Starting phenix.real_space_refine on Mon May 26 15:07:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g74_29796/05_2025/8g74_29796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g74_29796/05_2025/8g74_29796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g74_29796/05_2025/8g74_29796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g74_29796/05_2025/8g74_29796.map" model { file = "/net/cci-nas-00/data/ceres_data/8g74_29796/05_2025/8g74_29796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g74_29796/05_2025/8g74_29796.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 920 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 17494 2.51 5 N 4549 2.21 5 O 5376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 1.69s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27543 Number of models: 1 Model: "" Number of chains: 19 Chain: "E" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "A" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 8367 Classifications: {'peptide': 1071} Link IDs: {'PTRANS': 57, 'TRANS': 1013} Chain breaks: 4 Chain: "B" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "C" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "D" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 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: "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: "M" 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: "N" 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: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 17.54, per 1000 atoms: 0.64 Number of scatterers: 27543 At special positions: 0 Unit cell: (163.52, 148.19, 208.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 5376 8.00 N 4549 7.00 C 17494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " 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=2.06 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.05 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=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.04 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.05 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.02 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.02 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.02 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B1074 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 282 " " NAG D1304 " - " ASN D 331 " " NAG D1305 " - " ASN D 616 " " NAG D1306 " - " ASN D 657 " " NAG D1307 " - " ASN D 709 " " NAG D1308 " - " ASN D1074 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN D 717 " " NAG N 1 " - " ASN D 801 " " NAG O 1 " - " ASN D1098 " " NAG P 1 " - " ASN D1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.14 Conformation dependent library (CDL) restraints added in 3.6 seconds 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6430 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 54 sheets defined 23.1% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.50 Creating SS restraints... Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.878A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.601A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 759 removed outlier: 6.861A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 759 " --> pdb=" O TYR A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 759' Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.604A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.582A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.073A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.392A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.028A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.603A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.659A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.581A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.695A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 4.433A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.937A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.511A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.766A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.312A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.114A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.891A pdb=" N LYS C 64 " --> pdb=" O ASN C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.658A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 505 Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.574A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 891 removed outlier: 3.553A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 912 through 919 removed outlier: 3.975A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.602A pdb=" N THR D 941 " --> pdb=" O SER D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.945A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.776A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 3.962A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.155A pdb=" N GLY E 10 " --> pdb=" O THR E 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.550A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.341A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.933A pdb=" N ARG D 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU D 324 " --> pdb=" O ASN D 540 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N ASN D 542 " --> pdb=" O GLU D 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 55 Processing sheet with id=AA7, first strand: chain 'A' and resid 68 through 69 removed outlier: 3.731A pdb=" N ARG A 78 " --> pdb=" O HIS A 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.668A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.793A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.642A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.077A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.801A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB6, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.504A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.069A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.036A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.036A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.412A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.438A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.293A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.813A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.654A pdb=" N ARG B 78 " --> pdb=" O HIS B 69 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 153 through 157 removed outlier: 3.617A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.154A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.525A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.078A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.674A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.614A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.087A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.863A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.817A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.468A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.395A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.166A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.566A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 28 through 30 removed outlier: 8.212A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.938A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 68 through 70 removed outlier: 3.697A pdb=" N ARG D 78 " --> pdb=" O HIS D 69 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AE8, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.634A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER D 172 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 311 through 319 removed outlier: 6.926A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.687A pdb=" N LYS D 378 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.537A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.583A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.154A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.659A pdb=" N THR D1076 " --> pdb=" O SER D1097 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 718 through 728 removed outlier: 5.712A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.418A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.351A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 3003 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: 13.37 Time building geometry restraints manager: 8.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4476 1.29 - 1.42: 7438 1.42 - 1.56: 16089 1.56 - 1.69: 4 1.69 - 1.82: 160 Bond restraints: 28167 Sorted by residual: bond pdb=" C PRO B 899 " pdb=" O PRO B 899 " ideal model delta sigma weight residual 1.237 1.155 0.082 1.26e-02 6.30e+03 4.23e+01 bond pdb=" N VAL B1068 " pdb=" CA VAL B1068 " ideal model delta sigma weight residual 1.454 1.489 -0.035 7.70e-03 1.69e+04 2.05e+01 bond pdb=" N VAL D1068 " pdb=" CA VAL D1068 " ideal model delta sigma weight residual 1.457 1.491 -0.034 9.00e-03 1.23e+04 1.40e+01 bond pdb=" CA PRO D 25 " pdb=" C PRO D 25 " ideal model delta sigma weight residual 1.514 1.534 -0.020 5.50e-03 3.31e+04 1.34e+01 bond pdb=" C ALA B 903 " pdb=" O ALA B 903 " ideal model delta sigma weight residual 1.237 1.195 0.041 1.17e-02 7.31e+03 1.25e+01 ... (remaining 28162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 36527 2.02 - 4.04: 1624 4.04 - 6.06: 159 6.06 - 8.08: 20 8.08 - 10.11: 7 Bond angle restraints: 38337 Sorted by residual: angle pdb=" C ASP D 571 " pdb=" CA ASP D 571 " pdb=" CB ASP D 571 " ideal model delta sigma weight residual 110.04 119.71 -9.67 1.51e+00 4.39e-01 4.11e+01 angle pdb=" N ILE A 805 " pdb=" CA ILE A 805 " pdb=" C ILE A 805 " ideal model delta sigma weight residual 113.71 108.85 4.86 9.50e-01 1.11e+00 2.62e+01 angle pdb=" C CYS A 291 " pdb=" N ALA A 292 " pdb=" CA ALA A 292 " ideal model delta sigma weight residual 122.56 113.85 8.71 1.72e+00 3.38e-01 2.57e+01 angle pdb=" CA MET B 902 " pdb=" C MET B 902 " pdb=" N ALA B 903 " ideal model delta sigma weight residual 117.30 122.76 -5.46 1.16e+00 7.43e-01 2.21e+01 angle pdb=" N SER D 982 " pdb=" CA SER D 982 " pdb=" C SER D 982 " ideal model delta sigma weight residual 112.87 107.39 5.48 1.20e+00 6.94e-01 2.09e+01 ... (remaining 38332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.33: 16373 25.33 - 50.66: 859 50.66 - 75.98: 102 75.98 - 101.31: 41 101.31 - 126.64: 14 Dihedral angle restraints: 17389 sinusoidal: 7378 harmonic: 10011 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 16.95 76.05 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -161.97 75.97 1 1.00e+01 1.00e-02 7.27e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -154.53 68.53 1 1.00e+01 1.00e-02 6.09e+01 ... (remaining 17386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.299: 4460 0.299 - 0.597: 7 0.597 - 0.896: 1 0.896 - 1.195: 0 1.195 - 1.493: 1 Chirality restraints: 4469 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -0.91 -1.49 2.00e-01 2.50e+01 5.58e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.51e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.19e+01 ... (remaining 4466 not shown) Planarity restraints: 4953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " 0.357 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG A1304 " -0.088 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.143 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " -0.544 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D1303 " 0.358 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NAG D1303 " -0.092 2.00e-02 2.50e+03 pdb=" C8 NAG D1303 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG D1303 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG D1303 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1302 " -0.269 2.00e-02 2.50e+03 2.24e-01 6.28e+02 pdb=" C7 NAG A1302 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG A1302 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG A1302 " 0.373 2.00e-02 2.50e+03 pdb=" O7 NAG A1302 " 0.005 2.00e-02 2.50e+03 ... (remaining 4950 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 24 2.13 - 2.82: 8391 2.82 - 3.52: 36396 3.52 - 4.21: 64594 4.21 - 4.90: 111614 Nonbonded interactions: 221019 Sorted by model distance: nonbonded pdb=" O SER B 373 " pdb=" CD1 TRP B 436 " model vdw 1.439 3.260 nonbonded pdb=" CE1 PHE D 374 " pdb=" CE3 TRP D 436 " model vdw 1.493 3.640 nonbonded pdb=" OD1 ASN D 394 " pdb=" CG GLU D 516 " model vdw 1.546 3.440 nonbonded pdb=" CD ARG D 328 " pdb=" OD2 ASP D 578 " model vdw 1.550 3.440 nonbonded pdb=" CE1 PHE D 374 " pdb=" CZ3 TRP D 436 " model vdw 1.712 3.640 ... (remaining 221014 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' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147 or resid 1301 through 1307)) selection = (chain 'D' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147 or resid 1301 through 1307)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 7.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 1.390 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 66.620 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.140 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:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 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 : 0.006 0.258 28256 Z= 0.381 Angle : 0.918 28.915 38560 Z= 0.534 Chirality : 0.064 1.493 4469 Planarity : 0.011 0.306 4917 Dihedral : 15.492 126.640 10836 Min Nonbonded Distance : 1.439 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.43 % Favored : 96.40 % Rotamer: Outliers : 1.20 % Allowed : 13.63 % Favored : 85.17 % Cbeta Deviations : 0.06 % 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: -0.61 (0.14), residues: 3413 helix: 1.26 (0.20), residues: 690 sheet: -0.20 (0.17), residues: 842 loop : -1.15 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 886 HIS 0.021 0.002 HIS B 207 PHE 0.039 0.002 PHE B 400 TYR 0.032 0.002 TYR D 423 ARG 0.011 0.001 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.01958 ( 36) link_NAG-ASN : angle 5.55943 ( 108) link_BETA1-4 : bond 0.00680 ( 11) link_BETA1-4 : angle 1.54356 ( 33) hydrogen bonds : bond 0.14104 ( 1091) hydrogen bonds : angle 7.73805 ( 3003) SS BOND : bond 0.00972 ( 41) SS BOND : angle 2.36308 ( 82) covalent geometry : bond 0.00568 (28167) covalent geometry : angle 0.86420 (38337) Misc. bond : bond 0.25827 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 307 time to evaluate : 2.708 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: E 34 MET cc_start: 0.0926 (tmt) cc_final: 0.0541 (mpt) REVERT: A 59 PHE cc_start: 0.5550 (m-10) cc_final: 0.5296 (m-80) REVERT: A 266 TYR cc_start: 0.5140 (m-80) cc_final: 0.4813 (m-10) REVERT: A 281 GLU cc_start: 0.4694 (OUTLIER) cc_final: 0.4290 (tt0) REVERT: A 374 PHE cc_start: 0.5432 (m-80) cc_final: 0.4833 (m-80) REVERT: A 429 PHE cc_start: 0.8079 (t80) cc_final: 0.7832 (t80) REVERT: A 436 TRP cc_start: 0.6233 (p90) cc_final: 0.6022 (p90) REVERT: A 528 LYS cc_start: 0.7560 (ttmm) cc_final: 0.6588 (ttpt) REVERT: A 530 SER cc_start: 0.7674 (p) cc_final: 0.7365 (t) REVERT: A 779 GLN cc_start: 0.7915 (tt0) cc_final: 0.7160 (tp-100) REVERT: A 921 LYS cc_start: 0.7392 (tppt) cc_final: 0.6850 (mttp) REVERT: A 954 GLN cc_start: 0.8194 (mt0) cc_final: 0.7977 (mt0) REVERT: A 1010 GLN cc_start: 0.7387 (mm110) cc_final: 0.6428 (pt0) REVERT: A 1092 GLU cc_start: 0.7430 (pt0) cc_final: 0.7175 (pt0) REVERT: A 1119 ASN cc_start: 0.7325 (m-40) cc_final: 0.7056 (m110) REVERT: A 1125 ASN cc_start: 0.6018 (m-40) cc_final: 0.5286 (p0) REVERT: B 153 MET cc_start: 0.1511 (tpp) cc_final: -0.1148 (mtp) REVERT: B 269 TYR cc_start: 0.7676 (m-80) cc_final: 0.7423 (m-80) REVERT: B 304 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.6955 (mtpt) REVERT: B 338 PHE cc_start: 0.4173 (OUTLIER) cc_final: 0.3756 (m-10) REVERT: B 537 LYS cc_start: 0.6420 (tttt) cc_final: 0.5836 (tmtt) REVERT: B 546 LEU cc_start: 0.6092 (tt) cc_final: 0.5706 (mp) REVERT: B 947 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8121 (mttt) REVERT: B 994 ASP cc_start: 0.6414 (t70) cc_final: 0.6097 (t70) REVERT: D 153 MET cc_start: -0.0577 (mtm) cc_final: -0.1174 (mmm) REVERT: D 192 PHE cc_start: 0.6489 (m-80) cc_final: 0.6070 (m-80) REVERT: D 535 LYS cc_start: 0.5987 (mttt) cc_final: 0.5779 (mtmm) REVERT: D 583 GLU cc_start: 0.6801 (pt0) cc_final: 0.6448 (mp0) REVERT: D 780 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7390 (mt-10) REVERT: D 854 LYS cc_start: 0.4199 (ptpt) cc_final: 0.3776 (tptt) REVERT: D 1002 GLN cc_start: 0.7225 (tt0) cc_final: 0.6985 (tt0) REVERT: D 1017 GLU cc_start: 0.7171 (tt0) cc_final: 0.6959 (tt0) REVERT: D 1113 GLN cc_start: 0.8208 (mm110) cc_final: 0.7918 (mm-40) REVERT: D 1138 TYR cc_start: 0.7626 (t80) cc_final: 0.7341 (t80) outliers start: 36 outliers final: 16 residues processed: 337 average time/residue: 1.0348 time to fit residues: 425.1660 Evaluate side-chains 221 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 353 TRP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 645 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 chunk 144 optimal weight: 0.0170 chunk 88 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 138 optimal weight: 0.4980 chunk 268 optimal weight: 40.0000 chunk 104 optimal weight: 0.6980 chunk 163 optimal weight: 10.0000 chunk 200 optimal weight: 0.8980 chunk 311 optimal weight: 6.9990 overall best weight: 1.4220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 ASN E 58 GLN A 69 HIS A 188 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 354 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 764 ASN A 784 GLN A 901 GLN A 914 ASN A 960 ASN A1005 GLN A1010 GLN A1048 HIS A1101 HIS A1106 GLN B 69 HIS B 81 ASN B 137 ASN B 188 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 804 GLN B 901 GLN B 907 ASN B 935 GLN B1101 HIS B1119 ASN C 32 ASN D 69 HIS D 121 ASN ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 784 GLN D 901 GLN D 960 ASN D 969 ASN D 978 ASN D1088 HIS D1101 HIS D1113 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.232935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.157747 restraints weight = 33794.899| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 4.33 r_work: 0.3425 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 28256 Z= 0.186 Angle : 0.720 14.475 38560 Z= 0.359 Chirality : 0.049 0.364 4469 Planarity : 0.005 0.109 4917 Dihedral : 8.360 89.778 4722 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.92 % Rotamer: Outliers : 2.76 % Allowed : 13.56 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3413 helix: 1.45 (0.20), residues: 720 sheet: -0.01 (0.17), residues: 841 loop : -1.23 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 436 HIS 0.008 0.002 HIS B 66 PHE 0.031 0.002 PHE A 400 TYR 0.022 0.002 TYR D 351 ARG 0.005 0.001 ARG A 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 36) link_NAG-ASN : angle 3.45853 ( 108) link_BETA1-4 : bond 0.00362 ( 11) link_BETA1-4 : angle 1.44756 ( 33) hydrogen bonds : bond 0.05364 ( 1091) hydrogen bonds : angle 6.19503 ( 3003) SS BOND : bond 0.00713 ( 41) SS BOND : angle 1.90596 ( 82) covalent geometry : bond 0.00432 (28167) covalent geometry : angle 0.69148 (38337) Misc. bond : bond 0.00344 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 216 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.0853 (tmt) cc_final: -0.0303 (mpt) REVERT: E 51 ILE cc_start: 0.3868 (OUTLIER) cc_final: 0.3337 (tt) REVERT: A 51 THR cc_start: 0.6039 (p) cc_final: 0.5757 (t) REVERT: A 59 PHE cc_start: 0.5950 (m-10) cc_final: 0.5603 (m-80) REVERT: A 266 TYR cc_start: 0.5476 (m-80) cc_final: 0.5212 (m-10) REVERT: A 374 PHE cc_start: 0.5957 (m-80) cc_final: 0.5549 (m-80) REVERT: A 528 LYS cc_start: 0.7864 (ttmm) cc_final: 0.7585 (ttmm) REVERT: A 673 SER cc_start: 0.8128 (p) cc_final: 0.7906 (t) REVERT: A 779 GLN cc_start: 0.8790 (tt0) cc_final: 0.8409 (tp40) REVERT: A 921 LYS cc_start: 0.8410 (tppt) cc_final: 0.8090 (mtmp) REVERT: A 987 PRO cc_start: 0.7404 (Cg_exo) cc_final: 0.7077 (Cg_endo) REVERT: A 1010 GLN cc_start: 0.8429 (mm-40) cc_final: 0.7984 (pt0) REVERT: A 1119 ASN cc_start: 0.7981 (m-40) cc_final: 0.7296 (m110) REVERT: A 1125 ASN cc_start: 0.6996 (m-40) cc_final: 0.6453 (p0) REVERT: B 53 ASP cc_start: 0.7323 (t0) cc_final: 0.7052 (t0) REVERT: B 153 MET cc_start: 0.1142 (tpp) cc_final: -0.1280 (mtp) REVERT: B 338 PHE cc_start: 0.4353 (OUTLIER) cc_final: 0.3827 (m-10) REVERT: B 537 LYS cc_start: 0.7363 (tttt) cc_final: 0.6769 (tptp) REVERT: B 1010 GLN cc_start: 0.8691 (mm110) cc_final: 0.8216 (pt0) REVERT: C 82 MET cc_start: 0.0518 (mmm) cc_final: -0.1485 (ptp) REVERT: D 126 VAL cc_start: 0.6408 (OUTLIER) cc_final: 0.6013 (t) REVERT: D 153 MET cc_start: -0.0539 (mtm) cc_final: -0.1155 (mmm) REVERT: D 229 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6979 (mp) REVERT: D 238 PHE cc_start: 0.6597 (p90) cc_final: 0.6311 (p90) REVERT: D 796 ASP cc_start: 0.7546 (p0) cc_final: 0.7243 (t70) REVERT: D 854 LYS cc_start: 0.5306 (ptpt) cc_final: 0.4758 (tptt) outliers start: 83 outliers final: 34 residues processed: 282 average time/residue: 1.0528 time to fit residues: 364.4762 Evaluate side-chains 217 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 313 optimal weight: 0.7980 chunk 275 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 294 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 252 optimal weight: 9.9990 chunk 194 optimal weight: 0.8980 chunk 221 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 81 ASN B 245 HIS B 613 GLN B1002 GLN C 58 GLN D 121 ASN ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.233698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.159330 restraints weight = 34012.516| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 4.08 r_work: 0.3432 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 28256 Z= 0.128 Angle : 0.623 11.895 38560 Z= 0.309 Chirality : 0.046 0.286 4469 Planarity : 0.005 0.058 4917 Dihedral : 6.272 61.985 4698 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.61 % Favored : 97.33 % Rotamer: Outliers : 2.93 % Allowed : 13.86 % Favored : 83.21 % 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: -0.34 (0.14), residues: 3413 helix: 1.94 (0.20), residues: 683 sheet: -0.00 (0.16), residues: 867 loop : -1.20 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 353 HIS 0.005 0.001 HIS D1088 PHE 0.020 0.001 PHE A 400 TYR 0.018 0.001 TYR B1067 ARG 0.009 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00678 ( 36) link_NAG-ASN : angle 3.16852 ( 108) link_BETA1-4 : bond 0.00349 ( 11) link_BETA1-4 : angle 1.50322 ( 33) hydrogen bonds : bond 0.04579 ( 1091) hydrogen bonds : angle 5.77528 ( 3003) SS BOND : bond 0.00554 ( 41) SS BOND : angle 1.59902 ( 82) covalent geometry : bond 0.00292 (28167) covalent geometry : angle 0.59607 (38337) Misc. bond : bond 0.00125 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 201 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.0634 (tmt) cc_final: -0.0366 (mpt) REVERT: E 51 ILE cc_start: 0.3723 (OUTLIER) cc_final: 0.3155 (tt) REVERT: A 51 THR cc_start: 0.6217 (p) cc_final: 0.5808 (m) REVERT: A 70 VAL cc_start: 0.1799 (OUTLIER) cc_final: 0.1596 (m) REVERT: A 266 TYR cc_start: 0.5563 (m-80) cc_final: 0.5361 (m-10) REVERT: A 528 LYS cc_start: 0.7898 (ttmm) cc_final: 0.7560 (ttmm) REVERT: A 779 GLN cc_start: 0.8714 (tt0) cc_final: 0.8356 (tp-100) REVERT: A 921 LYS cc_start: 0.8385 (tppt) cc_final: 0.8103 (mttp) REVERT: A 987 PRO cc_start: 0.7438 (Cg_exo) cc_final: 0.7103 (Cg_endo) REVERT: A 1010 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8000 (pt0) REVERT: A 1119 ASN cc_start: 0.7879 (m-40) cc_final: 0.7226 (m110) REVERT: A 1125 ASN cc_start: 0.7340 (m-40) cc_final: 0.6846 (p0) REVERT: B 53 ASP cc_start: 0.7337 (t0) cc_final: 0.7059 (t0) REVERT: B 153 MET cc_start: 0.1489 (tpp) cc_final: -0.1318 (mtp) REVERT: B 201 PHE cc_start: 0.7501 (t80) cc_final: 0.7124 (t80) REVERT: B 266 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: B 271 GLN cc_start: 0.7477 (mt0) cc_final: 0.6835 (mp10) REVERT: B 534 VAL cc_start: 0.8187 (p) cc_final: 0.7797 (m) REVERT: B 537 LYS cc_start: 0.7517 (tttt) cc_final: 0.6852 (tmtt) REVERT: B 584 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7339 (mm) REVERT: B 740 MET cc_start: 0.8803 (tpp) cc_final: 0.8569 (tpp) REVERT: B 1005 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8428 (mt0) REVERT: B 1010 GLN cc_start: 0.8647 (mm110) cc_final: 0.8206 (pt0) REVERT: C 82 MET cc_start: 0.0569 (mmm) cc_final: -0.1042 (mtt) REVERT: D 126 VAL cc_start: 0.6379 (OUTLIER) cc_final: 0.5948 (t) REVERT: D 153 MET cc_start: -0.0409 (mtm) cc_final: -0.1023 (mmm) REVERT: D 194 PHE cc_start: 0.7562 (m-80) cc_final: 0.7358 (m-80) REVERT: D 229 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6846 (mp) REVERT: D 238 PHE cc_start: 0.6629 (p90) cc_final: 0.6354 (p90) REVERT: D 604 THR cc_start: 0.7530 (m) cc_final: 0.7139 (m) REVERT: D 854 LYS cc_start: 0.5077 (ptpt) cc_final: 0.4581 (tptt) REVERT: D 957 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8141 (mt0) outliers start: 88 outliers final: 42 residues processed: 272 average time/residue: 1.0832 time to fit residues: 361.0327 Evaluate side-chains 227 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 102 GLN Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 156 optimal weight: 20.0000 chunk 185 optimal weight: 0.7980 chunk 280 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 chunk 266 optimal weight: 8.9990 chunk 294 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 251 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A1135 ASN B 66 HIS B 613 GLN B1088 HIS C 58 GLN D 121 ASN D 146 HIS D 148 ASN ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 969 ASN D 978 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.224199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.162704 restraints weight = 33230.083| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.99 r_work: 0.3343 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.104 28256 Z= 0.346 Angle : 0.836 12.049 38560 Z= 0.417 Chirality : 0.055 0.345 4469 Planarity : 0.006 0.085 4917 Dihedral : 6.917 55.233 4693 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 4.55 % Allowed : 13.30 % Favored : 82.15 % 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: -0.72 (0.14), residues: 3413 helix: 1.13 (0.19), residues: 699 sheet: -0.11 (0.17), residues: 875 loop : -1.33 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 886 HIS 0.008 0.002 HIS B 519 PHE 0.032 0.003 PHE A 718 TYR 0.053 0.003 TYR A1067 ARG 0.014 0.001 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00765 ( 36) link_NAG-ASN : angle 3.83870 ( 108) link_BETA1-4 : bond 0.00409 ( 11) link_BETA1-4 : angle 2.18497 ( 33) hydrogen bonds : bond 0.06757 ( 1091) hydrogen bonds : angle 6.09557 ( 3003) SS BOND : bond 0.01378 ( 41) SS BOND : angle 2.02373 ( 82) covalent geometry : bond 0.00844 (28167) covalent geometry : angle 0.80517 (38337) Misc. bond : bond 0.00136 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 207 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 VAL cc_start: 0.1736 (OUTLIER) cc_final: 0.1519 (m) REVERT: A 273 ARG cc_start: 0.5025 (mmm-85) cc_final: 0.4280 (mmt180) REVERT: A 319 ARG cc_start: 0.7473 (ttm170) cc_final: 0.7139 (ptt-90) REVERT: A 528 LYS cc_start: 0.7900 (ttmm) cc_final: 0.7282 (ttpt) REVERT: A 543 PHE cc_start: 0.7390 (m-10) cc_final: 0.7056 (m-80) REVERT: A 564 GLN cc_start: 0.7470 (mt0) cc_final: 0.7081 (mt0) REVERT: A 574 ASP cc_start: 0.5630 (m-30) cc_final: 0.5405 (t0) REVERT: A 580 GLN cc_start: 0.7411 (mt0) cc_final: 0.7170 (mm110) REVERT: A 740 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8327 (ttp) REVERT: A 779 GLN cc_start: 0.8822 (tt0) cc_final: 0.8489 (tp40) REVERT: A 921 LYS cc_start: 0.8557 (tppt) cc_final: 0.8340 (mtmp) REVERT: A 987 PRO cc_start: 0.7859 (Cg_exo) cc_final: 0.7642 (Cg_endo) REVERT: B 53 ASP cc_start: 0.7681 (t0) cc_final: 0.7402 (t0) REVERT: B 153 MET cc_start: 0.1052 (tpp) cc_final: -0.1607 (mtt) REVERT: B 201 PHE cc_start: 0.7660 (t80) cc_final: 0.7339 (t80) REVERT: B 468 ILE cc_start: 0.3156 (OUTLIER) cc_final: 0.2872 (pp) REVERT: B 814 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.6902 (pptt) REVERT: B 1005 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8544 (mt0) REVERT: B 1010 GLN cc_start: 0.8643 (mm110) cc_final: 0.8349 (pt0) REVERT: D 28 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.5274 (m-80) REVERT: D 52 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7553 (mm-40) REVERT: D 153 MET cc_start: -0.0452 (mtm) cc_final: -0.1156 (mmp) REVERT: D 190 ARG cc_start: 0.6482 (mtt180) cc_final: 0.6261 (mtt90) REVERT: D 237 ARG cc_start: 0.7584 (mtt180) cc_final: 0.7279 (mtm180) REVERT: D 583 GLU cc_start: 0.6001 (mp0) cc_final: 0.5575 (tp30) REVERT: D 735 SER cc_start: 0.8407 (t) cc_final: 0.8204 (p) REVERT: D 854 LYS cc_start: 0.5507 (ptpt) cc_final: 0.5049 (tptt) REVERT: D 978 ASN cc_start: 0.8038 (t0) cc_final: 0.7252 (m-40) outliers start: 137 outliers final: 62 residues processed: 316 average time/residue: 1.0535 time to fit residues: 403.5770 Evaluate side-chains 249 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 180 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 28 TYR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 75 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 257 optimal weight: 3.9990 chunk 322 optimal weight: 0.9980 chunk 165 optimal weight: 20.0000 chunk 268 optimal weight: 30.0000 chunk 133 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 30 ASN B 66 HIS D 121 ASN ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1071 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.227667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.151853 restraints weight = 32935.829| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 4.16 r_work: 0.3333 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 28256 Z= 0.148 Angle : 0.643 10.771 38560 Z= 0.322 Chirality : 0.046 0.276 4469 Planarity : 0.005 0.056 4917 Dihedral : 6.032 53.691 4693 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.89 % Rotamer: Outliers : 3.56 % Allowed : 14.73 % Favored : 81.72 % 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: -0.53 (0.14), residues: 3413 helix: 1.59 (0.20), residues: 676 sheet: -0.12 (0.16), residues: 893 loop : -1.24 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 64 HIS 0.004 0.001 HIS B 66 PHE 0.030 0.002 PHE D 541 TYR 0.028 0.001 TYR A1067 ARG 0.007 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 36) link_NAG-ASN : angle 3.16292 ( 108) link_BETA1-4 : bond 0.00317 ( 11) link_BETA1-4 : angle 1.60346 ( 33) hydrogen bonds : bond 0.05046 ( 1091) hydrogen bonds : angle 5.74943 ( 3003) SS BOND : bond 0.00624 ( 41) SS BOND : angle 1.75989 ( 82) covalent geometry : bond 0.00343 (28167) covalent geometry : angle 0.61574 (38337) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 188 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.1521 (tmt) cc_final: 0.0448 (mpt) REVERT: A 127 VAL cc_start: 0.6896 (OUTLIER) cc_final: 0.6531 (m) REVERT: A 359 SER cc_start: 0.7439 (p) cc_final: 0.7165 (m) REVERT: A 528 LYS cc_start: 0.7860 (ttmm) cc_final: 0.7152 (ttpt) REVERT: A 564 GLN cc_start: 0.7338 (mt0) cc_final: 0.6880 (mt0) REVERT: A 574 ASP cc_start: 0.5491 (m-30) cc_final: 0.5270 (t0) REVERT: A 779 GLN cc_start: 0.8777 (tt0) cc_final: 0.8385 (tp40) REVERT: A 921 LYS cc_start: 0.8444 (tppt) cc_final: 0.8151 (mtmp) REVERT: A 987 PRO cc_start: 0.7772 (Cg_exo) cc_final: 0.7499 (Cg_endo) REVERT: A 1119 ASN cc_start: 0.8149 (m-40) cc_final: 0.7715 (m110) REVERT: B 53 ASP cc_start: 0.7426 (t0) cc_final: 0.7029 (t0) REVERT: B 68 ILE cc_start: 0.3074 (OUTLIER) cc_final: 0.2236 (mm) REVERT: B 153 MET cc_start: 0.0856 (tpp) cc_final: -0.1594 (mtt) REVERT: B 201 PHE cc_start: 0.7407 (t80) cc_final: 0.7148 (t80) REVERT: B 338 PHE cc_start: 0.4559 (OUTLIER) cc_final: 0.3885 (m-10) REVERT: B 468 ILE cc_start: 0.2890 (OUTLIER) cc_final: 0.2681 (pp) REVERT: B 578 ASP cc_start: 0.7702 (t70) cc_final: 0.7342 (t70) REVERT: B 654 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: B 814 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.7018 (mmtp) REVERT: B 964 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8179 (mptt) REVERT: B 990 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7438 (tm-30) REVERT: B 1005 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8515 (mt0) REVERT: B 1010 GLN cc_start: 0.8636 (mm110) cc_final: 0.8196 (pt0) REVERT: C 82 MET cc_start: 0.0432 (mmm) cc_final: -0.1255 (ptp) REVERT: D 28 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.5069 (m-80) REVERT: D 51 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.7948 (t) REVERT: D 153 MET cc_start: -0.0504 (mtm) cc_final: -0.1235 (mmp) REVERT: D 237 ARG cc_start: 0.7445 (mtt180) cc_final: 0.6951 (mtm180) REVERT: D 304 LYS cc_start: 0.8237 (mtpt) cc_final: 0.7562 (mmtm) REVERT: D 361 CYS cc_start: 0.6057 (OUTLIER) cc_final: 0.4845 (p) REVERT: D 583 GLU cc_start: 0.6015 (mp0) cc_final: 0.5537 (tp30) REVERT: D 703 ASN cc_start: 0.8378 (t0) cc_final: 0.8157 (t0) REVERT: D 735 SER cc_start: 0.8558 (t) cc_final: 0.8336 (p) REVERT: D 854 LYS cc_start: 0.5140 (ptpt) cc_final: 0.4602 (tptt) REVERT: D 978 ASN cc_start: 0.8020 (t0) cc_final: 0.7149 (m-40) REVERT: D 983 ARG cc_start: 0.6911 (ttp80) cc_final: 0.6603 (ttm170) outliers start: 107 outliers final: 54 residues processed: 276 average time/residue: 1.1129 time to fit residues: 374.1759 Evaluate side-chains 248 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 183 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 28 TYR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 1005 GLN Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 0 optimal weight: 20.0000 chunk 279 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 85 optimal weight: 0.0670 chunk 270 optimal weight: 8.9990 chunk 291 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN B 52 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.224466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.3823 r_free = 0.3823 target = 0.150097 restraints weight = 33108.720| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 4.28 r_work: 0.3287 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 28256 Z= 0.225 Angle : 0.698 11.448 38560 Z= 0.349 Chirality : 0.049 0.273 4469 Planarity : 0.005 0.065 4917 Dihedral : 6.096 58.482 4693 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 3.86 % Allowed : 14.79 % Favored : 81.35 % 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: -0.61 (0.14), residues: 3413 helix: 1.51 (0.20), residues: 681 sheet: -0.20 (0.16), residues: 904 loop : -1.28 (0.13), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 64 HIS 0.037 0.002 HIS B 66 PHE 0.032 0.002 PHE D 541 TYR 0.075 0.002 TYR A1067 ARG 0.009 0.001 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 36) link_NAG-ASN : angle 3.28297 ( 108) link_BETA1-4 : bond 0.00299 ( 11) link_BETA1-4 : angle 1.72833 ( 33) hydrogen bonds : bond 0.05676 ( 1091) hydrogen bonds : angle 5.81114 ( 3003) SS BOND : bond 0.00901 ( 41) SS BOND : angle 2.03123 ( 82) covalent geometry : bond 0.00539 (28167) covalent geometry : angle 0.66934 (38337) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 185 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.6928 (OUTLIER) cc_final: 0.6551 (m) REVERT: A 281 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5854 (tt0) REVERT: A 359 SER cc_start: 0.7451 (p) cc_final: 0.7153 (m) REVERT: A 528 LYS cc_start: 0.7861 (ttmm) cc_final: 0.7150 (ttpt) REVERT: A 740 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8306 (ttp) REVERT: A 779 GLN cc_start: 0.8846 (tt0) cc_final: 0.8446 (tp40) REVERT: A 921 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8229 (mtmp) REVERT: A 987 PRO cc_start: 0.7810 (Cg_exo) cc_final: 0.7548 (Cg_endo) REVERT: A 1119 ASN cc_start: 0.8248 (m-40) cc_final: 0.7815 (m110) REVERT: B 53 ASP cc_start: 0.7520 (t0) cc_final: 0.7058 (t0) REVERT: B 153 MET cc_start: 0.0638 (tpp) cc_final: -0.1744 (mtt) REVERT: B 338 PHE cc_start: 0.4582 (OUTLIER) cc_final: 0.3944 (m-10) REVERT: B 578 ASP cc_start: 0.7787 (t70) cc_final: 0.7433 (t70) REVERT: B 654 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: B 814 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7079 (mmtp) REVERT: B 990 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7489 (tm-30) REVERT: B 1005 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8577 (mt0) REVERT: B 1010 GLN cc_start: 0.8689 (mm110) cc_final: 0.8231 (pt0) REVERT: C 82 MET cc_start: 0.0361 (mmm) cc_final: -0.1317 (ptp) REVERT: D 28 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.5059 (m-80) REVERT: D 52 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7457 (mm-40) REVERT: D 153 MET cc_start: -0.0424 (mtm) cc_final: -0.1222 (mmp) REVERT: D 190 ARG cc_start: 0.6270 (mtt180) cc_final: 0.6060 (mtt90) REVERT: D 211 ASN cc_start: 0.2615 (OUTLIER) cc_final: 0.2319 (m-40) REVERT: D 233 ILE cc_start: 0.5032 (OUTLIER) cc_final: 0.4409 (tp) REVERT: D 237 ARG cc_start: 0.7576 (mtt180) cc_final: 0.7016 (mtm180) REVERT: D 304 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7556 (mmtm) REVERT: D 361 CYS cc_start: 0.6068 (OUTLIER) cc_final: 0.4647 (p) REVERT: D 583 GLU cc_start: 0.5889 (mp0) cc_final: 0.5411 (tp30) REVERT: D 661 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7744 (tt0) REVERT: D 735 SER cc_start: 0.8547 (t) cc_final: 0.8289 (p) REVERT: D 854 LYS cc_start: 0.5254 (ptpt) cc_final: 0.4703 (tptt) REVERT: D 978 ASN cc_start: 0.8087 (t0) cc_final: 0.7274 (m-40) REVERT: D 983 ARG cc_start: 0.7052 (ttp80) cc_final: 0.6816 (ttm170) outliers start: 116 outliers final: 63 residues processed: 279 average time/residue: 1.0574 time to fit residues: 359.7621 Evaluate side-chains 251 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 175 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 28 TYR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1005 GLN Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 171 optimal weight: 10.0000 chunk 170 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 303 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 59 optimal weight: 20.0000 chunk 230 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 354 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN D 121 ASN D 137 ASN ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 ASN D 762 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.226630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.165136 restraints weight = 33064.793| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.08 r_work: 0.3387 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28256 Z= 0.122 Angle : 0.599 11.803 38560 Z= 0.300 Chirality : 0.045 0.252 4469 Planarity : 0.004 0.055 4917 Dihedral : 5.528 58.982 4693 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 2.86 % Allowed : 15.79 % Favored : 81.35 % 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: -0.40 (0.14), residues: 3413 helix: 1.81 (0.20), residues: 681 sheet: -0.09 (0.16), residues: 906 loop : -1.20 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 64 HIS 0.008 0.001 HIS B 69 PHE 0.033 0.001 PHE D 541 TYR 0.017 0.001 TYR B1067 ARG 0.008 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 36) link_NAG-ASN : angle 2.80341 ( 108) link_BETA1-4 : bond 0.00341 ( 11) link_BETA1-4 : angle 1.48106 ( 33) hydrogen bonds : bond 0.04500 ( 1091) hydrogen bonds : angle 5.55689 ( 3003) SS BOND : bond 0.00461 ( 41) SS BOND : angle 1.67572 ( 82) covalent geometry : bond 0.00278 (28167) covalent geometry : angle 0.57562 (38337) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 187 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.1331 (tmt) cc_final: 0.0354 (mpt) REVERT: A 127 VAL cc_start: 0.7047 (OUTLIER) cc_final: 0.6661 (m) REVERT: A 281 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5712 (tt0) REVERT: A 359 SER cc_start: 0.7484 (p) cc_final: 0.7282 (m) REVERT: A 528 LYS cc_start: 0.7867 (ttmm) cc_final: 0.7263 (ttpt) REVERT: A 779 GLN cc_start: 0.8654 (tt0) cc_final: 0.8390 (tp40) REVERT: A 987 PRO cc_start: 0.7803 (Cg_exo) cc_final: 0.7521 (Cg_endo) REVERT: A 1119 ASN cc_start: 0.8044 (m-40) cc_final: 0.7500 (m110) REVERT: B 53 ASP cc_start: 0.7499 (t0) cc_final: 0.7079 (t0) REVERT: B 68 ILE cc_start: 0.3657 (OUTLIER) cc_final: 0.3314 (pp) REVERT: B 153 MET cc_start: 0.0538 (tpp) cc_final: -0.1759 (mtt) REVERT: B 338 PHE cc_start: 0.4650 (OUTLIER) cc_final: 0.3813 (m-10) REVERT: B 654 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: B 814 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.7092 (mmtp) REVERT: B 990 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7602 (tm-30) REVERT: B 1010 GLN cc_start: 0.8587 (mm110) cc_final: 0.8349 (pt0) REVERT: C 82 MET cc_start: 0.0653 (mmm) cc_final: -0.1111 (ptp) REVERT: D 51 THR cc_start: 0.8679 (p) cc_final: 0.8146 (t) REVERT: D 126 VAL cc_start: 0.6997 (OUTLIER) cc_final: 0.6568 (t) REVERT: D 153 MET cc_start: -0.0333 (mtm) cc_final: -0.1078 (mmp) REVERT: D 200 TYR cc_start: 0.6979 (m-80) cc_final: 0.6396 (m-80) REVERT: D 211 ASN cc_start: 0.2749 (OUTLIER) cc_final: 0.2461 (m-40) REVERT: D 237 ARG cc_start: 0.7579 (mtt180) cc_final: 0.7220 (mtm180) REVERT: D 304 LYS cc_start: 0.8233 (mtpt) cc_final: 0.7735 (mmtm) REVERT: D 361 CYS cc_start: 0.6244 (OUTLIER) cc_final: 0.5139 (p) REVERT: D 583 GLU cc_start: 0.5881 (mp0) cc_final: 0.5423 (tp30) REVERT: D 854 LYS cc_start: 0.5534 (ptpt) cc_final: 0.5000 (tptt) REVERT: D 978 ASN cc_start: 0.8085 (t0) cc_final: 0.7374 (m-40) outliers start: 86 outliers final: 45 residues processed: 256 average time/residue: 1.0862 time to fit residues: 339.8071 Evaluate side-chains 226 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 921 LYS Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1005 GLN Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 162 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 217 optimal weight: 4.9990 chunk 274 optimal weight: 9.9990 chunk 303 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 280 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 44 GLN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN D 121 ASN ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 703 ASN D 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.223916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.163160 restraints weight = 33154.439| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.02 r_work: 0.3351 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 28256 Z= 0.228 Angle : 0.705 18.744 38560 Z= 0.351 Chirality : 0.050 0.440 4469 Planarity : 0.005 0.070 4917 Dihedral : 5.931 59.400 4693 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.37 % Rotamer: Outliers : 3.22 % Allowed : 15.56 % Favored : 81.22 % 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: -0.54 (0.14), residues: 3413 helix: 1.63 (0.20), residues: 679 sheet: -0.24 (0.16), residues: 905 loop : -1.21 (0.13), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 64 HIS 0.006 0.002 HIS A1064 PHE 0.033 0.002 PHE D 541 TYR 0.036 0.002 TYR A1067 ARG 0.007 0.001 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 36) link_NAG-ASN : angle 3.52299 ( 108) link_BETA1-4 : bond 0.00376 ( 11) link_BETA1-4 : angle 1.73786 ( 33) hydrogen bonds : bond 0.05709 ( 1091) hydrogen bonds : angle 5.75658 ( 3003) SS BOND : bond 0.00918 ( 41) SS BOND : angle 1.91276 ( 82) covalent geometry : bond 0.00547 (28167) covalent geometry : angle 0.67415 (38337) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 174 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.7034 (OUTLIER) cc_final: 0.6635 (m) REVERT: A 281 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5848 (tt0) REVERT: A 359 SER cc_start: 0.7498 (p) cc_final: 0.7256 (m) REVERT: A 386 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7412 (mttt) REVERT: A 564 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7078 (mt0) REVERT: A 740 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8388 (ttp) REVERT: A 779 GLN cc_start: 0.8770 (tt0) cc_final: 0.8471 (tp40) REVERT: A 987 PRO cc_start: 0.7884 (Cg_exo) cc_final: 0.7643 (Cg_endo) REVERT: A 1119 ASN cc_start: 0.8224 (m-40) cc_final: 0.7762 (m110) REVERT: B 53 ASP cc_start: 0.7539 (t0) cc_final: 0.7076 (t0) REVERT: B 68 ILE cc_start: 0.3685 (OUTLIER) cc_final: 0.3378 (pp) REVERT: B 153 MET cc_start: 0.0691 (tpp) cc_final: 0.0417 (tpp) REVERT: B 338 PHE cc_start: 0.4823 (OUTLIER) cc_final: 0.4003 (m-10) REVERT: B 654 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: B 814 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.6765 (pptt) REVERT: B 990 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7675 (tm-30) REVERT: B 1010 GLN cc_start: 0.8608 (mm110) cc_final: 0.8343 (pt0) REVERT: C 82 MET cc_start: 0.0545 (mmm) cc_final: -0.1334 (ptp) REVERT: D 28 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.5177 (m-80) REVERT: D 52 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7444 (mm-40) REVERT: D 153 MET cc_start: -0.0289 (mtm) cc_final: -0.1106 (mmp) REVERT: D 211 ASN cc_start: 0.2820 (OUTLIER) cc_final: 0.2536 (m-40) REVERT: D 237 ARG cc_start: 0.7653 (mtt180) cc_final: 0.7173 (mtm180) REVERT: D 304 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7736 (mmtm) REVERT: D 361 CYS cc_start: 0.6260 (OUTLIER) cc_final: 0.4798 (p) REVERT: D 583 GLU cc_start: 0.5920 (mp0) cc_final: 0.5435 (tp30) REVERT: D 854 LYS cc_start: 0.5394 (ptpt) cc_final: 0.4937 (tptt) REVERT: D 978 ASN cc_start: 0.8142 (t0) cc_final: 0.7439 (m-40) outliers start: 97 outliers final: 59 residues processed: 245 average time/residue: 1.0543 time to fit residues: 315.6631 Evaluate side-chains 235 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 163 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 28 TYR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 921 LYS Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1005 GLN Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 248 optimal weight: 9.9990 chunk 313 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 309 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 300 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 93 optimal weight: 0.0870 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN D 207 HIS ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.226153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.165565 restraints weight = 33194.966| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.10 r_work: 0.3378 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 28256 Z= 0.131 Angle : 0.612 12.174 38560 Z= 0.306 Chirality : 0.045 0.265 4469 Planarity : 0.005 0.056 4917 Dihedral : 5.482 57.924 4693 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.37 % Favored : 96.54 % Rotamer: Outliers : 2.46 % Allowed : 16.46 % Favored : 81.08 % 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: -0.38 (0.14), residues: 3413 helix: 1.88 (0.20), residues: 673 sheet: -0.14 (0.16), residues: 917 loop : -1.15 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 436 HIS 0.003 0.001 HIS B 69 PHE 0.035 0.001 PHE D 541 TYR 0.025 0.001 TYR A1067 ARG 0.006 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 36) link_NAG-ASN : angle 2.88209 ( 108) link_BETA1-4 : bond 0.00335 ( 11) link_BETA1-4 : angle 1.47637 ( 33) hydrogen bonds : bond 0.04641 ( 1091) hydrogen bonds : angle 5.56412 ( 3003) SS BOND : bond 0.00547 ( 41) SS BOND : angle 1.91897 ( 82) covalent geometry : bond 0.00303 (28167) covalent geometry : angle 0.58602 (38337) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 179 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.7059 (OUTLIER) cc_final: 0.6674 (m) REVERT: A 273 ARG cc_start: 0.4546 (mmm-85) cc_final: 0.4295 (mmm-85) REVERT: A 281 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5767 (tt0) REVERT: A 779 GLN cc_start: 0.8665 (tt0) cc_final: 0.8407 (tp40) REVERT: A 987 PRO cc_start: 0.7783 (Cg_exo) cc_final: 0.7499 (Cg_endo) REVERT: A 1119 ASN cc_start: 0.8088 (m-40) cc_final: 0.7579 (m110) REVERT: B 53 ASP cc_start: 0.7527 (t0) cc_final: 0.7047 (t0) REVERT: B 68 ILE cc_start: 0.3751 (OUTLIER) cc_final: 0.3459 (pp) REVERT: B 153 MET cc_start: 0.0768 (tpp) cc_final: -0.1568 (mtt) REVERT: B 338 PHE cc_start: 0.4791 (OUTLIER) cc_final: 0.3910 (m-10) REVERT: B 654 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7684 (tm-30) REVERT: B 814 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.7120 (mmtp) REVERT: B 990 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7638 (tm-30) REVERT: B 1010 GLN cc_start: 0.8582 (mm110) cc_final: 0.8348 (pt0) REVERT: C 82 MET cc_start: 0.0470 (mmm) cc_final: -0.1447 (ptp) REVERT: D 51 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8180 (t) REVERT: D 153 MET cc_start: -0.0288 (mtm) cc_final: -0.0954 (mmp) REVERT: D 200 TYR cc_start: 0.6962 (m-80) cc_final: 0.6415 (m-80) REVERT: D 211 ASN cc_start: 0.3041 (OUTLIER) cc_final: 0.2795 (m-40) REVERT: D 237 ARG cc_start: 0.7667 (mtt180) cc_final: 0.7201 (mtm180) REVERT: D 304 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7731 (mmtm) REVERT: D 361 CYS cc_start: 0.6242 (OUTLIER) cc_final: 0.5054 (p) REVERT: D 583 GLU cc_start: 0.5879 (mp0) cc_final: 0.5451 (tp30) REVERT: D 854 LYS cc_start: 0.5608 (ptpt) cc_final: 0.5084 (tptt) REVERT: D 978 ASN cc_start: 0.8121 (t0) cc_final: 0.7425 (m-40) outliers start: 74 outliers final: 50 residues processed: 238 average time/residue: 1.0665 time to fit residues: 308.8827 Evaluate side-chains 231 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 172 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 921 LYS Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 1005 GLN Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 153 optimal weight: 20.0000 chunk 294 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 238 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 259 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 137 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 52 GLN B 134 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 703 ASN D 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.224932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.165214 restraints weight = 32874.204| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.00 r_work: 0.3362 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 28256 Z= 0.195 Angle : 0.667 12.496 38560 Z= 0.335 Chirality : 0.048 0.269 4469 Planarity : 0.005 0.061 4917 Dihedral : 5.710 59.304 4693 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.22 % Rotamer: Outliers : 2.53 % Allowed : 16.36 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.47 (0.14), residues: 3413 helix: 1.74 (0.20), residues: 681 sheet: -0.17 (0.17), residues: 868 loop : -1.18 (0.13), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 152 HIS 0.006 0.001 HIS D 207 PHE 0.039 0.002 PHE D 541 TYR 0.033 0.002 TYR A1067 ARG 0.006 0.001 ARG D 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 36) link_NAG-ASN : angle 3.07467 ( 108) link_BETA1-4 : bond 0.00327 ( 11) link_BETA1-4 : angle 1.61713 ( 33) hydrogen bonds : bond 0.05360 ( 1091) hydrogen bonds : angle 5.68870 ( 3003) SS BOND : bond 0.00804 ( 41) SS BOND : angle 2.10824 ( 82) covalent geometry : bond 0.00466 (28167) covalent geometry : angle 0.64006 (38337) Misc. bond : bond 0.00023 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 175 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.7056 (OUTLIER) cc_final: 0.6670 (m) REVERT: A 281 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5764 (tt0) REVERT: A 779 GLN cc_start: 0.8749 (tt0) cc_final: 0.8473 (tp40) REVERT: A 987 PRO cc_start: 0.7857 (Cg_exo) cc_final: 0.7595 (Cg_endo) REVERT: A 1119 ASN cc_start: 0.8152 (m-40) cc_final: 0.7677 (m110) REVERT: B 53 ASP cc_start: 0.7584 (t0) cc_final: 0.7116 (t0) REVERT: B 68 ILE cc_start: 0.3728 (OUTLIER) cc_final: 0.3447 (pp) REVERT: B 153 MET cc_start: 0.0731 (tpp) cc_final: -0.1579 (mtt) REVERT: B 338 PHE cc_start: 0.4913 (OUTLIER) cc_final: 0.4052 (m-10) REVERT: B 654 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: B 814 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6751 (pptt) REVERT: B 990 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7686 (tm-30) REVERT: B 1005 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8513 (mt0) REVERT: B 1010 GLN cc_start: 0.8548 (mm110) cc_final: 0.8334 (pt0) REVERT: C 82 MET cc_start: 0.0423 (mmm) cc_final: -0.1458 (ptp) REVERT: D 28 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.5128 (m-80) REVERT: D 51 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8171 (t) REVERT: D 153 MET cc_start: -0.0405 (mtm) cc_final: -0.1086 (mmp) REVERT: D 200 TYR cc_start: 0.7002 (m-80) cc_final: 0.6457 (m-80) REVERT: D 211 ASN cc_start: 0.3090 (OUTLIER) cc_final: 0.2856 (p0) REVERT: D 237 ARG cc_start: 0.7868 (mtt180) cc_final: 0.7206 (mtm180) REVERT: D 304 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7699 (mmtm) REVERT: D 583 GLU cc_start: 0.5915 (mp0) cc_final: 0.5503 (tp30) REVERT: D 854 LYS cc_start: 0.5550 (ptpt) cc_final: 0.5020 (tptt) REVERT: D 978 ASN cc_start: 0.8167 (t0) cc_final: 0.7471 (m-40) outliers start: 76 outliers final: 52 residues processed: 237 average time/residue: 1.0656 time to fit residues: 309.4164 Evaluate side-chains 231 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 169 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 28 TYR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 921 LYS Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 1005 GLN Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 226 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 309 optimal weight: 0.7980 chunk 329 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN B 14 GLN B 52 GLN B 87 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.221561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.142132 restraints weight = 32726.703| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.44 r_work: 0.3242 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 28256 Z= 0.282 Angle : 0.769 14.170 38560 Z= 0.386 Chirality : 0.052 0.282 4469 Planarity : 0.006 0.073 4917 Dihedral : 6.337 59.427 4690 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 2.73 % Allowed : 16.52 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3413 helix: 1.43 (0.20), residues: 668 sheet: -0.37 (0.16), residues: 876 loop : -1.38 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 152 HIS 0.008 0.002 HIS A1064 PHE 0.035 0.002 PHE D 541 TYR 0.041 0.002 TYR A1067 ARG 0.007 0.001 ARG D 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 36) link_NAG-ASN : angle 3.41522 ( 108) link_BETA1-4 : bond 0.00358 ( 11) link_BETA1-4 : angle 1.81289 ( 33) hydrogen bonds : bond 0.06133 ( 1091) hydrogen bonds : angle 5.88433 ( 3003) SS BOND : bond 0.01197 ( 41) SS BOND : angle 2.72738 ( 82) covalent geometry : bond 0.00680 (28167) covalent geometry : angle 0.73660 (38337) Misc. bond : bond 0.00023 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30353.36 seconds wall clock time: 522 minutes 9.00 seconds (31329.00 seconds total)