " - pdb=" SG CYS C 577 " distance=2.04 Simple disulfide: pdb=" SG CYS C 604 " - pdb=" SG CYS C 638 " distance=2.03 Simple disulfide: pdb=" SG CYS C 651 " - pdb=" SG CYS C 660 " distance=2.03 Simple disulfide: pdb=" SG CYS C 724 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 729 " - pdb=" SG CYS C 735 " distance=2.03 Simple disulfide: pdb=" SG CYS C 826 " - pdb=" SG CYS C 837 " distance=2.03 Simple disulfide: pdb=" SG CYS C1018 " - pdb=" SG CYS C1029 " distance=2.03 Simple disulfide: pdb=" SG CYS C1068 " - pdb=" SG CYS C1112 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1303 " - " ASN A 646 " " NAG A1305 " - " ASN A 703 " " NAG A1308 " - " ASN A 116 " " NAG A1309 " - " ASN A 273 " " NAG A1310 " - " ASN A 334 " " NAG A1311 " - " ASN A1084 " " NAG A1312 " - " ASN A1120 " " NAG B1304 " - " ASN B 646 " " NAG B1306 " - " ASN B 703 " " NAG B1309 " - " ASN B 116 " " NAG B1310 " - " ASN B 273 " " NAG B1311 " - " ASN B 334 " " NAG B1312 " - " ASN B1084 " " NAG B1313 " - " ASN B1120 " " NAG B1314 " - " ASN B 163 " " NAG C1305 " - " ASN C 646 " " NAG C1307 " - " ASN C 703 " " NAG C1310 " - " ASN C 116 " " NAG C1311 " - " ASN C 273 " " NAG C1312 " - " ASN C 334 " " NAG C1313 " - " ASN C1084 " " NAG C1314 " - " ASN C1120 " " NAG C1315 " - " ASN C 163 " " NAG D 1 " - " ASN A 787 " " NAG E 1 " - " ASN A 231 " " NAG F 1 " - " ASN A 361 " " NAG G 1 " - " ASN B 787 " " NAG H 1 " - " ASN B 231 " " NAG I 1 " - " ASN B 361 " " NAG J 1 " - " ASN C 787 " " NAG K 1 " - " ASN C 231 " " NAG L 1 " - " ASN C 361 " Time building additional restraints: 6.56 Conformation dependent library (CDL) restraints added in 3.4 seconds 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6024 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 46 sheets defined 23.6% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.47 Creating SS restraints... Processing helix chain 'A' and resid 285 through 295 Processing helix chain 'A' and resid 340 through 344 removed outlier: 3.749A pdb=" N TRP A 344 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.726A pdb=" N VAL A 358 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.719A pdb=" N LEU A 379 " --> pdb=" O PRO A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 408 through 414 removed outlier: 3.624A pdb=" N ASP A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 611 removed outlier: 4.100A pdb=" N MET A 610 " --> pdb=" O ASP A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 625 removed outlier: 3.740A pdb=" N TYR A 623 " --> pdb=" O ASP A 619 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 625 " --> pdb=" O ARG A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 737 removed outlier: 3.539A pdb=" N SER A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 737 " --> pdb=" O THR A 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 732 through 737' Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 742 through 768 removed outlier: 3.711A pdb=" N LEU A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 752 " --> pdb=" O GLN A 748 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 755 " --> pdb=" O ARG A 751 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 759 " --> pdb=" O GLY A 755 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR A 764 " --> pdb=" O GLN A 760 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 809 Processing helix chain 'A' and resid 822 through 828 Processing helix chain 'A' and resid 834 through 841 Processing helix chain 'A' and resid 852 through 871 Processing helix chain 'A' and resid 872 through 876 Processing helix chain 'A' and resid 883 through 894 Processing helix chain 'A' and resid 899 through 905 removed outlier: 3.660A pdb=" N TYR A 903 " --> pdb=" O GLN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 926 Processing helix chain 'A' and resid 928 through 930 No H-bonds generated for 'chain 'A' and resid 928 through 930' Processing helix chain 'A' and resid 931 through 951 removed outlier: 3.523A pdb=" N GLN A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 945 " --> pdb=" O ASN A 941 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN A 951 " --> pdb=" O THR A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 954 No H-bonds generated for 'chain 'A' and resid 952 through 954' Processing helix chain 'A' and resid 962 through 970 removed outlier: 4.014A pdb=" N ILE A 966 " --> pdb=" O VAL A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 1019 removed outlier: 3.624A pdb=" N VAL A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 993 " --> pdb=" O SER A 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.688A pdb=" N ASN B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.856A pdb=" N LEU B 379 " --> pdb=" O PRO B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 402 Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'B' and resid 612 through 616 removed outlier: 3.993A pdb=" N ILE B 616 " --> pdb=" O ALA B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 622 Processing helix chain 'B' and resid 732 through 740 removed outlier: 3.539A pdb=" N SER B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 769 removed outlier: 3.751A pdb=" N CYS B 746 " --> pdb=" O TYR B 742 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 764 " --> pdb=" O GLN B 760 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 809 Processing helix chain 'B' and resid 834 through 841 Processing helix chain 'B' and resid 852 through 871 removed outlier: 3.752A pdb=" N THR B 869 " --> pdb=" O SER B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 876 Processing helix chain 'B' and resid 883 through 894 Processing helix chain 'B' and resid 899 through 905 removed outlier: 3.841A pdb=" N TYR B 903 " --> pdb=" O GLN B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 926 Processing helix chain 'B' and resid 931 through 951 removed outlier: 3.783A pdb=" N GLN B 935 " --> pdb=" O LEU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 954 No H-bonds generated for 'chain 'B' and resid 952 through 954' Processing helix chain 'B' and resid 962 through 968 removed outlier: 3.910A pdb=" N ILE B 966 " --> pdb=" O VAL B 962 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 967 " --> pdb=" O LEU B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 1019 removed outlier: 3.682A pdb=" N VAL B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 982 " --> pdb=" O GLN B 978 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 993 " --> pdb=" O SER B 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.667A pdb=" N VAL C 332 " --> pdb=" O PRO C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 removed outlier: 3.703A pdb=" N VAL C 358 " --> pdb=" O ASP C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 removed outlier: 3.834A pdb=" N LEU C 379 " --> pdb=" O PRO C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 414 Processing helix chain 'C' and resid 606 through 610 removed outlier: 3.932A pdb=" N THR C 609 " --> pdb=" O ASP C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 625 removed outlier: 4.079A pdb=" N TYR C 623 " --> pdb=" O ASP C 619 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE C 625 " --> pdb=" O ARG C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 737 Processing helix chain 'C' and resid 739 through 741 No H-bonds generated for 'chain 'C' and resid 739 through 741' Processing helix chain 'C' and resid 742 through 768 removed outlier: 3.820A pdb=" N LEU C 749 " --> pdb=" O PHE C 745 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 752 " --> pdb=" O GLN C 748 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU C 759 " --> pdb=" O GLY C 755 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR C 764 " --> pdb=" O GLN C 760 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 792 removed outlier: 3.689A pdb=" N LEU C 792 " --> pdb=" O SER C 789 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 789 through 792' Processing helix chain 'C' and resid 802 through 809 Processing helix chain 'C' and resid 822 through 827 Processing helix chain 'C' and resid 834 through 841 Processing helix chain 'C' and resid 852 through 870 Processing helix chain 'C' and resid 883 through 896 removed outlier: 3.866A pdb=" N ALA C 889 " --> pdb=" O ALA C 885 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR C 890 " --> pdb=" O MET C 886 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 895 " --> pdb=" O ARG C 891 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY C 896 " --> pdb=" O PHE C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 905 removed outlier: 4.389A pdb=" N TYR C 903 " --> pdb=" O GLN C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 927 Processing helix chain 'C' and resid 931 through 951 removed outlier: 3.520A pdb=" N GLN C 935 " --> pdb=" O LEU C 931 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 950 " --> pdb=" O ASN C 946 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 951 " --> pdb=" O THR C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 968 removed outlier: 3.689A pdb=" N ILE C 966 " --> pdb=" O VAL C 962 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 967 " --> pdb=" O LEU C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 1019 removed outlier: 3.661A pdb=" N ASP C 980 " --> pdb=" O GLU C 976 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG C 981 " --> pdb=" O VAL C 977 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 982 " --> pdb=" O GLN C 978 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR C 993 " --> pdb=" O SER C 989 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 8.125A pdb=" N ASN A 66 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N HIS A 260 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 258 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 255 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU A 198 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS A 225 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL A 200 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR A 204 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N VAL A 219 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N PHE A 41 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 removed outlier: 3.523A pdb=" N ARG B 554 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 562 " --> pdb=" O GLY B 553 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP B 561 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 535 " --> pdb=" O PHE B 528 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 60 removed outlier: 3.653A pdb=" N ASP A 269 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP A 278 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 89 removed outlier: 6.464A pdb=" N ILE A 130 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG A 168 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE A 132 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR A 166 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL A 134 " --> pdb=" O CYS A 164 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N CYS A 164 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 156 removed outlier: 6.309A pdb=" N ASN A 148 " --> pdb=" O PRO A 152 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 154 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE A 145 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 302 through 305 Processing sheet with id=AA7, first strand: chain 'A' and resid 316 through 319 removed outlier: 3.554A pdb=" N VAL A 317 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 540 " --> pdb=" O ASP A 573 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASP A 561 " --> pdb=" O ILE A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.645A pdb=" N GLU A 345 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A 387 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.450A pdb=" N CYS A 352 " --> pdb=" O CYS A 512 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 440 through 442 Processing sheet with id=AB2, first strand: chain 'A' and resid 643 through 644 removed outlier: 6.431A pdb=" N ALA A 643 " --> pdb=" O ALA A 680 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR A 682 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 697 through 714 removed outlier: 6.861A pdb=" N THR A 697 " --> pdb=" O THR A1062 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR A1062 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA A 699 " --> pdb=" O ASN A1060 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASN A1060 " --> pdb=" O ALA A 699 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU A1058 " --> pdb=" O PRO A 701 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A1042 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET A1036 " --> pdb=" O VAL A1051 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR A1053 " --> pdb=" O HIS A1034 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N HIS A1034 " --> pdb=" O TYR A1053 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 719 through 722 removed outlier: 4.521A pdb=" N LYS A 719 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 773 through 774 Processing sheet with id=AB6, first strand: chain 'A' and resid 782 through 783 Processing sheet with id=AB7, first strand: chain 'A' and resid 1106 through 1111 removed outlier: 4.912A pdb=" N ALA A1073 " --> pdb=" O SER A1109 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A1119 " --> pdb=" O ALA A1066 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1080 through 1083 Processing sheet with id=AB9, first strand: chain 'B' and resid 41 through 42 removed outlier: 6.869A pdb=" N PHE B 41 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N VAL B 219 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR B 204 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL B 200 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS B 225 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU B 198 " --> pdb=" O LYS B 225 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS B 185 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 100 " --> pdb=" O HIS B 185 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 258 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 53 through 60 removed outlier: 4.300A pdb=" N ASP B 278 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 88 through 89 removed outlier: 3.543A pdb=" N VAL B 122 " --> pdb=" O ASP B 133 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 151 through 156 removed outlier: 5.880A pdb=" N ASN B 148 " --> pdb=" O PRO B 152 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B 154 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP B 156 " --> pdb=" O MET B 144 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE B 145 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 302 through 306 removed outlier: 3.635A pdb=" N THR B 306 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL B 582 " --> pdb=" O THR B 306 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 345 through 349 removed outlier: 3.664A pdb=" N GLU B 345 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL B 387 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 352 through 353 removed outlier: 6.319A pdb=" N CYS B 352 " --> pdb=" O CYS B 512 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 440 through 442 Processing sheet with id=AC8, first strand: chain 'B' and resid 643 through 644 removed outlier: 6.266A pdb=" N ALA B 643 " --> pdb=" O ALA B 680 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N THR B 682 " --> pdb=" O ALA B 643 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 697 through 714 removed outlier: 6.865A pdb=" N GLN B1057 " --> pdb=" O MET B 702 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE B 704 " --> pdb=" O PRO B1055 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE B 706 " --> pdb=" O TYR B1053 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N TYR B1053 " --> pdb=" O ILE B 706 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 708 " --> pdb=" O VAL B1051 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B1051 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR B 710 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU B1049 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL B 712 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL B1047 " --> pdb=" O VAL B 712 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLY B1045 " --> pdb=" O PRO B 714 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B1042 " --> pdb=" O GLY B1045 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR B1053 " --> pdb=" O HIS B1034 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS B1034 " --> pdb=" O TYR B1053 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 697 through 714 removed outlier: 6.865A pdb=" N GLN B1057 " --> pdb=" O MET B 702 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE B 704 " --> pdb=" O PRO B1055 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE B 706 " --> pdb=" O TYR B1053 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N TYR B1053 " --> pdb=" O ILE B 706 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 708 " --> pdb=" O VAL B1051 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B1051 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR B 710 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU B1049 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL B 712 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL B1047 " --> pdb=" O VAL B 712 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLY B1045 " --> pdb=" O PRO B 714 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N THR B1062 " --> pdb=" O THR B1083 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B1064 " --> pdb=" O PHE B1081 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE B1081 " --> pdb=" O ALA B1064 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 719 through 722 removed outlier: 4.521A pdb=" N LYS B 719 " --> pdb=" O LEU B 847 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 782 through 783 Processing sheet with id=AD4, first strand: chain 'B' and resid 1106 through 1111 removed outlier: 5.103A pdb=" N ALA B1073 " --> pdb=" O SER B1109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.623A pdb=" N THR C 34 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEU C 198 " --> pdb=" O LYS C 225 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS C 225 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL C 200 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR C 204 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N VAL C 219 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE C 41 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 54 through 60 removed outlier: 4.208A pdb=" N ASP C 278 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 88 through 89 Processing sheet with id=AD8, first strand: chain 'C' and resid 151 through 158 removed outlier: 6.207A pdb=" N ASN C 148 " --> pdb=" O PRO C 152 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR C 158 " --> pdb=" O ASP C 142 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N ASP C 142 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 9.889A pdb=" N MET C 239 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU C 241 " --> pdb=" O PRO C 143 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE C 145 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 301 through 305 Processing sheet with id=AE1, first strand: chain 'C' and resid 345 through 349 removed outlier: 3.844A pdb=" N GLU C 345 " --> pdb=" O TYR C 391 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL C 387 " --> pdb=" O ILE C 349 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 352 through 353 removed outlier: 6.663A pdb=" N CYS C 352 " --> pdb=" O CYS C 512 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 440 through 442 Processing sheet with id=AE4, first strand: chain 'C' and resid 526 through 530 removed outlier: 3.845A pdb=" N GLY C 535 " --> pdb=" O PHE C 528 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP C 561 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY C 553 " --> pdb=" O ASP C 561 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 643 through 649 removed outlier: 6.117A pdb=" N ALA C 643 " --> pdb=" O ALA C 680 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N THR C 682 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ASP C 645 " --> pdb=" O THR C 682 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE C 659 " --> pdb=" O ILE C 655 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 697 through 714 removed outlier: 6.757A pdb=" N THR C 697 " --> pdb=" O THR C1062 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR C1062 " --> pdb=" O THR C 697 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA C 699 " --> pdb=" O ASN C1060 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN C1060 " --> pdb=" O ALA C 699 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU C1058 " --> pdb=" O PRO C 701 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY C1045 " --> pdb=" O ALA C1041 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA C1041 " --> pdb=" O GLY C1045 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL C1047 " --> pdb=" O PRO C1039 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU C1049 " --> pdb=" O SER C1037 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER C1037 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL C1051 " --> pdb=" O LEU C1035 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 697 through 714 removed outlier: 6.757A pdb=" N THR C 697 " --> pdb=" O THR C1062 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR C1062 " --> pdb=" O THR C 697 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA C 699 " --> pdb=" O ASN C1060 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN C1060 " --> pdb=" O ALA C 699 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU C1058 " --> pdb=" O PRO C 701 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE C1081 " --> pdb=" O ALA C1064 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 719 through 722 removed outlier: 4.502A pdb=" N LYS C 719 " --> pdb=" O LEU C 847 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 782 through 783 Processing sheet with id=AF1, first strand: chain 'C' and resid 1106 through 1111 removed outlier: 4.722A pdb=" N ALA C1073 " --> pdb=" O SER C1109 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C1119 " --> pdb=" O ALA C1066 " (cutoff:3.500A) 932 hydrogen bonds defined for protein. 2535 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: 12.76 Time building geometry restraints manager: 7.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8202 1.35 - 1.47: 6928 1.47 - 1.59: 11297 1.59 - 1.72: 0 1.72 - 1.84: 186 Bond restraints: 26613 Sorted by residual: bond pdb=" CA PHE A 270 " pdb=" C PHE A 270 " ideal model delta sigma weight residual 1.522 1.485 0.038 1.20e-02 6.94e+03 9.86e+00 bond pdb=" C LYS B 450 " pdb=" N PRO B 451 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.08e-02 8.57e+03 8.31e+00 bond pdb=" N ASP A 271 " pdb=" CA ASP A 271 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.41e-02 5.03e+03 7.97e+00 bond pdb=" N PHE A 270 " pdb=" CA PHE A 270 " ideal model delta sigma weight residual 1.454 1.480 -0.026 1.23e-02 6.61e+03 4.36e+00 bond pdb=" CA ASP B 115 " pdb=" CB ASP B 115 " ideal model delta sigma weight residual 1.534 1.509 0.025 1.45e-02 4.76e+03 3.07e+00 ... (remaining 26608 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 35483 1.90 - 3.79: 609 3.79 - 5.69: 64 5.69 - 7.59: 20 7.59 - 9.48: 4 Bond angle restraints: 36180 Sorted by residual: angle pdb=" CA PHE A 270 " pdb=" C PHE A 270 " pdb=" O PHE A 270 " ideal model delta sigma weight residual 121.11 115.77 5.34 1.13e+00 7.83e-01 2.24e+01 angle pdb=" CA ASP A 271 " pdb=" CB ASP A 271 " pdb=" CG ASP A 271 " ideal model delta sigma weight residual 112.60 116.80 -4.20 1.00e+00 1.00e+00 1.77e+01 angle pdb=" C ILE A 335 " pdb=" N THR A 336 " pdb=" CA THR A 336 " ideal model delta sigma weight residual 121.54 129.53 -7.99 1.91e+00 2.74e-01 1.75e+01 angle pdb=" CA ASP B 115 " pdb=" CB ASP B 115 " pdb=" CG ASP B 115 " ideal model delta sigma weight residual 112.60 116.78 -4.18 1.00e+00 1.00e+00 1.74e+01 angle pdb=" CA ASP A 271 " pdb=" C ASP A 271 " pdb=" O ASP A 271 " ideal model delta sigma weight residual 120.89 116.37 4.52 1.11e+00 8.12e-01 1.66e+01 ... (remaining 36175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.35: 15192 23.35 - 46.69: 1194 46.69 - 70.04: 186 70.04 - 93.38: 36 93.38 - 116.73: 6 Dihedral angle restraints: 16614 sinusoidal: 7236 harmonic: 9378 Sorted by residual: dihedral pdb=" CB CYS B 20 " pdb=" SG CYS B 20 " pdb=" SG CYS B 140 " pdb=" CB CYS B 140 " ideal model delta sinusoidal sigma weight residual 93.00 -177.62 -89.38 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS C 729 " pdb=" SG CYS C 729 " pdb=" SG CYS C 735 " pdb=" CB CYS C 735 " ideal model delta sinusoidal sigma weight residual 93.00 -179.91 -87.09 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" CB CYS A 604 " pdb=" SG CYS A 604 " pdb=" SG CYS A 638 " pdb=" CB CYS A 638 " ideal model delta sinusoidal sigma weight residual 93.00 20.04 72.96 1 1.00e+01 1.00e-02 6.79e+01 ... (remaining 16611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3912 0.087 - 0.174: 322 0.174 - 0.260: 12 0.260 - 0.347: 0 0.347 - 0.434: 1 Chirality restraints: 4247 Sorted by residual: chirality pdb=" CG LEU B 114 " pdb=" CB LEU B 114 " pdb=" CD1 LEU B 114 " pdb=" CD2 LEU B 114 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" C1 NAG A1312 " pdb=" ND2 ASN A1120 " pdb=" C2 NAG A1312 " pdb=" O5 NAG A1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C1 NAG C1315 " pdb=" ND2 ASN C 163 " pdb=" C2 NAG C1315 " pdb=" O5 NAG C1315 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 4244 not shown) Planarity restraints: 4634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 565 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO C 566 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 566 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 566 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 269 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C ASP A 269 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP A 269 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 270 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 904 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" CD GLU B 904 " -0.038 2.00e-02 2.50e+03 pdb=" OE1 GLU B 904 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 904 " 0.014 2.00e-02 2.50e+03 ... (remaining 4631 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2003 2.74 - 3.28: 23102 3.28 - 3.82: 40681 3.82 - 4.36: 47158 4.36 - 4.90: 85603 Nonbonded interactions: 198547 Sorted by model distance: nonbonded pdb=" OG1 THR C1102 " pdb=" OD1 ASP C1104 " model vdw 2.206 3.040 nonbonded pdb=" OG1 THR A1102 " pdb=" OD1 ASP A1104 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR B 42 " pdb=" O HIS B 59 " model vdw 2.306 3.040 nonbonded pdb=" O TYR C 304 " pdb=" OG SER C 583 " model vdw 2.308 3.040 nonbonded pdb=" O SER B1097 " pdb=" OG SER B1097 " model vdw 2.324 3.040 ... (remaining 198542 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 19 through 1127 or resid 1303 through 1313)) selection = (chain 'B' and (resid 19 through 1127 or resid 1303 through 1313)) selection = (chain 'C' and (resid 19 through 1127 or resid 1303 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 64.490 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26705 Z= 0.141 Angle : 0.616 9.484 36411 Z= 0.333 Chirality : 0.046 0.434 4247 Planarity : 0.005 0.065 4602 Dihedral : 16.055 116.728 10455 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.65 % Allowed : 21.66 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.60 (0.14), residues: 3198 helix: -0.62 (0.18), residues: 705 sheet: 0.05 (0.20), residues: 735 loop : -1.79 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 428 HIS 0.003 0.001 HIS C 170 PHE 0.019 0.001 PHE C 549 TYR 0.021 0.001 TYR B 356 ARG 0.007 0.000 ARG B1093 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 32) link_NAG-ASN : angle 2.19760 ( 96) link_BETA1-4 : bond 0.00545 ( 12) link_BETA1-4 : angle 2.05679 ( 36) link_ALPHA1-3 : bond 0.00641 ( 3) link_ALPHA1-3 : angle 1.56985 ( 9) hydrogen bonds : bond 0.23704 ( 915) hydrogen bonds : angle 8.38438 ( 2535) SS BOND : bond 0.00364 ( 45) SS BOND : angle 1.17044 ( 90) covalent geometry : bond 0.00262 (26613) covalent geometry : angle 0.60036 (36180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 236 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7447 (mm) REVERT: A 300 GLU cc_start: 0.7673 (mp0) cc_final: 0.7245 (mm-30) REVERT: A 316 GLU cc_start: 0.7589 (mp0) cc_final: 0.7202 (mp0) REVERT: A 516 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7370 (mm-40) REVERT: A 678 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7992 (pt) REVERT: A 696 ASN cc_start: 0.8146 (t0) cc_final: 0.7849 (t0) REVERT: A 929 THR cc_start: 0.5230 (t) cc_final: 0.5013 (t) REVERT: A 1077 ARG cc_start: 0.7993 (tpp80) cc_final: 0.7651 (mtt-85) REVERT: A 1093 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7527 (mtt90) REVERT: B 172 PHE cc_start: 0.5783 (OUTLIER) cc_final: 0.4080 (t80) REVERT: B 208 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7354 (m-30) REVERT: B 294 THR cc_start: 0.7112 (OUTLIER) cc_final: 0.6781 (p) REVERT: B 554 ARG cc_start: 0.7555 (ptp-170) cc_final: 0.6752 (mtp85) REVERT: B 593 SER cc_start: 0.8536 (t) cc_final: 0.8079 (p) REVERT: B 936 ASP cc_start: 0.7755 (t0) cc_final: 0.7533 (t0) REVERT: B 965 ASP cc_start: 0.7967 (p0) cc_final: 0.7292 (m-30) REVERT: B 966 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8008 (mt) REVERT: B 1107 PHE cc_start: 0.8489 (p90) cc_final: 0.8078 (p90) REVERT: B 1111 ASN cc_start: 0.7556 (OUTLIER) cc_final: 0.7019 (p0) REVERT: C 53 ARG cc_start: 0.7044 (mtm-85) cc_final: 0.6426 (mtm180) REVERT: C 184 LYS cc_start: 0.7393 (tppt) cc_final: 0.6756 (mmmt) REVERT: C 325 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: C 346 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.7816 (ttm170) REVERT: C 619 ASP cc_start: 0.7149 (m-30) cc_final: 0.6797 (m-30) REVERT: C 690 ASP cc_start: 0.6967 (p0) cc_final: 0.6704 (t0) REVERT: C 1024 LYS cc_start: 0.8978 (mmmm) cc_final: 0.8728 (mmtm) REVERT: C 1036 MET cc_start: 0.8724 (mtm) cc_final: 0.8447 (mtp) outliers start: 102 outliers final: 85 residues processed: 323 average time/residue: 0.3297 time to fit residues: 174.6924 Evaluate side-chains 316 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 222 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 687 ASP Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1111 ASN Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 527 ASN Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 724 CYS Chi-restraints excluded: chain C residue 764 THR Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 853 ASP Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 1068 CYS Chi-restraints excluded: chain C residue 1106 THR Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1127 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 9.9990 chunk 243 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 291 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 842 ASN A1057 GLN B 260 HIS B 893 ASN B 908 GLN B 940 GLN C 322 ASN C 760 GLN C 905 ASN C 908 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.129182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.105715 restraints weight = 33361.272| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.72 r_work: 0.2962 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 26705 Z= 0.297 Angle : 0.740 16.770 36411 Z= 0.383 Chirality : 0.050 0.216 4247 Planarity : 0.005 0.057 4602 Dihedral : 9.372 100.989 4957 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 6.12 % Allowed : 19.08 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.14), residues: 3198 helix: -0.14 (0.19), residues: 729 sheet: 0.00 (0.19), residues: 762 loop : -1.83 (0.13), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 428 HIS 0.007 0.002 HIS C1044 PHE 0.042 0.002 PHE C 546 TYR 0.022 0.002 TYR C1053 ARG 0.005 0.001 ARG A1025 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 32) link_NAG-ASN : angle 2.38088 ( 96) link_BETA1-4 : bond 0.00663 ( 12) link_BETA1-4 : angle 2.22365 ( 36) link_ALPHA1-3 : bond 0.00940 ( 3) link_ALPHA1-3 : angle 2.52609 ( 9) hydrogen bonds : bond 0.07809 ( 915) hydrogen bonds : angle 6.20582 ( 2535) SS BOND : bond 0.00773 ( 45) SS BOND : angle 1.93371 ( 90) covalent geometry : bond 0.00738 (26613) covalent geometry : angle 0.72153 (36180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 232 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 GLU cc_start: 0.7540 (mp0) cc_final: 0.7311 (mp0) REVERT: A 316 GLU cc_start: 0.7483 (mp0) cc_final: 0.7096 (mp0) REVERT: A 448 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8171 (ttmm) REVERT: A 516 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7352 (mm-40) REVERT: A 554 ARG cc_start: 0.7638 (mtp85) cc_final: 0.7395 (mtp85) REVERT: A 696 ASN cc_start: 0.8202 (t0) cc_final: 0.7746 (t0) REVERT: A 890 TYR cc_start: 0.8486 (t80) cc_final: 0.8245 (t80) REVERT: A 893 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8419 (m110) REVERT: A 1090 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8796 (tp) REVERT: A 1093 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.7542 (mtt90) REVERT: B 153 TYR cc_start: 0.5624 (OUTLIER) cc_final: 0.5348 (p90) REVERT: B 300 GLU cc_start: 0.7988 (mp0) cc_final: 0.7639 (mm-30) REVERT: B 554 ARG cc_start: 0.7607 (ptp-170) cc_final: 0.7365 (ptp-110) REVERT: B 593 SER cc_start: 0.8667 (t) cc_final: 0.8193 (p) REVERT: B 890 TYR cc_start: 0.8472 (t80) cc_final: 0.8084 (t80) REVERT: B 1092 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8308 (mt0) REVERT: C 49 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.6493 (mpp80) REVERT: C 230 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8362 (pt) REVERT: C 330 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8359 (t0) REVERT: C 502 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8267 (m-80) REVERT: C 565 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7638 (t70) REVERT: C 619 ASP cc_start: 0.7115 (m-30) cc_final: 0.6768 (m-30) REVERT: C 760 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8055 (mp-120) REVERT: C 1024 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8634 (mmtm) outliers start: 171 outliers final: 118 residues processed: 380 average time/residue: 0.3184 time to fit residues: 201.7576 Evaluate side-chains 342 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 213 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 448 LYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 893 ASN Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 810 ASN Chi-restraints excluded: chain B residue 839 GLN Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 893 ASN Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 941 ASN Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain B residue 1092 GLN Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 502 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 724 CYS Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 810 ASN Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 853 ASP Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 980 ASP Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1068 CYS Chi-restraints excluded: chain C residue 1086 THR Chi-restraints excluded: chain C residue 1103 THR Chi-restraints excluded: chain C residue 1118 ILE Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 306 optimal weight: 4.9990 chunk 226 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 198 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 308 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 893 ASN B 940 GLN C 203 ASN C 531 ASN C 941 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.133496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.113076 restraints weight = 33156.138| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.46 r_work: 0.3039 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 26705 Z= 0.113 Angle : 0.552 9.415 36411 Z= 0.286 Chirality : 0.043 0.205 4247 Planarity : 0.004 0.044 4602 Dihedral : 8.291 97.671 4892 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.40 % Allowed : 20.80 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.06 (0.14), residues: 3198 helix: 0.53 (0.20), residues: 717 sheet: 0.07 (0.19), residues: 750 loop : -1.65 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 428 HIS 0.002 0.001 HIS C 167 PHE 0.012 0.001 PHE C 549 TYR 0.019 0.001 TYR C1053 ARG 0.002 0.000 ARG C 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 32) link_NAG-ASN : angle 2.06002 ( 96) link_BETA1-4 : bond 0.00399 ( 12) link_BETA1-4 : angle 1.84030 ( 36) link_ALPHA1-3 : bond 0.01069 ( 3) link_ALPHA1-3 : angle 2.48984 ( 9) hydrogen bonds : bond 0.05454 ( 915) hydrogen bonds : angle 5.59696 ( 2535) SS BOND : bond 0.00381 ( 45) SS BOND : angle 1.48620 ( 90) covalent geometry : bond 0.00245 (26613) covalent geometry : angle 0.53363 (36180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 234 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 GLU cc_start: 0.7382 (mp0) cc_final: 0.7177 (mp0) REVERT: A 316 GLU cc_start: 0.7450 (mp0) cc_final: 0.7114 (mp0) REVERT: A 516 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7287 (mm-40) REVERT: A 600 GLN cc_start: 0.8540 (tm-30) cc_final: 0.7805 (tt0) REVERT: A 696 ASN cc_start: 0.8192 (t0) cc_final: 0.7838 (t0) REVERT: A 830 VAL cc_start: 0.4591 (OUTLIER) cc_final: 0.4252 (t) REVERT: A 890 TYR cc_start: 0.8381 (t80) cc_final: 0.8095 (t80) REVERT: A 893 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8420 (m110) REVERT: B 208 ASP cc_start: 0.7599 (m-30) cc_final: 0.7303 (m-30) REVERT: B 504 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7712 (mt) REVERT: B 554 ARG cc_start: 0.7686 (ptp-170) cc_final: 0.7382 (ptp-110) REVERT: B 593 SER cc_start: 0.8643 (t) cc_final: 0.8226 (p) REVERT: B 966 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8174 (mt) REVERT: B 1111 ASN cc_start: 0.7526 (OUTLIER) cc_final: 0.7243 (p0) REVERT: C 49 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.6508 (mpp80) REVERT: C 230 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7876 (pt) REVERT: C 325 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: C 502 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8159 (m-80) REVERT: C 565 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7609 (t70) REVERT: C 1024 LYS cc_start: 0.8840 (mmmm) cc_final: 0.8606 (mmtm) outliers start: 123 outliers final: 85 residues processed: 339 average time/residue: 0.3471 time to fit residues: 195.6159 Evaluate side-chains 315 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 220 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 893 ASN Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 893 ASN Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1111 ASN Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1118 ILE Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 502 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 724 CYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 917 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 980 ASP Chi-restraints excluded: chain C residue 1118 ILE Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 305 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 74 optimal weight: 7.9990 chunk 295 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 893 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109843 restraints weight = 33462.760| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.52 r_work: 0.2980 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 26705 Z= 0.204 Angle : 0.648 11.744 36411 Z= 0.332 Chirality : 0.047 0.479 4247 Planarity : 0.004 0.049 4602 Dihedral : 8.294 92.044 4874 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.73 % Allowed : 19.62 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.14), residues: 3198 helix: 0.50 (0.20), residues: 726 sheet: 0.01 (0.19), residues: 756 loop : -1.71 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 428 HIS 0.006 0.001 HIS C1044 PHE 0.033 0.002 PHE C 546 TYR 0.020 0.002 TYR B 256 ARG 0.003 0.000 ARG A1093 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 32) link_NAG-ASN : angle 2.29136 ( 96) link_BETA1-4 : bond 0.00526 ( 12) link_BETA1-4 : angle 2.03044 ( 36) link_ALPHA1-3 : bond 0.01237 ( 3) link_ALPHA1-3 : angle 2.79077 ( 9) hydrogen bonds : bond 0.06528 ( 915) hydrogen bonds : angle 5.53624 ( 2535) SS BOND : bond 0.00588 ( 45) SS BOND : angle 1.86736 ( 90) covalent geometry : bond 0.00499 (26613) covalent geometry : angle 0.62768 (36180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 227 time to evaluate : 2.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 GLU cc_start: 0.7563 (mp0) cc_final: 0.7356 (mp0) REVERT: A 316 GLU cc_start: 0.7576 (mp0) cc_final: 0.7160 (mp0) REVERT: A 516 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7258 (mm-40) REVERT: A 554 ARG cc_start: 0.7547 (mtt-85) cc_final: 0.7089 (mtp85) REVERT: A 600 GLN cc_start: 0.8572 (tm-30) cc_final: 0.7906 (tt0) REVERT: A 696 ASN cc_start: 0.8203 (t0) cc_final: 0.7827 (t0) REVERT: A 888 MET cc_start: 0.8646 (mmm) cc_final: 0.8189 (mmm) REVERT: A 893 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8476 (m110) REVERT: B 208 ASP cc_start: 0.7550 (m-30) cc_final: 0.7261 (m-30) REVERT: B 300 GLU cc_start: 0.7964 (mp0) cc_final: 0.7676 (mm-30) REVERT: B 504 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7828 (mt) REVERT: B 554 ARG cc_start: 0.7700 (ptp-170) cc_final: 0.7360 (ptp-110) REVERT: B 593 SER cc_start: 0.8659 (t) cc_final: 0.8203 (p) REVERT: C 49 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.6582 (mpp80) REVERT: C 230 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8208 (pt) REVERT: C 330 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8338 (t0) REVERT: C 346 ARG cc_start: 0.9414 (OUTLIER) cc_final: 0.8889 (ttm170) REVERT: C 565 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7500 (t70) REVERT: C 1024 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8612 (mmtm) outliers start: 160 outliers final: 114 residues processed: 366 average time/residue: 0.3326 time to fit residues: 201.1007 Evaluate side-chains 337 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 216 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 HIS Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 893 ASN Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 893 ASN Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 941 ASN Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1118 ILE Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 724 CYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 980 ASP Chi-restraints excluded: chain C residue 1068 CYS Chi-restraints excluded: chain C residue 1086 THR Chi-restraints excluded: chain C residue 1118 ILE Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1127 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 108 optimal weight: 0.0370 chunk 165 optimal weight: 7.9990 chunk 50 optimal weight: 0.0970 chunk 173 optimal weight: 0.5980 chunk 280 optimal weight: 0.9980 chunk 316 optimal weight: 1.9990 chunk 287 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 893 ASN C 893 ASN C 941 ASN C1057 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.134255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.113793 restraints weight = 33426.764| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.52 r_work: 0.3044 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 26705 Z= 0.101 Angle : 0.531 9.407 36411 Z= 0.274 Chirality : 0.042 0.285 4247 Planarity : 0.003 0.040 4602 Dihedral : 7.578 88.375 4869 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.33 % Allowed : 21.05 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.92 (0.14), residues: 3198 helix: 0.78 (0.20), residues: 744 sheet: 0.14 (0.19), residues: 753 loop : -1.65 (0.13), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 428 HIS 0.002 0.000 HIS C 167 PHE 0.013 0.001 PHE C 549 TYR 0.017 0.001 TYR C1053 ARG 0.005 0.000 ARG B1093 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 32) link_NAG-ASN : angle 2.03842 ( 96) link_BETA1-4 : bond 0.00407 ( 12) link_BETA1-4 : angle 1.79028 ( 36) link_ALPHA1-3 : bond 0.01443 ( 3) link_ALPHA1-3 : angle 2.62616 ( 9) hydrogen bonds : bond 0.04756 ( 915) hydrogen bonds : angle 5.22974 ( 2535) SS BOND : bond 0.00475 ( 45) SS BOND : angle 1.51304 ( 90) covalent geometry : bond 0.00208 (26613) covalent geometry : angle 0.51200 (36180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 235 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 GLU cc_start: 0.7510 (mp0) cc_final: 0.7117 (mp0) REVERT: A 331 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: A 516 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7240 (mm-40) REVERT: A 554 ARG cc_start: 0.7472 (mtt-85) cc_final: 0.7143 (mtp85) REVERT: A 600 GLN cc_start: 0.8546 (tm-30) cc_final: 0.7907 (tt0) REVERT: A 696 ASN cc_start: 0.8195 (t0) cc_final: 0.7847 (t0) REVERT: A 888 MET cc_start: 0.8673 (mmm) cc_final: 0.8254 (mmm) REVERT: A 1093 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7570 (mtt90) REVERT: B 133 ASP cc_start: 0.8487 (p0) cc_final: 0.8170 (p0) REVERT: B 154 LYS cc_start: 0.7610 (tppp) cc_final: 0.6993 (tttm) REVERT: B 208 ASP cc_start: 0.7524 (m-30) cc_final: 0.7229 (m-30) REVERT: B 504 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7759 (mt) REVERT: B 554 ARG cc_start: 0.7699 (ptp-170) cc_final: 0.7432 (ptp-110) REVERT: B 593 SER cc_start: 0.8652 (t) cc_final: 0.8157 (p) REVERT: B 966 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8159 (mt) REVERT: C 33 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7185 (mt0) REVERT: C 49 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.6520 (mpp80) REVERT: C 230 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7842 (pt) REVERT: C 502 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8064 (m-80) REVERT: C 565 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7365 (t70) REVERT: C 893 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8504 (m110) REVERT: C 950 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8429 (mttt) REVERT: C 1024 LYS cc_start: 0.8852 (mmmm) cc_final: 0.8629 (mmtm) REVERT: C 1036 MET cc_start: 0.8754 (mtm) cc_final: 0.8487 (mtp) outliers start: 121 outliers final: 91 residues processed: 340 average time/residue: 0.3457 time to fit residues: 192.7697 Evaluate side-chains 319 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 218 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 HIS Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 1092 GLN Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 893 ASN Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain C residue 33 GLN Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 502 PHE Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 CYS Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 CYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 893 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 917 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 980 ASP Chi-restraints excluded: chain C residue 1068 CYS Chi-restraints excluded: chain C residue 1118 ILE Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1127 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 308 optimal weight: 4.9990 chunk 220 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 278 optimal weight: 0.0040 chunk 112 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 217 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 893 ASN B 940 GLN C 893 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.130999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.107609 restraints weight = 33340.468| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.75 r_work: 0.2985 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26705 Z= 0.158 Angle : 0.581 9.316 36411 Z= 0.299 Chirality : 0.045 0.267 4247 Planarity : 0.004 0.042 4602 Dihedral : 7.596 84.217 4863 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.26 % Allowed : 20.19 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.92 (0.14), residues: 3198 helix: 0.76 (0.20), residues: 744 sheet: 0.13 (0.19), residues: 759 loop : -1.66 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 428 HIS 0.004 0.001 HIS A 202 PHE 0.024 0.001 PHE C 546 TYR 0.018 0.001 TYR C1053 ARG 0.006 0.000 ARG B1093 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 32) link_NAG-ASN : angle 2.03329 ( 96) link_BETA1-4 : bond 0.00468 ( 12) link_BETA1-4 : angle 1.89298 ( 36) link_ALPHA1-3 : bond 0.01406 ( 3) link_ALPHA1-3 : angle 2.50976 ( 9) hydrogen bonds : bond 0.05593 ( 915) hydrogen bonds : angle 5.23626 ( 2535) SS BOND : bond 0.00478 ( 45) SS BOND : angle 1.65030 ( 90) covalent geometry : bond 0.00381 (26613) covalent geometry : angle 0.56268 (36180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 225 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8942 (tp) REVERT: A 316 GLU cc_start: 0.7492 (mp0) cc_final: 0.7127 (mp0) REVERT: A 331 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7701 (mt-10) REVERT: A 448 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8149 (ttmm) REVERT: A 516 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7224 (mm-40) REVERT: A 600 GLN cc_start: 0.8579 (tm-30) cc_final: 0.7955 (tt0) REVERT: A 696 ASN cc_start: 0.8157 (t0) cc_final: 0.7835 (t0) REVERT: A 888 MET cc_start: 0.8720 (mmm) cc_final: 0.8314 (mmm) REVERT: A 1093 ARG cc_start: 0.7941 (ttm-80) cc_final: 0.7559 (mtt90) REVERT: B 133 ASP cc_start: 0.8668 (p0) cc_final: 0.8267 (p0) REVERT: B 208 ASP cc_start: 0.7519 (m-30) cc_final: 0.7239 (m-30) REVERT: B 300 GLU cc_start: 0.7972 (mp0) cc_final: 0.7611 (mm-30) REVERT: B 504 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7940 (mt) REVERT: B 554 ARG cc_start: 0.7636 (ptp-170) cc_final: 0.7327 (ptp-110) REVERT: B 593 SER cc_start: 0.8642 (t) cc_final: 0.8112 (p) REVERT: C 49 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.6533 (mpp80) REVERT: C 230 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8047 (pt) REVERT: C 325 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: C 330 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8217 (t0) REVERT: C 346 ARG cc_start: 0.9391 (OUTLIER) cc_final: 0.9121 (ttm170) REVERT: C 502 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8279 (m-80) REVERT: C 565 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7455 (t70) REVERT: C 893 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8445 (m110) REVERT: C 936 ASP cc_start: 0.8166 (t0) cc_final: 0.7790 (t0) REVERT: C 1024 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8610 (mmtm) outliers start: 147 outliers final: 118 residues processed: 350 average time/residue: 0.3335 time to fit residues: 193.4044 Evaluate side-chains 353 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 223 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 448 LYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 HIS Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1092 GLN Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 893 ASN Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 502 PHE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 CYS Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 CYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 893 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 917 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 980 ASP Chi-restraints excluded: chain C residue 1068 CYS Chi-restraints excluded: chain C residue 1086 THR Chi-restraints excluded: chain C residue 1103 THR Chi-restraints excluded: chain C residue 1118 ILE Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1127 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 297 optimal weight: 4.9990 chunk 251 optimal weight: 0.9980 chunk 265 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 217 optimal weight: 0.9990 chunk 301 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 893 ASN C 506 ASN C 893 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.131928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.111552 restraints weight = 33317.691| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.50 r_work: 0.3011 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26705 Z= 0.146 Angle : 0.574 9.345 36411 Z= 0.296 Chirality : 0.044 0.252 4247 Planarity : 0.004 0.043 4602 Dihedral : 7.504 79.714 4861 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.59 % Allowed : 19.76 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.14), residues: 3198 helix: 0.79 (0.20), residues: 744 sheet: 0.21 (0.19), residues: 729 loop : -1.67 (0.13), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 428 HIS 0.004 0.001 HIS C1044 PHE 0.022 0.001 PHE C 546 TYR 0.018 0.001 TYR C1053 ARG 0.005 0.000 ARG B1093 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 32) link_NAG-ASN : angle 2.01010 ( 96) link_BETA1-4 : bond 0.00464 ( 12) link_BETA1-4 : angle 1.87768 ( 36) link_ALPHA1-3 : bond 0.01344 ( 3) link_ALPHA1-3 : angle 2.50124 ( 9) hydrogen bonds : bond 0.05518 ( 915) hydrogen bonds : angle 5.21158 ( 2535) SS BOND : bond 0.00471 ( 45) SS BOND : angle 1.63636 ( 90) covalent geometry : bond 0.00349 (26613) covalent geometry : angle 0.55609 (36180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 223 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8907 (tp) REVERT: A 316 GLU cc_start: 0.7523 (mp0) cc_final: 0.7171 (mp0) REVERT: A 331 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: A 516 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7215 (mm-40) REVERT: A 554 ARG cc_start: 0.7506 (mtt-85) cc_final: 0.7050 (mtp85) REVERT: A 600 GLN cc_start: 0.8594 (tm-30) cc_final: 0.7979 (tt0) REVERT: A 696 ASN cc_start: 0.8136 (t0) cc_final: 0.7857 (t0) REVERT: A 830 VAL cc_start: 0.4444 (OUTLIER) cc_final: 0.4067 (t) REVERT: A 888 MET cc_start: 0.8685 (mmm) cc_final: 0.8298 (mmm) REVERT: A 890 TYR cc_start: 0.8411 (t80) cc_final: 0.8197 (t80) REVERT: A 1093 ARG cc_start: 0.7900 (ttm-80) cc_final: 0.7533 (mtt90) REVERT: B 133 ASP cc_start: 0.8572 (p0) cc_final: 0.8259 (p0) REVERT: B 208 ASP cc_start: 0.7527 (m-30) cc_final: 0.7242 (m-30) REVERT: B 300 GLU cc_start: 0.7934 (mp0) cc_final: 0.7650 (mm-30) REVERT: B 323 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7462 (mt) REVERT: B 504 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7931 (mt) REVERT: B 554 ARG cc_start: 0.7630 (ptp-170) cc_final: 0.7336 (ptp-110) REVERT: B 593 SER cc_start: 0.8617 (t) cc_final: 0.8114 (p) REVERT: B 1092 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8123 (mt0) REVERT: C 49 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.6567 (mpp80) REVERT: C 230 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8021 (pt) REVERT: C 325 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: C 330 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8222 (t0) REVERT: C 346 ARG cc_start: 0.9387 (OUTLIER) cc_final: 0.9124 (ttm170) REVERT: C 502 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8260 (m-80) REVERT: C 518 THR cc_start: 0.7654 (OUTLIER) cc_final: 0.7091 (p) REVERT: C 565 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7413 (t70) REVERT: C 893 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8440 (m110) REVERT: C 936 ASP cc_start: 0.8147 (t0) cc_final: 0.7919 (t0) REVERT: C 1024 LYS cc_start: 0.8842 (mmmm) cc_final: 0.8609 (mmtm) outliers start: 156 outliers final: 126 residues processed: 355 average time/residue: 0.3286 time to fit residues: 192.9180 Evaluate side-chains 361 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 220 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 HIS Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1092 GLN Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 893 ASN Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain B residue 1092 GLN Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 502 PHE Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 CYS Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 CYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 893 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 980 ASP Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1068 CYS Chi-restraints excluded: chain C residue 1086 THR Chi-restraints excluded: chain C residue 1103 THR Chi-restraints excluded: chain C residue 1118 ILE Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1127 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 130 optimal weight: 10.0000 chunk 271 optimal weight: 8.9990 chunk 262 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 213 optimal weight: 0.0870 chunk 221 optimal weight: 8.9990 chunk 242 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 219 optimal weight: 10.0000 chunk 279 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 overall best weight: 2.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 893 ASN B 905 ASN B 940 GLN C 506 ASN C 893 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.110067 restraints weight = 33386.906| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.50 r_work: 0.2993 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 26705 Z= 0.193 Angle : 0.623 9.992 36411 Z= 0.320 Chirality : 0.046 0.257 4247 Planarity : 0.004 0.046 4602 Dihedral : 7.667 74.358 4861 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 5.91 % Allowed : 19.62 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.98 (0.14), residues: 3198 helix: 0.71 (0.20), residues: 744 sheet: 0.18 (0.19), residues: 729 loop : -1.70 (0.13), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 428 HIS 0.005 0.001 HIS C1044 PHE 0.029 0.002 PHE C 546 TYR 0.019 0.002 TYR B 256 ARG 0.004 0.000 ARG B1093 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 32) link_NAG-ASN : angle 2.06389 ( 96) link_BETA1-4 : bond 0.00530 ( 12) link_BETA1-4 : angle 1.99835 ( 36) link_ALPHA1-3 : bond 0.01300 ( 3) link_ALPHA1-3 : angle 2.55281 ( 9) hydrogen bonds : bond 0.06142 ( 915) hydrogen bonds : angle 5.29174 ( 2535) SS BOND : bond 0.00615 ( 45) SS BOND : angle 1.79531 ( 90) covalent geometry : bond 0.00473 (26613) covalent geometry : angle 0.60435 (36180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 218 time to evaluate : 2.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 GLU cc_start: 0.7530 (mp0) cc_final: 0.7152 (mp0) REVERT: A 331 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: A 448 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8082 (ttmm) REVERT: A 516 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7256 (mm-40) REVERT: A 554 ARG cc_start: 0.7575 (mtt-85) cc_final: 0.7070 (mtp85) REVERT: A 600 GLN cc_start: 0.8554 (tm-30) cc_final: 0.7944 (tt0) REVERT: A 696 ASN cc_start: 0.8156 (t0) cc_final: 0.7876 (t0) REVERT: A 888 MET cc_start: 0.8705 (mmm) cc_final: 0.8311 (mmm) REVERT: A 890 TYR cc_start: 0.8444 (t80) cc_final: 0.8198 (t80) REVERT: A 1093 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7542 (mtt90) REVERT: B 133 ASP cc_start: 0.8654 (p0) cc_final: 0.8322 (p0) REVERT: B 208 ASP cc_start: 0.7524 (m-30) cc_final: 0.7237 (m-30) REVERT: B 300 GLU cc_start: 0.7937 (mp0) cc_final: 0.7655 (mm-30) REVERT: B 504 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8192 (mt) REVERT: B 554 ARG cc_start: 0.7464 (ptp-170) cc_final: 0.7163 (ptp-110) REVERT: B 593 SER cc_start: 0.8611 (t) cc_final: 0.8109 (p) REVERT: B 1092 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: C 49 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.6586 (mpp80) REVERT: C 230 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8179 (pt) REVERT: C 325 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: C 330 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8240 (t0) REVERT: C 346 ARG cc_start: 0.9396 (OUTLIER) cc_final: 0.9131 (ttm170) REVERT: C 502 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8340 (m-80) REVERT: C 565 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7394 (t70) REVERT: C 893 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8416 (m110) REVERT: C 1024 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8619 (mmtm) outliers start: 165 outliers final: 133 residues processed: 360 average time/residue: 0.3659 time to fit residues: 221.3129 Evaluate side-chains 359 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 214 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 448 LYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 HIS Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1092 GLN Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 893 ASN Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain B residue 1092 GLN Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 502 PHE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 CYS Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 CYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 893 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 980 ASP Chi-restraints excluded: chain C residue 1068 CYS Chi-restraints excluded: chain C residue 1086 THR Chi-restraints excluded: chain C residue 1103 THR Chi-restraints excluded: chain C residue 1118 ILE Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1127 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 291 optimal weight: 0.4980 chunk 145 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 725 ASN B 893 ASN C 506 ASN C 893 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.111083 restraints weight = 33406.839| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.52 r_work: 0.3006 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26705 Z= 0.149 Angle : 0.589 9.818 36411 Z= 0.303 Chirality : 0.044 0.251 4247 Planarity : 0.004 0.045 4602 Dihedral : 7.516 67.971 4861 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.44 % Allowed : 20.37 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.14), residues: 3198 helix: 0.79 (0.20), residues: 744 sheet: 0.19 (0.19), residues: 729 loop : -1.69 (0.13), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 428 HIS 0.004 0.001 HIS A 202 PHE 0.022 0.001 PHE C 546 TYR 0.018 0.001 TYR C1053 ARG 0.005 0.000 ARG B1093 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 32) link_NAG-ASN : angle 2.02817 ( 96) link_BETA1-4 : bond 0.00474 ( 12) link_BETA1-4 : angle 1.91851 ( 36) link_ALPHA1-3 : bond 0.01327 ( 3) link_ALPHA1-3 : angle 2.46469 ( 9) hydrogen bonds : bond 0.05669 ( 915) hydrogen bonds : angle 5.22282 ( 2535) SS BOND : bond 0.00501 ( 45) SS BOND : angle 1.64001 ( 90) covalent geometry : bond 0.00354 (26613) covalent geometry : angle 0.57133 (36180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 217 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 GLU cc_start: 0.7521 (mp0) cc_final: 0.7153 (mp0) REVERT: A 331 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: A 448 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8076 (ttmm) REVERT: A 516 GLN cc_start: 0.7618 (mm-40) cc_final: 0.7217 (mm-40) REVERT: A 554 ARG cc_start: 0.7552 (mtt-85) cc_final: 0.7108 (mtp85) REVERT: A 600 GLN cc_start: 0.8525 (tm-30) cc_final: 0.7932 (tt0) REVERT: A 696 ASN cc_start: 0.8089 (t0) cc_final: 0.7846 (t0) REVERT: A 888 MET cc_start: 0.8700 (mmm) cc_final: 0.8305 (mmm) REVERT: A 890 TYR cc_start: 0.8437 (t80) cc_final: 0.8217 (t80) REVERT: A 1093 ARG cc_start: 0.7914 (ttm-80) cc_final: 0.7534 (mtt90) REVERT: B 133 ASP cc_start: 0.8607 (p0) cc_final: 0.8300 (p0) REVERT: B 208 ASP cc_start: 0.7486 (m-30) cc_final: 0.7197 (m-30) REVERT: B 300 GLU cc_start: 0.7907 (mp0) cc_final: 0.7643 (mm-30) REVERT: B 323 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7432 (mt) REVERT: B 504 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7965 (mt) REVERT: B 554 ARG cc_start: 0.7623 (ptp-170) cc_final: 0.7318 (ptp-110) REVERT: B 593 SER cc_start: 0.8518 (t) cc_final: 0.8059 (p) REVERT: B 1092 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8151 (mt0) REVERT: C 49 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.6567 (mpp80) REVERT: C 230 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8054 (pt) REVERT: C 325 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: C 330 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8232 (t0) REVERT: C 346 ARG cc_start: 0.9393 (OUTLIER) cc_final: 0.9134 (ttm170) REVERT: C 502 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8260 (m-80) REVERT: C 565 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7410 (t70) REVERT: C 893 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8393 (m110) REVERT: C 1024 LYS cc_start: 0.8837 (mmmm) cc_final: 0.8614 (mmtm) outliers start: 152 outliers final: 132 residues processed: 346 average time/residue: 0.3491 time to fit residues: 200.5628 Evaluate side-chains 362 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 217 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 448 LYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 HIS Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1092 GLN Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 893 ASN Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain B residue 1092 GLN Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 502 PHE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 CYS Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 CYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 893 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 917 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 980 ASP Chi-restraints excluded: chain C residue 1068 CYS Chi-restraints excluded: chain C residue 1086 THR Chi-restraints excluded: chain C residue 1103 THR Chi-restraints excluded: chain C residue 1118 ILE Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1127 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 301 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 306 optimal weight: 4.9990 chunk 285 optimal weight: 0.7980 chunk 276 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 205 optimal weight: 0.7980 chunk 288 optimal weight: 0.0270 chunk 9 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 893 ASN C 189 HIS C 506 ASN C 760 GLN C 790 GLN C 893 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.133731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113573 restraints weight = 33223.985| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.48 r_work: 0.3047 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 26705 Z= 0.104 Angle : 0.534 9.817 36411 Z= 0.276 Chirality : 0.043 0.234 4247 Planarity : 0.003 0.040 4602 Dihedral : 7.013 59.626 4859 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.22 % Allowed : 21.52 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.14), residues: 3198 helix: 0.97 (0.20), residues: 744 sheet: 0.25 (0.19), residues: 729 loop : -1.62 (0.13), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 428 HIS 0.002 0.000 HIS C1074 PHE 0.013 0.001 PHE C 549 TYR 0.017 0.001 TYR C1053 ARG 0.004 0.000 ARG B1093 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 32) link_NAG-ASN : angle 1.94371 ( 96) link_BETA1-4 : bond 0.00418 ( 12) link_BETA1-4 : angle 1.79098 ( 36) link_ALPHA1-3 : bond 0.01262 ( 3) link_ALPHA1-3 : angle 2.18630 ( 9) hydrogen bonds : bond 0.04735 ( 915) hydrogen bonds : angle 5.06616 ( 2535) SS BOND : bond 0.00379 ( 45) SS BOND : angle 1.34828 ( 90) covalent geometry : bond 0.00225 (26613) covalent geometry : angle 0.51804 (36180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 226 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 GLU cc_start: 0.7483 (mp0) cc_final: 0.7122 (mp0) REVERT: A 331 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: A 516 GLN cc_start: 0.7604 (mm-40) cc_final: 0.7219 (mm-40) REVERT: A 554 ARG cc_start: 0.7489 (mtt-85) cc_final: 0.7125 (mtp85) REVERT: A 600 GLN cc_start: 0.8546 (tm-30) cc_final: 0.7962 (tt0) REVERT: A 678 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8642 (mt) REVERT: A 696 ASN cc_start: 0.8128 (t0) cc_final: 0.7902 (t0) REVERT: A 888 MET cc_start: 0.8694 (mmm) cc_final: 0.8310 (mmm) REVERT: A 890 TYR cc_start: 0.8412 (t80) cc_final: 0.8208 (t80) REVERT: A 1093 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.7544 (mtt90) REVERT: B 133 ASP cc_start: 0.8438 (p0) cc_final: 0.8187 (p0) REVERT: B 208 ASP cc_start: 0.7480 (m-30) cc_final: 0.7173 (m-30) REVERT: B 504 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7736 (mt) REVERT: B 554 ARG cc_start: 0.7601 (ptp-170) cc_final: 0.7311 (ptp-110) REVERT: B 593 SER cc_start: 0.8528 (t) cc_final: 0.8063 (p) REVERT: B 966 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8178 (mt) REVERT: B 1107 PHE cc_start: 0.8415 (p90) cc_final: 0.8083 (p90) REVERT: C 49 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.6534 (mpp80) REVERT: C 230 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7875 (pt) REVERT: C 325 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: C 346 ARG cc_start: 0.9391 (OUTLIER) cc_final: 0.9169 (ttm170) REVERT: C 502 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8095 (m-80) REVERT: C 565 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7388 (t70) REVERT: C 760 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8476 (mm-40) REVERT: C 893 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8514 (m110) REVERT: C 1024 LYS cc_start: 0.8832 (mmmm) cc_final: 0.8587 (mmtm) REVERT: C 1036 MET cc_start: 0.8724 (mtm) cc_final: 0.8471 (mtp) outliers start: 118 outliers final: 95 residues processed: 326 average time/residue: 0.3464 time to fit residues: 187.0918 Evaluate side-chains 330 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 223 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 HIS Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1092 GLN Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 893 ASN Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 502 PHE Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 CYS Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 CYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 893 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 980 ASP Chi-restraints excluded: chain C residue 1068 CYS Chi-restraints excluded: chain C residue 1118 ILE Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1127 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 19 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 315 optimal weight: 10.0000 chunk 314 optimal weight: 0.9990 chunk 316 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 165 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 ASN C 760 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.133721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.112777 restraints weight = 33480.057| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.59 r_work: 0.3013 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.176 26705 Z= 0.155 Angle : 0.691 59.183 36411 Z= 0.382 Chirality : 0.043 0.234 4247 Planarity : 0.004 0.096 4602 Dihedral : 6.960 59.631 4854 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.08 % Allowed : 21.63 % Favored : 74.29 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % 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: -0.79 (0.14), residues: 3198 helix: 1.00 (0.20), residues: 744 sheet: 0.25 (0.19), residues: 729 loop : -1.62 (0.13), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 428 HIS 0.002 0.000 HIS C1074 PHE 0.013 0.001 PHE C 549 TYR 0.017 0.001 TYR C1053 ARG 0.003 0.000 ARG C 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 32) link_NAG-ASN : angle 1.94123 ( 96) link_BETA1-4 : bond 0.00393 ( 12) link_BETA1-4 : angle 1.79177 ( 36) link_ALPHA1-3 : bond 0.01337 ( 3) link_ALPHA1-3 : angle 2.39899 ( 9) hydrogen bonds : bond 0.04816 ( 915) hydrogen bonds : angle 5.07193 ( 2535) SS BOND : bond 0.00683 ( 45) SS BOND : angle 2.31014 ( 90) covalent geometry : bond 0.00325 (26613) covalent geometry : angle 0.67261 (36180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13593.61 seconds wall clock time: 234 minutes 14.09 seconds (14054.09 seconds total)