Starting phenix.real_space_refine on Sun Jun 22 09:59:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c1v_16383/06_2025/8c1v_16383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c1v_16383/06_2025/8c1v_16383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c1v_16383/06_2025/8c1v_16383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c1v_16383/06_2025/8c1v_16383.map" model { file = "/net/cci-nas-00/data/ceres_data/8c1v_16383/06_2025/8c1v_16383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c1v_16383/06_2025/8c1v_16383.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 16329 2.51 5 N 4158 2.21 5 O 4998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25590 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7822 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 954} Chain breaks: 8 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 7822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7822 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 954} Chain breaks: 8 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 7822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7822 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 954} Chain breaks: 8 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 470 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "E" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 470 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "F" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 470 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} 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: "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: "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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: "C" 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: 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 Time building chain proxies: 16.33, per 1000 atoms: 0.64 Number of scatterers: 25590 At special positions: 0 Unit cell: (140.22, 132.84, 191.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4998 8.00 N 4158 7.00 C 16329 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A1098 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 234 " " NAG A1311 " - " ASN A 603 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 343 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 61 " " NAG B1310 " - " ASN B 234 " " NAG B1311 " - " ASN B 603 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 343 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 234 " " NAG C1311 " - " ASN C 603 " " NAG C1312 " - " ASN C 165 " " NAG C1313 " - " ASN C 343 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN C 717 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN C1134 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B1134 " Time building additional restraints: 6.14 Conformation dependent library (CDL) restraints added in 3.2 seconds 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5982 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 45 sheets defined 22.9% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.566A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.626A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.409A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 390' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.740A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.722A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.673A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.908A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.676A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 937 removed outlier: 3.699A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 966 removed outlier: 4.367A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.618A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.045A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.736A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.654A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.626A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 385 through 390 removed outlier: 4.408A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 390' Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.741A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 738 through 743 removed outlier: 3.961A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.679A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.885A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.578A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.558A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 938 removed outlier: 3.684A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 938 " --> pdb=" O ILE C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 967 removed outlier: 4.283A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN C 953 " --> pdb=" O GLN C 949 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.574A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.032A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.969A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.558A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.626A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 385 through 390 removed outlier: 4.409A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 390' Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.740A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 738 through 743 removed outlier: 4.055A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.008A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.608A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.628A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.098A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.585A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.349A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.504A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 967 removed outlier: 4.274A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN B 953 " --> pdb=" O GLN B 949 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.595A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.020A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.018A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.540A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 210 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 10.038A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.728A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.824A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.972A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 7.248A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.897A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.881A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.528A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.807A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.807A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.202A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.358A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.796A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.718A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.174A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.292A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 311 through 318 removed outlier: 7.193A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.897A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.473A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.505A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.505A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.251A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AD2, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.683A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.505A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.110A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.369A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 311 through 318 removed outlier: 7.297A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.897A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.132A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.749A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.749A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.210A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE7, first strand: chain 'D' and resid 48 through 52 removed outlier: 4.327A pdb=" N GLY D 49 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA D 41 " --> pdb=" O GLY D 49 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D 26 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU D 25 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR D 3 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE D 4 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU D 57 " --> pdb=" O ILE D 4 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 48 through 52 removed outlier: 4.328A pdb=" N GLY E 49 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA E 41 " --> pdb=" O GLY E 49 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU E 26 " --> pdb=" O LYS E 42 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU E 25 " --> pdb=" O TYR E 3 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR E 3 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE E 4 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU E 57 " --> pdb=" O ILE E 4 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 48 through 52 removed outlier: 4.326A pdb=" N GLY F 49 " --> pdb=" O ALA F 41 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA F 41 " --> pdb=" O GLY F 49 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU F 26 " --> pdb=" O LYS F 42 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU F 25 " --> pdb=" O TYR F 3 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR F 3 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE F 4 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU F 57 " --> pdb=" O ILE F 4 " (cutoff:3.500A) 890 hydrogen bonds defined for protein. 2454 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.61 Time building geometry restraints manager: 7.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8101 1.34 - 1.47: 6598 1.47 - 1.59: 11332 1.59 - 1.72: 0 1.72 - 1.84: 129 Bond restraints: 26160 Sorted by residual: bond pdb=" N PHE B 329 " pdb=" CA PHE B 329 " ideal model delta sigma weight residual 1.455 1.434 0.021 7.00e-03 2.04e+04 8.72e+00 bond pdb=" N PHE E 10 " pdb=" CA PHE E 10 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.23e-02 6.61e+03 5.75e+00 bond pdb=" N PHE F 10 " pdb=" CA PHE F 10 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.23e-02 6.61e+03 5.68e+00 bond pdb=" N PHE D 10 " pdb=" CA PHE D 10 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.23e-02 6.61e+03 5.49e+00 bond pdb=" CA ILE B 332 " pdb=" C ILE B 332 " ideal model delta sigma weight residual 1.524 1.506 0.019 8.60e-03 1.35e+04 4.63e+00 ... (remaining 26155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 35143 2.42 - 4.84: 418 4.84 - 7.26: 25 7.26 - 9.68: 12 9.68 - 12.10: 3 Bond angle restraints: 35601 Sorted by residual: angle pdb=" N LYS A 529 " pdb=" CA LYS A 529 " pdb=" C LYS A 529 " ideal model delta sigma weight residual 111.28 120.42 -9.14 1.09e+00 8.42e-01 7.04e+01 angle pdb=" C PHE A 329 " pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta sigma weight residual 119.78 128.21 -8.43 1.03e+00 9.43e-01 6.70e+01 angle pdb=" N ASN A 331 " pdb=" CA ASN A 331 " pdb=" C ASN A 331 " ideal model delta sigma weight residual 109.96 98.61 11.35 1.49e+00 4.50e-01 5.80e+01 angle pdb=" C PHE B 329 " pdb=" N PRO B 330 " pdb=" CA PRO B 330 " ideal model delta sigma weight residual 119.78 127.15 -7.37 1.03e+00 9.43e-01 5.12e+01 angle pdb=" N ILE A 332 " pdb=" CA ILE A 332 " pdb=" C ILE A 332 " ideal model delta sigma weight residual 108.65 118.46 -9.81 1.45e+00 4.76e-01 4.58e+01 ... (remaining 35596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 14508 17.10 - 34.20: 1328 34.20 - 51.30: 297 51.30 - 68.40: 55 68.40 - 85.50: 30 Dihedral angle restraints: 16218 sinusoidal: 6927 harmonic: 9291 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -0.50 -85.50 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -0.52 -85.48 1 1.00e+01 1.00e-02 8.84e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -16.53 -69.47 1 1.00e+01 1.00e-02 6.23e+01 ... (remaining 16215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3764 0.088 - 0.175: 408 0.175 - 0.263: 12 0.263 - 0.350: 7 0.350 - 0.438: 3 Chirality restraints: 4194 Sorted by residual: chirality pdb=" CA CYS A 336 " pdb=" N CYS A 336 " pdb=" C CYS A 336 " pdb=" CB CYS A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 4191 not shown) Planarity restraints: 4584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " -0.066 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO A 337 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.031 2.00e-02 2.50e+03 2.73e-02 9.30e+00 pdb=" CG ASN A 331 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.031 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 327 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.44e+00 pdb=" C VAL B 327 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL B 327 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG B 328 " -0.017 2.00e-02 2.50e+03 ... (remaining 4581 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 92 2.44 - 3.05: 17007 3.05 - 3.67: 38091 3.67 - 4.28: 55476 4.28 - 4.90: 92144 Nonbonded interactions: 202810 Sorted by model distance: nonbonded pdb=" OG SER B 530 " pdb=" OE1 GLN B 580 " model vdw 1.819 3.040 nonbonded pdb=" O PRO C 412 " pdb=" CG2 THR E 54 " model vdw 1.923 3.460 nonbonded pdb=" O PRO B 412 " pdb=" CG2 THR F 54 " model vdw 1.923 3.460 nonbonded pdb=" O PRO A 412 " pdb=" CG2 THR D 54 " model vdw 1.924 3.460 nonbonded pdb=" OE1 GLN B 414 " pdb=" CA GLY F 37 " model vdw 1.992 3.440 ... (remaining 202805 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.060 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 60.040 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.150 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:13.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 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 : 0.004 0.077 26250 Z= 0.184 Angle : 0.620 16.402 35832 Z= 0.340 Chirality : 0.048 0.438 4194 Planarity : 0.004 0.102 4539 Dihedral : 13.676 80.638 10119 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.40 % Favored : 95.57 % Rotamer: Outliers : 0.40 % Allowed : 1.09 % Favored : 98.51 % Cbeta Deviations : 0.03 % 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: -0.12 (0.15), residues: 3138 helix: 1.69 (0.24), residues: 579 sheet: 0.59 (0.22), residues: 591 loop : -0.87 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 886 HIS 0.002 0.000 HIS C1088 PHE 0.033 0.001 PHE E 10 TYR 0.008 0.001 TYR B 904 ARG 0.005 0.000 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.01310 ( 45) link_NAG-ASN : angle 2.27889 ( 135) link_BETA1-4 : bond 0.00241 ( 6) link_BETA1-4 : angle 0.97587 ( 18) hydrogen bonds : bond 0.26393 ( 856) hydrogen bonds : angle 9.41164 ( 2454) SS BOND : bond 0.00432 ( 39) SS BOND : angle 0.99082 ( 78) covalent geometry : bond 0.00350 (26160) covalent geometry : angle 0.60347 (35601) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 468 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 ILE cc_start: 0.6908 (mt) cc_final: 0.6638 (pt) REVERT: B 203 ILE cc_start: 0.6616 (mm) cc_final: 0.6338 (mm) REVERT: B 269 TYR cc_start: 0.7926 (m-80) cc_final: 0.7412 (m-80) outliers start: 11 outliers final: 5 residues processed: 479 average time/residue: 1.0214 time to fit residues: 597.0921 Evaluate side-chains 200 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 195 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.7980 chunk 241 optimal weight: 40.0000 chunk 133 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 249 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 chunk 288 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 450 ASN A 901 GLN A1002 GLN A1101 HIS A1135 ASN C 52 GLN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 907 ASN C 969 ASN C1036 GLN B 907 ASN B1002 GLN B1010 GLN B1054 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.154165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.102390 restraints weight = 55049.233| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.75 r_work: 0.3513 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26250 Z= 0.179 Angle : 0.659 12.715 35832 Z= 0.333 Chirality : 0.048 0.224 4194 Planarity : 0.004 0.063 4539 Dihedral : 6.731 59.859 4491 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.84 % Allowed : 11.92 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.57 (0.15), residues: 3138 helix: 0.89 (0.21), residues: 639 sheet: 0.21 (0.20), residues: 630 loop : -1.07 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 353 HIS 0.006 0.001 HIS A1064 PHE 0.019 0.002 PHE C 92 TYR 0.019 0.002 TYR C 170 ARG 0.007 0.001 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 45) link_NAG-ASN : angle 1.62071 ( 135) link_BETA1-4 : bond 0.00348 ( 6) link_BETA1-4 : angle 0.89455 ( 18) hydrogen bonds : bond 0.04662 ( 856) hydrogen bonds : angle 6.41172 ( 2454) SS BOND : bond 0.00488 ( 39) SS BOND : angle 1.41210 ( 78) covalent geometry : bond 0.00404 (26160) covalent geometry : angle 0.64950 (35601) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 209 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8472 (m-80) cc_final: 0.8259 (m-80) REVERT: A 365 TYR cc_start: 0.8437 (m-80) cc_final: 0.8082 (m-10) REVERT: A 765 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8342 (ptp-110) REVERT: A 981 LEU cc_start: 0.8601 (mt) cc_final: 0.7756 (pp) REVERT: C 58 PHE cc_start: 0.7965 (m-10) cc_final: 0.7757 (m-10) REVERT: C 269 TYR cc_start: 0.8294 (m-80) cc_final: 0.7969 (m-80) REVERT: B 332 ILE cc_start: 0.8431 (mm) cc_final: 0.8216 (tp) REVERT: B 699 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7238 (mt) REVERT: B 855 PHE cc_start: 0.6212 (p90) cc_final: 0.5900 (p90) REVERT: B 947 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8309 (mttp) outliers start: 78 outliers final: 29 residues processed: 267 average time/residue: 1.0043 time to fit residues: 328.3899 Evaluate side-chains 171 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain E residue 3 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 83 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 295 optimal weight: 0.0970 chunk 142 optimal weight: 0.0570 chunk 100 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 148 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN C 957 GLN B 957 GLN E 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.152609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.099955 restraints weight = 54072.714| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.25 r_work: 0.3447 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26250 Z= 0.136 Angle : 0.576 9.919 35832 Z= 0.289 Chirality : 0.046 0.213 4194 Planarity : 0.004 0.077 4539 Dihedral : 6.040 59.929 4485 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.62 % Allowed : 14.29 % Favored : 83.10 % 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: -0.65 (0.14), residues: 3138 helix: 0.76 (0.21), residues: 651 sheet: 0.22 (0.20), residues: 627 loop : -1.14 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 38 HIS 0.004 0.001 HIS A1064 PHE 0.014 0.001 PHE A 65 TYR 0.021 0.001 TYR F 3 ARG 0.009 0.001 ARG E 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 45) link_NAG-ASN : angle 1.61091 ( 135) link_BETA1-4 : bond 0.00358 ( 6) link_BETA1-4 : angle 0.90080 ( 18) hydrogen bonds : bond 0.04088 ( 856) hydrogen bonds : angle 5.95939 ( 2454) SS BOND : bond 0.00307 ( 39) SS BOND : angle 0.90047 ( 78) covalent geometry : bond 0.00314 (26160) covalent geometry : angle 0.56735 (35601) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 163 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8595 (m-80) cc_final: 0.8288 (m-80) REVERT: A 203 ILE cc_start: 0.7156 (mm) cc_final: 0.6915 (mp) REVERT: A 269 TYR cc_start: 0.8577 (m-80) cc_final: 0.8318 (m-10) REVERT: A 740 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.6906 (tmt) REVERT: A 855 PHE cc_start: 0.5670 (OUTLIER) cc_final: 0.5009 (p90) REVERT: A 947 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8373 (mptt) REVERT: C 332 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.6337 (tp) REVERT: C 697 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7304 (mtt) REVERT: C 1050 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8508 (ptp) REVERT: B 66 HIS cc_start: 0.6607 (OUTLIER) cc_final: 0.6203 (t-170) REVERT: B 773 GLU cc_start: 0.8785 (tt0) cc_final: 0.8582 (tt0) REVERT: B 776 LYS cc_start: 0.9081 (ttpt) cc_final: 0.8869 (tttm) REVERT: B 947 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8066 (mttp) REVERT: B 1050 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8741 (ptm) REVERT: E 39 TRP cc_start: 0.8279 (m-10) cc_final: 0.7836 (t-100) outliers start: 72 outliers final: 29 residues processed: 216 average time/residue: 0.8028 time to fit residues: 222.2052 Evaluate side-chains 172 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain E residue 3 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 54 optimal weight: 0.9990 chunk 264 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 317 optimal weight: 7.9990 chunk 151 optimal weight: 0.5980 chunk 218 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 978 ASN C1005 GLN B 87 ASN B 450 ASN B 658 ASN B 957 GLN B1005 GLN F 47 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.146975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.093022 restraints weight = 52926.307| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.17 r_work: 0.3286 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 26250 Z= 0.217 Angle : 0.645 10.817 35832 Z= 0.323 Chirality : 0.048 0.254 4194 Planarity : 0.004 0.062 4539 Dihedral : 5.968 59.842 4482 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.93 % Allowed : 15.16 % Favored : 80.92 % 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: -0.84 (0.14), residues: 3138 helix: 0.33 (0.20), residues: 660 sheet: 0.24 (0.19), residues: 666 loop : -1.23 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 353 HIS 0.006 0.001 HIS C1088 PHE 0.025 0.002 PHE C 92 TYR 0.020 0.002 TYR F 3 ARG 0.009 0.001 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 45) link_NAG-ASN : angle 1.89904 ( 135) link_BETA1-4 : bond 0.00917 ( 6) link_BETA1-4 : angle 1.24074 ( 18) hydrogen bonds : bond 0.03964 ( 856) hydrogen bonds : angle 5.95883 ( 2454) SS BOND : bond 0.00642 ( 39) SS BOND : angle 1.66689 ( 78) covalent geometry : bond 0.00513 (26160) covalent geometry : angle 0.63065 (35601) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 137 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8822 (m-80) cc_final: 0.8449 (m-80) REVERT: A 318 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.8052 (p90) REVERT: A 365 TYR cc_start: 0.8169 (m-10) cc_final: 0.7861 (m-10) REVERT: A 740 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7471 (tmt) REVERT: A 947 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8392 (mptt) REVERT: A 1076 THR cc_start: 0.9434 (OUTLIER) cc_final: 0.9156 (p) REVERT: C 332 ILE cc_start: 0.6694 (OUTLIER) cc_final: 0.6436 (tp) REVERT: C 342 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7701 (t80) REVERT: C 581 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8196 (p) REVERT: C 934 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8369 (mp) REVERT: B 66 HIS cc_start: 0.7022 (OUTLIER) cc_final: 0.6583 (t-170) REVERT: B 755 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8523 (tp-100) REVERT: B 776 LYS cc_start: 0.9208 (ttpt) cc_final: 0.8994 (tttp) REVERT: B 855 PHE cc_start: 0.6313 (OUTLIER) cc_final: 0.5998 (p90) outliers start: 108 outliers final: 41 residues processed: 226 average time/residue: 1.0811 time to fit residues: 313.4179 Evaluate side-chains 165 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 113 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain E residue 3 TYR Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain F residue 50 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 147 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 139 optimal weight: 30.0000 chunk 101 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 97 optimal weight: 0.1980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 957 GLN A 978 ASN C 774 GLN C1005 GLN B 125 ASN B 957 GLN B1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.147318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.093114 restraints weight = 53358.149| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.72 r_work: 0.3324 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26250 Z= 0.147 Angle : 0.574 10.506 35832 Z= 0.284 Chirality : 0.046 0.237 4194 Planarity : 0.004 0.060 4539 Dihedral : 5.710 59.381 4482 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.42 % Allowed : 16.58 % Favored : 80.01 % 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: -0.89 (0.14), residues: 3138 helix: 0.44 (0.20), residues: 651 sheet: 0.08 (0.18), residues: 693 loop : -1.29 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 64 HIS 0.003 0.001 HIS A1088 PHE 0.020 0.001 PHE C 92 TYR 0.021 0.001 TYR B 365 ARG 0.006 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 45) link_NAG-ASN : angle 1.78914 ( 135) link_BETA1-4 : bond 0.00390 ( 6) link_BETA1-4 : angle 0.98433 ( 18) hydrogen bonds : bond 0.03525 ( 856) hydrogen bonds : angle 5.70878 ( 2454) SS BOND : bond 0.00365 ( 39) SS BOND : angle 1.04466 ( 78) covalent geometry : bond 0.00348 (26160) covalent geometry : angle 0.56239 (35601) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 118 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8781 (m-80) cc_final: 0.8445 (m-80) REVERT: A 269 TYR cc_start: 0.8472 (m-10) cc_final: 0.8230 (m-10) REVERT: A 360 ASN cc_start: 0.7978 (m-40) cc_final: 0.7485 (p0) REVERT: A 365 TYR cc_start: 0.8245 (m-10) cc_final: 0.8043 (m-10) REVERT: A 581 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8058 (p) REVERT: A 855 PHE cc_start: 0.5792 (OUTLIER) cc_final: 0.4955 (p90) REVERT: A 947 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8305 (mptt) REVERT: A 1076 THR cc_start: 0.9425 (OUTLIER) cc_final: 0.9211 (p) REVERT: C 332 ILE cc_start: 0.6662 (OUTLIER) cc_final: 0.6424 (OUTLIER) REVERT: C 581 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8157 (p) REVERT: C 696 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8559 (t) REVERT: B 111 ASP cc_start: 0.7944 (p0) cc_final: 0.7164 (p0) REVERT: B 754 LEU cc_start: 0.9142 (pp) cc_final: 0.8938 (pt) REVERT: B 855 PHE cc_start: 0.6353 (OUTLIER) cc_final: 0.5993 (p90) REVERT: E 50 LEU cc_start: 0.8741 (tp) cc_final: 0.8523 (tp) outliers start: 94 outliers final: 37 residues processed: 195 average time/residue: 0.7647 time to fit residues: 194.1578 Evaluate side-chains 151 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 107 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain E residue 3 TYR Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 32 optimal weight: 30.0000 chunk 220 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 181 optimal weight: 0.4980 chunk 152 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 290 optimal weight: 0.0370 chunk 45 optimal weight: 6.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 957 GLN A1005 GLN C1005 GLN B 957 GLN B1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.146483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.091411 restraints weight = 52684.465| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.73 r_work: 0.3291 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26250 Z= 0.154 Angle : 0.579 10.532 35832 Z= 0.286 Chirality : 0.046 0.245 4194 Planarity : 0.004 0.061 4539 Dihedral : 5.574 59.372 4482 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.89 % Allowed : 16.43 % Favored : 79.68 % 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: -0.90 (0.14), residues: 3138 helix: 0.45 (0.20), residues: 654 sheet: -0.04 (0.18), residues: 711 loop : -1.26 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 104 HIS 0.003 0.001 HIS A1088 PHE 0.019 0.001 PHE C 92 TYR 0.017 0.001 TYR D 55 ARG 0.006 0.000 ARG D 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 45) link_NAG-ASN : angle 1.81361 ( 135) link_BETA1-4 : bond 0.00281 ( 6) link_BETA1-4 : angle 0.95338 ( 18) hydrogen bonds : bond 0.03437 ( 856) hydrogen bonds : angle 5.61472 ( 2454) SS BOND : bond 0.00417 ( 39) SS BOND : angle 1.13284 ( 78) covalent geometry : bond 0.00365 (26160) covalent geometry : angle 0.56696 (35601) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 111 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8807 (m-80) cc_final: 0.8448 (m-80) REVERT: A 269 TYR cc_start: 0.8462 (m-10) cc_final: 0.8154 (m-10) REVERT: A 318 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7893 (p90) REVERT: A 360 ASN cc_start: 0.7949 (m-40) cc_final: 0.7505 (p0) REVERT: A 365 TYR cc_start: 0.8234 (m-10) cc_final: 0.7926 (m-10) REVERT: A 581 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8091 (p) REVERT: A 855 PHE cc_start: 0.5850 (OUTLIER) cc_final: 0.5649 (p90) REVERT: A 947 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8281 (mptt) REVERT: C 118 LEU cc_start: 0.7088 (mp) cc_final: 0.6690 (tp) REVERT: C 332 ILE cc_start: 0.6658 (OUTLIER) cc_final: 0.6394 (OUTLIER) REVERT: C 696 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8517 (t) REVERT: C 725 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8624 (tt0) REVERT: B 66 HIS cc_start: 0.7006 (OUTLIER) cc_final: 0.6607 (t-90) REVERT: B 755 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8472 (tp40) REVERT: B 855 PHE cc_start: 0.6383 (OUTLIER) cc_final: 0.6008 (p90) REVERT: E 53 ARG cc_start: 0.8062 (tpm-80) cc_final: 0.7614 (mmp80) outliers start: 107 outliers final: 53 residues processed: 202 average time/residue: 0.8039 time to fit residues: 212.0720 Evaluate side-chains 164 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 102 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain F residue 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 129 optimal weight: 0.4980 chunk 212 optimal weight: 7.9990 chunk 181 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 299 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 220 optimal weight: 0.6980 chunk 210 optimal weight: 6.9990 chunk 182 optimal weight: 0.0970 chunk 153 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN C1005 GLN B 957 GLN B1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.147150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.092619 restraints weight = 53056.901| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.73 r_work: 0.3321 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26250 Z= 0.112 Angle : 0.553 11.149 35832 Z= 0.272 Chirality : 0.045 0.252 4194 Planarity : 0.004 0.062 4539 Dihedral : 5.373 59.712 4482 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.54 % Allowed : 18.14 % Favored : 79.32 % 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: -0.82 (0.14), residues: 3138 helix: 0.60 (0.20), residues: 648 sheet: -0.01 (0.18), residues: 711 loop : -1.22 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 104 HIS 0.003 0.001 HIS A 49 PHE 0.017 0.001 PHE C 92 TYR 0.038 0.001 TYR E 3 ARG 0.003 0.000 ARG E 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 45) link_NAG-ASN : angle 1.72628 ( 135) link_BETA1-4 : bond 0.00451 ( 6) link_BETA1-4 : angle 0.95870 ( 18) hydrogen bonds : bond 0.03240 ( 856) hydrogen bonds : angle 5.46871 ( 2454) SS BOND : bond 0.00428 ( 39) SS BOND : angle 1.05934 ( 78) covalent geometry : bond 0.00258 (26160) covalent geometry : angle 0.54139 (35601) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 120 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8750 (m-80) cc_final: 0.8433 (m-80) REVERT: A 269 TYR cc_start: 0.8448 (m-10) cc_final: 0.8244 (m-10) REVERT: A 360 ASN cc_start: 0.7933 (m-40) cc_final: 0.7492 (p0) REVERT: A 365 TYR cc_start: 0.8266 (m-80) cc_final: 0.7909 (m-10) REVERT: A 581 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8056 (p) REVERT: A 740 MET cc_start: 0.8592 (tpp) cc_final: 0.8332 (tpt) REVERT: C 118 LEU cc_start: 0.7063 (mp) cc_final: 0.6676 (tp) REVERT: C 332 ILE cc_start: 0.6687 (OUTLIER) cc_final: 0.6433 (tp) REVERT: C 342 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7640 (t80) REVERT: B 111 ASP cc_start: 0.7862 (p0) cc_final: 0.7623 (t0) REVERT: B 855 PHE cc_start: 0.6391 (OUTLIER) cc_final: 0.5952 (p90) REVERT: E 40 ILE cc_start: 0.9343 (mm) cc_final: 0.8592 (pp) outliers start: 70 outliers final: 39 residues processed: 180 average time/residue: 0.7617 time to fit residues: 178.0929 Evaluate side-chains 147 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 56 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 304 optimal weight: 40.0000 chunk 128 optimal weight: 4.9990 chunk 259 optimal weight: 0.8980 chunk 36 optimal weight: 20.0000 chunk 226 optimal weight: 0.6980 chunk 225 optimal weight: 2.9990 chunk 252 optimal weight: 0.3980 chunk 96 optimal weight: 0.0870 chunk 193 optimal weight: 0.7980 chunk 32 optimal weight: 30.0000 chunk 89 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 957 GLN A1005 GLN C 978 ASN C1005 GLN B 957 GLN B1005 GLN B1142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.146785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.092084 restraints weight = 52664.577| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.73 r_work: 0.3309 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26250 Z= 0.122 Angle : 0.561 10.919 35832 Z= 0.277 Chirality : 0.045 0.242 4194 Planarity : 0.004 0.064 4539 Dihedral : 5.326 59.858 4482 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.87 % Allowed : 18.14 % Favored : 78.99 % 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: -0.81 (0.14), residues: 3138 helix: 0.62 (0.20), residues: 648 sheet: -0.01 (0.18), residues: 711 loop : -1.23 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 104 HIS 0.004 0.001 HIS A1088 PHE 0.026 0.001 PHE A 168 TYR 0.036 0.001 TYR E 3 ARG 0.004 0.000 ARG E 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 45) link_NAG-ASN : angle 1.73090 ( 135) link_BETA1-4 : bond 0.00349 ( 6) link_BETA1-4 : angle 0.92781 ( 18) hydrogen bonds : bond 0.03227 ( 856) hydrogen bonds : angle 5.39641 ( 2454) SS BOND : bond 0.00334 ( 39) SS BOND : angle 1.02001 ( 78) covalent geometry : bond 0.00286 (26160) covalent geometry : angle 0.55055 (35601) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 105 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8755 (m-80) cc_final: 0.8444 (m-80) REVERT: A 269 TYR cc_start: 0.8401 (m-10) cc_final: 0.8139 (m-10) REVERT: A 360 ASN cc_start: 0.7954 (m-40) cc_final: 0.7520 (p0) REVERT: A 365 TYR cc_start: 0.8270 (m-80) cc_final: 0.7913 (m-10) REVERT: A 581 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8061 (p) REVERT: A 602 THR cc_start: 0.8918 (m) cc_final: 0.8707 (p) REVERT: C 118 LEU cc_start: 0.7085 (mp) cc_final: 0.6707 (tp) REVERT: C 332 ILE cc_start: 0.6723 (OUTLIER) cc_final: 0.6451 (tp) REVERT: C 342 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7629 (t80) REVERT: B 66 HIS cc_start: 0.7087 (OUTLIER) cc_final: 0.6660 (t-90) REVERT: B 755 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8470 (tp-100) REVERT: B 855 PHE cc_start: 0.6432 (OUTLIER) cc_final: 0.5986 (p90) REVERT: B 886 TRP cc_start: 0.7996 (p90) cc_final: 0.7777 (p90) REVERT: B 934 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8681 (tt) REVERT: D 28 ILE cc_start: 0.5018 (OUTLIER) cc_final: 0.4716 (pp) REVERT: F 38 TRP cc_start: 0.5648 (m100) cc_final: 0.5313 (m100) outliers start: 79 outliers final: 47 residues processed: 173 average time/residue: 0.8242 time to fit residues: 193.5703 Evaluate side-chains 157 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 102 time to evaluate : 5.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 56 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 284 optimal weight: 0.8980 chunk 317 optimal weight: 30.0000 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 304 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 131 optimal weight: 0.0030 chunk 271 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN A1005 GLN C1005 GLN B 957 GLN B1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.143674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.090333 restraints weight = 51084.072| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.21 r_work: 0.3267 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26250 Z= 0.129 Angle : 0.570 10.698 35832 Z= 0.281 Chirality : 0.045 0.232 4194 Planarity : 0.004 0.065 4539 Dihedral : 5.327 59.508 4482 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.69 % Allowed : 18.58 % Favored : 78.74 % 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: -0.82 (0.14), residues: 3138 helix: 0.61 (0.20), residues: 651 sheet: -0.06 (0.18), residues: 714 loop : -1.22 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 104 HIS 0.004 0.001 HIS A1088 PHE 0.015 0.001 PHE C 92 TYR 0.022 0.001 TYR E 3 ARG 0.002 0.000 ARG E 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 45) link_NAG-ASN : angle 1.75140 ( 135) link_BETA1-4 : bond 0.00321 ( 6) link_BETA1-4 : angle 0.92141 ( 18) hydrogen bonds : bond 0.03229 ( 856) hydrogen bonds : angle 5.37508 ( 2454) SS BOND : bond 0.00386 ( 39) SS BOND : angle 1.12105 ( 78) covalent geometry : bond 0.00304 (26160) covalent geometry : angle 0.55878 (35601) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 110 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8763 (m-80) cc_final: 0.8443 (m-80) REVERT: A 269 TYR cc_start: 0.8418 (m-10) cc_final: 0.8146 (m-10) REVERT: A 360 ASN cc_start: 0.8005 (m-40) cc_final: 0.7591 (p0) REVERT: A 365 TYR cc_start: 0.8297 (m-80) cc_final: 0.7850 (m-10) REVERT: A 581 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8117 (p) REVERT: C 118 LEU cc_start: 0.7100 (mp) cc_final: 0.6729 (tp) REVERT: C 332 ILE cc_start: 0.6742 (OUTLIER) cc_final: 0.6455 (tp) REVERT: B 66 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.6769 (t-90) REVERT: B 134 GLN cc_start: 0.7988 (pm20) cc_final: 0.7732 (pm20) REVERT: B 755 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8483 (tp-100) REVERT: B 855 PHE cc_start: 0.6411 (OUTLIER) cc_final: 0.5917 (p90) REVERT: B 934 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8671 (tt) REVERT: D 28 ILE cc_start: 0.5016 (OUTLIER) cc_final: 0.4711 (pp) outliers start: 74 outliers final: 50 residues processed: 175 average time/residue: 0.7117 time to fit residues: 164.5863 Evaluate side-chains 160 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 103 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain E residue 56 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 193 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 132 optimal weight: 30.0000 chunk 35 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 247 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 957 GLN A1005 GLN C1005 GLN B 957 GLN B1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.143233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.089750 restraints weight = 50747.467| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.25 r_work: 0.3254 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26250 Z= 0.143 Angle : 0.588 10.634 35832 Z= 0.289 Chirality : 0.046 0.234 4194 Planarity : 0.004 0.060 4539 Dihedral : 5.363 59.154 4482 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.73 % Allowed : 18.76 % Favored : 78.52 % 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: -0.84 (0.14), residues: 3138 helix: 0.59 (0.20), residues: 651 sheet: -0.07 (0.18), residues: 714 loop : -1.22 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP F 38 HIS 0.004 0.001 HIS A1088 PHE 0.023 0.001 PHE A 168 TYR 0.021 0.001 TYR E 3 ARG 0.003 0.000 ARG E 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 45) link_NAG-ASN : angle 1.78772 ( 135) link_BETA1-4 : bond 0.00276 ( 6) link_BETA1-4 : angle 0.90973 ( 18) hydrogen bonds : bond 0.03281 ( 856) hydrogen bonds : angle 5.40287 ( 2454) SS BOND : bond 0.00445 ( 39) SS BOND : angle 1.37659 ( 78) covalent geometry : bond 0.00339 (26160) covalent geometry : angle 0.57562 (35601) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 110 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8771 (m-80) cc_final: 0.8471 (m-80) REVERT: A 360 ASN cc_start: 0.7947 (m-40) cc_final: 0.7560 (p0) REVERT: A 365 TYR cc_start: 0.8317 (m-80) cc_final: 0.7833 (m-10) REVERT: A 581 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8123 (p) REVERT: C 118 LEU cc_start: 0.7124 (mp) cc_final: 0.6753 (tp) REVERT: C 332 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6470 (tp) REVERT: B 66 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.6808 (t-90) REVERT: B 755 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8476 (tp-100) REVERT: B 855 PHE cc_start: 0.6377 (OUTLIER) cc_final: 0.5896 (p90) REVERT: B 934 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8661 (tt) REVERT: D 28 ILE cc_start: 0.4995 (OUTLIER) cc_final: 0.4689 (pp) REVERT: F 38 TRP cc_start: 0.5238 (m100) cc_final: 0.4938 (m100) REVERT: F 52 PRO cc_start: 0.8518 (Cg_exo) cc_final: 0.8278 (Cg_endo) outliers start: 75 outliers final: 50 residues processed: 177 average time/residue: 0.7238 time to fit residues: 168.9373 Evaluate side-chains 156 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 99 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 188 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 244 optimal weight: 0.0670 chunk 216 optimal weight: 0.8980 chunk 68 optimal weight: 0.0570 chunk 313 optimal weight: 30.0000 chunk 164 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 957 GLN A1005 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN B 957 GLN B1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.146854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.092455 restraints weight = 52842.336| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.71 r_work: 0.3315 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26250 Z= 0.115 Angle : 0.578 11.135 35832 Z= 0.284 Chirality : 0.045 0.226 4194 Planarity : 0.004 0.059 4539 Dihedral : 5.266 59.625 4482 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.29 % Allowed : 19.45 % Favored : 78.26 % 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: -0.81 (0.14), residues: 3138 helix: 0.59 (0.20), residues: 648 sheet: -0.09 (0.18), residues: 738 loop : -1.19 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 38 HIS 0.003 0.001 HIS A1088 PHE 0.016 0.001 PHE C 220 TYR 0.020 0.001 TYR E 3 ARG 0.002 0.000 ARG E 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 45) link_NAG-ASN : angle 1.71605 ( 135) link_BETA1-4 : bond 0.00354 ( 6) link_BETA1-4 : angle 0.90960 ( 18) hydrogen bonds : bond 0.03134 ( 856) hydrogen bonds : angle 5.30743 ( 2454) SS BOND : bond 0.00303 ( 39) SS BOND : angle 1.40799 ( 78) covalent geometry : bond 0.00267 (26160) covalent geometry : angle 0.56573 (35601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23700.63 seconds wall clock time: 407 minutes 47.22 seconds (24467.22 seconds total)