Starting phenix.real_space_refine on Tue Jun 24 12:12:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g74_29796/06_2025/8g74_29796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g74_29796/06_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_29796/06_2025/8g74_29796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g74_29796/06_2025/8g74_29796.map" model { file = "/net/cci-nas-00/data/ceres_data/8g74_29796/06_2025/8g74_29796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g74_29796/06_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): 2.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 18.83, per 1000 atoms: 0.68 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: 6.46 Conformation dependent library (CDL) restraints added in 3.4 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: 3.87 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: 14.06 Time building geometry restraints manager: 7.85 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: 9.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.050 Extract box with map and model: 1.360 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 67.630 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.310 ------------------------------------------------------------------------------- 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 : 2.753 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: 1.3430 time to fit residues: 550.6103 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 : 4.162 ------------------------------------------------------------------------------- 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 = 0.157752 restraints weight = 33794.898| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 4.33 r_work: 0.3423 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 2.834 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: 0.0852 (tmt) cc_final: -0.0298 (mpt) REVERT: E 51 ILE cc_start: 0.3868 (OUTLIER) cc_final: 0.3319 (tt) REVERT: A 51 THR cc_start: 0.6040 (p) cc_final: 0.5763 (t) REVERT: A 59 PHE cc_start: 0.5942 (m-10) cc_final: 0.5591 (m-80) REVERT: A 266 TYR cc_start: 0.5414 (m-80) cc_final: 0.5158 (m-10) REVERT: A 374 PHE cc_start: 0.5939 (m-80) cc_final: 0.5529 (m-80) REVERT: A 528 LYS cc_start: 0.7865 (ttmm) cc_final: 0.7587 (ttmm) REVERT: A 673 SER cc_start: 0.8127 (p) cc_final: 0.7905 (t) REVERT: A 779 GLN cc_start: 0.8775 (tt0) cc_final: 0.8401 (tp40) REVERT: A 921 LYS cc_start: 0.8401 (tppt) cc_final: 0.8094 (mtmp) REVERT: A 987 PRO cc_start: 0.7405 (Cg_exo) cc_final: 0.7074 (Cg_endo) REVERT: A 1010 GLN cc_start: 0.8427 (mm-40) cc_final: 0.7987 (pt0) REVERT: A 1119 ASN cc_start: 0.7986 (m-40) cc_final: 0.7296 (m110) REVERT: A 1125 ASN cc_start: 0.6985 (m-40) cc_final: 0.6445 (p0) REVERT: B 53 ASP cc_start: 0.7310 (t0) cc_final: 0.7039 (t0) REVERT: B 153 MET cc_start: 0.1168 (tpp) cc_final: -0.1260 (mtp) REVERT: B 338 PHE cc_start: 0.4326 (OUTLIER) cc_final: 0.3825 (m-10) REVERT: B 537 LYS cc_start: 0.7376 (tttt) cc_final: 0.6779 (tptp) REVERT: B 1010 GLN cc_start: 0.8699 (mm110) cc_final: 0.8219 (pt0) REVERT: C 82 MET cc_start: 0.0498 (mmm) cc_final: -0.1475 (ptp) REVERT: D 126 VAL cc_start: 0.6404 (OUTLIER) cc_final: 0.6007 (t) REVERT: D 153 MET cc_start: -0.0533 (mtm) cc_final: -0.1153 (mmm) REVERT: D 229 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6967 (mp) REVERT: D 238 PHE cc_start: 0.6610 (p90) cc_final: 0.6320 (p90) REVERT: D 796 ASP cc_start: 0.7549 (p0) cc_final: 0.7247 (t70) REVERT: D 854 LYS cc_start: 0.5305 (ptpt) cc_final: 0.4752 (tptt) outliers start: 83 outliers final: 34 residues processed: 282 average time/residue: 1.2178 time to fit residues: 421.6743 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 : 3.578 ------------------------------------------------------------------------------- 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: 0.9980 chunk 275 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 294 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 252 optimal weight: 9.9990 chunk 194 optimal weight: 0.8980 chunk 221 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.233535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.176300 restraints weight = 33754.233| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.90 r_work: 0.3530 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28256 Z= 0.130 Angle : 0.626 11.962 38560 Z= 0.311 Chirality : 0.046 0.287 4469 Planarity : 0.005 0.058 4917 Dihedral : 6.339 63.213 4698 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.67 % Favored : 97.25 % Rotamer: Outliers : 2.96 % Allowed : 13.83 % 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: -0.35 (0.14), residues: 3413 helix: 1.92 (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 0.022 0.001 PHE A 400 TYR 0.018 0.001 TYR B1067 ARG 0.010 0.001 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 36) link_NAG-ASN : angle 3.25694 ( 108) link_BETA1-4 : bond 0.00416 ( 11) link_BETA1-4 : angle 1.57346 ( 33) hydrogen bonds : bond 0.04634 ( 1091) hydrogen bonds : angle 5.79715 ( 3003) SS BOND : bond 0.00473 ( 41) SS BOND : angle 1.58090 ( 82) covalent geometry : bond 0.00296 (28167) covalent geometry : angle 0.59779 (38337) Misc. bond : bond 0.00024 ( 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 291 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 202 time to evaluate : 3.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.0674 (tmt) cc_final: -0.0339 (mpt) REVERT: E 51 ILE cc_start: 0.3723 (OUTLIER) cc_final: 0.3275 (tt) REVERT: A 51 THR cc_start: 0.6574 (p) cc_final: 0.6093 (m) REVERT: A 70 VAL cc_start: 0.1619 (OUTLIER) cc_final: 0.1395 (m) REVERT: A 266 TYR cc_start: 0.6138 (m-80) cc_final: 0.5875 (m-10) REVERT: A 528 LYS cc_start: 0.7922 (ttmm) cc_final: 0.7609 (ttmm) REVERT: A 779 GLN cc_start: 0.8635 (tt0) cc_final: 0.8388 (tp-100) REVERT: A 987 PRO cc_start: 0.7468 (Cg_exo) cc_final: 0.7182 (Cg_endo) REVERT: A 1010 GLN cc_start: 0.8349 (mm-40) cc_final: 0.8103 (pt0) REVERT: A 1119 ASN cc_start: 0.7873 (m-40) cc_final: 0.7185 (m110) REVERT: A 1125 ASN cc_start: 0.7257 (m-40) cc_final: 0.6949 (p0) REVERT: B 53 ASP cc_start: 0.7390 (t0) cc_final: 0.7150 (t0) REVERT: B 153 MET cc_start: 0.1480 (tpp) cc_final: -0.1324 (mtp) REVERT: B 201 PHE cc_start: 0.7594 (t80) cc_final: 0.7302 (t80) REVERT: B 266 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.7573 (m-80) REVERT: B 269 TYR cc_start: 0.8085 (m-80) cc_final: 0.7727 (m-80) REVERT: B 271 GLN cc_start: 0.7410 (mt0) cc_final: 0.6925 (mp10) REVERT: B 740 MET cc_start: 0.8813 (tpp) cc_final: 0.8612 (tpp) REVERT: B 1005 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8362 (mt0) REVERT: B 1010 GLN cc_start: 0.8565 (mm110) cc_final: 0.8324 (pt0) REVERT: C 82 MET cc_start: 0.0778 (mmm) cc_final: -0.1011 (mtt) REVERT: D 126 VAL cc_start: 0.6596 (OUTLIER) cc_final: 0.6147 (t) REVERT: D 153 MET cc_start: -0.0355 (mtm) cc_final: -0.1012 (mmm) REVERT: D 229 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7137 (mp) REVERT: D 238 PHE cc_start: 0.7011 (p90) cc_final: 0.6757 (p90) REVERT: D 604 THR cc_start: 0.7457 (m) cc_final: 0.7035 (m) REVERT: D 854 LYS cc_start: 0.5260 (ptpt) cc_final: 0.4853 (tptt) REVERT: D 957 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8071 (mt0) outliers start: 89 outliers final: 46 residues processed: 274 average time/residue: 1.5403 time to fit residues: 520.8089 Evaluate side-chains 228 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 3.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 86 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 552 LEU 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 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 316 SER 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 979 ASP 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: 0.5980 chunk 280 optimal weight: 0.0270 chunk 53 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 266 optimal weight: 10.0000 chunk 294 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 overall best weight: 2.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 914 ASN A1135 ASN B 66 HIS B 613 GLN D 121 ASN ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 969 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.227469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.161930 restraints weight = 33340.024| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.11 r_work: 0.3369 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 28256 Z= 0.202 Angle : 0.692 11.231 38560 Z= 0.345 Chirality : 0.049 0.276 4469 Planarity : 0.005 0.059 4917 Dihedral : 6.021 57.132 4693 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.25 % Rotamer: Outliers : 4.22 % Allowed : 13.33 % Favored : 82.45 % 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: -0.46 (0.14), residues: 3413 helix: 1.71 (0.20), residues: 681 sheet: 0.04 (0.17), residues: 859 loop : -1.28 (0.13), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 152 HIS 0.005 0.002 HIS A1064 PHE 0.031 0.002 PHE D 541 TYR 0.035 0.002 TYR A1067 ARG 0.011 0.001 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00579 ( 36) link_NAG-ASN : angle 3.38183 ( 108) link_BETA1-4 : bond 0.00314 ( 11) link_BETA1-4 : angle 1.75738 ( 33) hydrogen bonds : bond 0.05574 ( 1091) hydrogen bonds : angle 5.80233 ( 3003) SS BOND : bond 0.00890 ( 41) SS BOND : angle 1.84562 ( 82) covalent geometry : bond 0.00481 (28167) covalent geometry : angle 0.66271 (38337) Misc. bond : bond 0.00017 ( 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 323 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 196 time to evaluate : 2.961 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: 0.0987 (tmt) cc_final: -0.0056 (mpt) REVERT: E 51 ILE cc_start: 0.3891 (OUTLIER) cc_final: 0.3428 (tt) REVERT: A 51 THR cc_start: 0.6637 (p) cc_final: 0.6284 (m) REVERT: A 70 VAL cc_start: 0.1716 (OUTLIER) cc_final: 0.1497 (m) REVERT: A 266 TYR cc_start: 0.6277 (m-80) cc_final: 0.6049 (m-10) REVERT: A 528 LYS cc_start: 0.7913 (ttmm) cc_final: 0.7227 (ttpt) REVERT: A 543 PHE cc_start: 0.7326 (m-10) cc_final: 0.7038 (m-80) REVERT: A 564 GLN cc_start: 0.7443 (mt0) cc_final: 0.7026 (mt0) REVERT: A 574 ASP cc_start: 0.5645 (m-30) cc_final: 0.5322 (t0) REVERT: A 779 GLN cc_start: 0.8782 (tt0) cc_final: 0.8469 (tp40) REVERT: A 933 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8446 (mtmt) REVERT: A 987 PRO cc_start: 0.7662 (Cg_exo) cc_final: 0.7403 (Cg_endo) REVERT: A 1119 ASN cc_start: 0.8121 (m-40) cc_final: 0.7890 (m-40) REVERT: A 1125 ASN cc_start: 0.8108 (m-40) cc_final: 0.7882 (p0) REVERT: B 53 ASP cc_start: 0.7584 (t0) cc_final: 0.7319 (t0) REVERT: B 153 MET cc_start: 0.1232 (tpp) cc_final: -0.1491 (mtt) REVERT: B 201 PHE cc_start: 0.7581 (t80) cc_final: 0.7336 (t80) REVERT: B 266 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7878 (m-80) REVERT: B 271 GLN cc_start: 0.7638 (mt0) cc_final: 0.7343 (mt0) REVERT: B 338 PHE cc_start: 0.4424 (OUTLIER) cc_final: 0.3797 (m-10) REVERT: B 468 ILE cc_start: 0.2981 (OUTLIER) cc_final: 0.2735 (pp) REVERT: B 534 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8061 (m) REVERT: B 574 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7039 (m-30) REVERT: B 814 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.6732 (pptt) REVERT: B 1005 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8517 (mt0) REVERT: B 1010 GLN cc_start: 0.8584 (mm110) cc_final: 0.8301 (pt0) REVERT: D 28 TYR cc_start: 0.6914 (OUTLIER) cc_final: 0.5064 (m-80) REVERT: D 45 SER cc_start: 0.8389 (p) cc_final: 0.8182 (t) REVERT: D 52 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7344 (mm-40) REVERT: D 153 MET cc_start: -0.0365 (mtm) cc_final: -0.1110 (mmp) REVERT: D 229 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7179 (mp) REVERT: D 237 ARG cc_start: 0.7505 (mtt180) cc_final: 0.7154 (mtm180) REVERT: D 565 PHE cc_start: 0.5953 (m-80) cc_final: 0.5700 (m-10) REVERT: D 583 GLU cc_start: 0.5976 (mp0) cc_final: 0.5581 (tp30) REVERT: D 854 LYS cc_start: 0.5362 (ptpt) cc_final: 0.4867 (tptt) REVERT: D 978 ASN cc_start: 0.7815 (t160) cc_final: 0.7086 (m-40) REVERT: D 979 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7737 (OUTLIER) REVERT: D 988 GLU cc_start: 0.7661 (tp30) cc_final: 0.7275 (tt0) REVERT: D 1038 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8362 (mppt) REVERT: D 1125 ASN cc_start: 0.7749 (m-40) cc_final: 0.7534 (p0) outliers start: 127 outliers final: 60 residues processed: 295 average time/residue: 1.0787 time to fit residues: 388.9576 Evaluate side-chains 254 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 180 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE 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 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 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 740 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 933 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 1050 MET 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 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 338 PHE 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 534 VAL 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 719 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 229 LEU 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 534 VAL Chi-restraints excluded: chain D residue 551 VAL 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 957 GLN Chi-restraints excluded: chain D residue 979 ASP Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1038 LYS 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: 8.9990 chunk 137 optimal weight: 10.0000 chunk 254 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 257 optimal weight: 0.1980 chunk 322 optimal weight: 5.9990 chunk 165 optimal weight: 30.0000 chunk 268 optimal weight: 30.0000 chunk 133 optimal weight: 20.0000 chunk 113 optimal weight: 0.6980 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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** A 804 GLN A1010 GLN B 30 ASN B 52 GLN B 66 HIS B1088 HIS D 121 ASN D 146 HIS D 148 ASN ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN D1071 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.226147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.163804 restraints weight = 33192.918| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.99 r_work: 0.3374 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 28256 Z= 0.205 Angle : 0.669 10.472 38560 Z= 0.336 Chirality : 0.048 0.272 4469 Planarity : 0.005 0.060 4917 Dihedral : 5.907 53.000 4693 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 4.19 % Allowed : 13.96 % Favored : 81.85 % 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: -0.51 (0.14), residues: 3413 helix: 1.53 (0.20), residues: 688 sheet: -0.07 (0.16), residues: 899 loop : -1.24 (0.13), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 152 HIS 0.005 0.001 HIS A1064 PHE 0.030 0.002 PHE D 541 TYR 0.070 0.002 TYR A1067 ARG 0.013 0.001 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 36) link_NAG-ASN : angle 3.18591 ( 108) link_BETA1-4 : bond 0.00299 ( 11) link_BETA1-4 : angle 1.69074 ( 33) hydrogen bonds : bond 0.05409 ( 1091) hydrogen bonds : angle 5.75455 ( 3003) SS BOND : bond 0.00819 ( 41) SS BOND : angle 1.73785 ( 82) covalent geometry : bond 0.00486 (28167) covalent geometry : angle 0.64271 (38337) Misc. bond : bond 0.00041 ( 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 320 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 194 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.1020 (tmt) cc_final: 0.0151 (mpt) REVERT: E 51 ILE cc_start: 0.4104 (OUTLIER) cc_final: 0.3695 (tt) REVERT: A 70 VAL cc_start: 0.1657 (OUTLIER) cc_final: 0.1450 (m) REVERT: A 127 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6639 (m) REVERT: A 528 LYS cc_start: 0.7936 (ttmm) cc_final: 0.7298 (ttpt) REVERT: A 564 GLN cc_start: 0.7385 (mt0) cc_final: 0.6961 (mt0) REVERT: A 779 GLN cc_start: 0.8745 (tt0) cc_final: 0.8448 (tp40) REVERT: A 933 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8433 (mtmt) REVERT: A 987 PRO cc_start: 0.7783 (Cg_exo) cc_final: 0.7542 (Cg_endo) REVERT: A 1119 ASN cc_start: 0.8134 (m-40) cc_final: 0.7626 (m110) REVERT: B 53 ASP cc_start: 0.7570 (t0) cc_final: 0.7284 (t0) REVERT: B 153 MET cc_start: 0.0825 (tpp) cc_final: -0.1646 (mtt) REVERT: B 201 PHE cc_start: 0.7552 (t80) cc_final: 0.7321 (t80) REVERT: B 266 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: B 338 PHE cc_start: 0.4537 (OUTLIER) cc_final: 0.3839 (m-10) REVERT: B 468 ILE cc_start: 0.3036 (OUTLIER) cc_final: 0.2770 (pp) REVERT: B 578 ASP cc_start: 0.7629 (t70) cc_final: 0.7397 (t70) REVERT: B 654 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7501 (tm-30) REVERT: B 814 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.7096 (mmtp) REVERT: B 973 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8522 (pp) REVERT: B 990 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7616 (tm-30) REVERT: B 1005 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8500 (mt0) REVERT: B 1010 GLN cc_start: 0.8563 (mm110) cc_final: 0.8327 (pt0) REVERT: C 82 MET cc_start: 0.0718 (mmm) cc_final: -0.1112 (ptp) REVERT: D 28 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.5097 (m-80) REVERT: D 52 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7411 (mm-40) REVERT: D 153 MET cc_start: -0.0456 (mtm) cc_final: -0.1181 (mmp) REVERT: D 237 ARG cc_start: 0.7435 (mtt180) cc_final: 0.7156 (mtm180) REVERT: D 361 CYS cc_start: 0.6327 (OUTLIER) cc_final: 0.5097 (p) REVERT: D 551 VAL cc_start: 0.6380 (OUTLIER) cc_final: 0.6048 (t) REVERT: D 565 PHE cc_start: 0.6033 (m-80) cc_final: 0.5820 (m-10) REVERT: D 583 GLU cc_start: 0.6034 (mp0) cc_final: 0.5596 (tp30) REVERT: D 661 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: D 854 LYS cc_start: 0.5383 (ptpt) cc_final: 0.4924 (tptt) REVERT: D 978 ASN cc_start: 0.7863 (t160) cc_final: 0.7194 (m-40) REVERT: D 1038 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8339 (mppt) outliers start: 126 outliers final: 61 residues processed: 292 average time/residue: 1.0843 time to fit residues: 388.8143 Evaluate side-chains 253 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 175 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain A residue 70 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 407 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 654 GLU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 933 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 66 HIS 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 338 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 468 ILE 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 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 814 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 973 ILE 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 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 551 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1005 GLN Chi-restraints excluded: chain D residue 1038 LYS 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: 0.2980 chunk 123 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 291 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** B1088 HIS C 58 GLN C 102 GLN D 121 ASN ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.227435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.165548 restraints weight = 33519.309| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.06 r_work: 0.3402 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3494 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 : 0.604 11.014 38560 Z= 0.302 Chirality : 0.045 0.248 4469 Planarity : 0.004 0.056 4917 Dihedral : 5.457 57.163 4693 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.16 % Favored : 96.75 % Rotamer: Outliers : 3.32 % Allowed : 15.09 % Favored : 81.58 % 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: 1.84 (0.20), residues: 682 sheet: -0.02 (0.16), residues: 904 loop : -1.16 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 64 HIS 0.024 0.001 HIS B 66 PHE 0.031 0.001 PHE D 541 TYR 0.018 0.001 TYR B1067 ARG 0.008 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 36) link_NAG-ASN : angle 2.91183 ( 108) link_BETA1-4 : bond 0.00330 ( 11) link_BETA1-4 : angle 1.50873 ( 33) hydrogen bonds : bond 0.04580 ( 1091) hydrogen bonds : angle 5.53882 ( 3003) SS BOND : bond 0.00524 ( 41) SS BOND : angle 1.66309 ( 82) covalent geometry : bond 0.00293 (28167) covalent geometry : angle 0.57930 (38337) Misc. bond : bond 0.00020 ( 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 286 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 186 time to evaluate : 3.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.0976 (tmt) cc_final: 0.0140 (mpt) REVERT: E 51 ILE cc_start: 0.4115 (OUTLIER) cc_final: 0.3714 (tt) REVERT: A 51 THR cc_start: 0.6690 (p) cc_final: 0.6442 (m) REVERT: A 70 VAL cc_start: 0.1633 (OUTLIER) cc_final: 0.1407 (m) REVERT: A 127 VAL cc_start: 0.7059 (OUTLIER) cc_final: 0.6684 (m) REVERT: A 359 SER cc_start: 0.7486 (p) cc_final: 0.7281 (m) REVERT: A 528 LYS cc_start: 0.7900 (ttmm) cc_final: 0.7270 (ttpt) REVERT: A 564 GLN cc_start: 0.7409 (mt0) cc_final: 0.6983 (mt0) REVERT: A 779 GLN cc_start: 0.8663 (tt0) cc_final: 0.8395 (tp40) REVERT: A 933 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8371 (mtmt) REVERT: A 987 PRO cc_start: 0.7810 (Cg_exo) cc_final: 0.7523 (Cg_endo) REVERT: A 1010 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8094 (pt0) REVERT: A 1119 ASN cc_start: 0.8016 (m-40) cc_final: 0.7479 (m110) REVERT: B 53 ASP cc_start: 0.7522 (t0) cc_final: 0.7227 (t0) REVERT: B 68 ILE cc_start: 0.3604 (OUTLIER) cc_final: 0.3278 (pp) REVERT: B 153 MET cc_start: 0.0742 (tpp) cc_final: -0.1662 (mtt) REVERT: B 338 PHE cc_start: 0.4546 (OUTLIER) cc_final: 0.3758 (m-10) REVERT: B 468 ILE cc_start: 0.3026 (OUTLIER) cc_final: 0.2736 (pp) REVERT: B 654 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: B 814 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.7085 (mmtp) REVERT: B 990 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7604 (tm-30) REVERT: B 1010 GLN cc_start: 0.8557 (mm110) cc_final: 0.8313 (pt0) REVERT: C 82 MET cc_start: 0.0420 (mmm) cc_final: -0.1300 (ptp) REVERT: D 126 VAL cc_start: 0.6860 (OUTLIER) cc_final: 0.6404 (t) REVERT: D 153 MET cc_start: -0.0322 (mtm) cc_final: -0.1058 (mmp) REVERT: D 237 ARG cc_start: 0.7597 (mtt180) cc_final: 0.7213 (mtm180) REVERT: D 304 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7792 (mmtm) REVERT: D 361 CYS cc_start: 0.6301 (OUTLIER) cc_final: 0.5332 (p) REVERT: D 565 PHE cc_start: 0.5905 (m-80) cc_final: 0.5665 (m-10) REVERT: D 583 GLU cc_start: 0.5991 (mp0) cc_final: 0.5624 (tp30) REVERT: D 703 ASN cc_start: 0.8307 (t0) cc_final: 0.8077 (t0) REVERT: D 854 LYS cc_start: 0.5252 (ptpt) cc_final: 0.4804 (tptt) REVERT: D 978 ASN cc_start: 0.7931 (t160) cc_final: 0.7191 (m-40) outliers start: 100 outliers final: 53 residues processed: 269 average time/residue: 1.0616 time to fit residues: 351.8944 Evaluate side-chains 239 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 175 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain A residue 70 VAL 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 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 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 933 LYS 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 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 468 ILE 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 32 ASN 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 126 VAL Chi-restraints excluded: chain D residue 267 VAL 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 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 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 171 optimal weight: 8.9990 chunk 170 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 303 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 159 optimal weight: 9.9990 chunk 59 optimal weight: 0.0020 chunk 230 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 overall best weight: 1.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 ASN ** 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** B1088 HIS D 121 ASN ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN D 978 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.226182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.167831 restraints weight = 33144.452| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.95 r_work: 0.3414 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 28256 Z= 0.167 Angle : 0.643 19.049 38560 Z= 0.320 Chirality : 0.047 0.323 4469 Planarity : 0.005 0.057 4917 Dihedral : 5.460 59.926 4692 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 3.46 % Allowed : 14.83 % 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: -0.37 (0.14), residues: 3413 helix: 1.76 (0.20), residues: 689 sheet: -0.05 (0.16), residues: 923 loop : -1.17 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 436 HIS 0.005 0.001 HIS A1064 PHE 0.033 0.002 PHE D 541 TYR 0.028 0.002 TYR A1067 ARG 0.008 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00579 ( 36) link_NAG-ASN : angle 3.45752 ( 108) link_BETA1-4 : bond 0.00303 ( 11) link_BETA1-4 : angle 1.59127 ( 33) hydrogen bonds : bond 0.05072 ( 1091) hydrogen bonds : angle 5.59777 ( 3003) SS BOND : bond 0.00703 ( 41) SS BOND : angle 1.68576 ( 82) covalent geometry : bond 0.00391 (28167) covalent geometry : angle 0.61120 (38337) Misc. bond : bond 0.00025 ( 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 289 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 185 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 32 ASN cc_start: 0.5048 (OUTLIER) cc_final: 0.4754 (m-40) REVERT: E 34 MET cc_start: 0.1139 (tmt) cc_final: 0.0361 (mpt) REVERT: A 70 VAL cc_start: 0.1676 (OUTLIER) cc_final: 0.1461 (m) REVERT: A 127 VAL cc_start: 0.7046 (OUTLIER) cc_final: 0.6663 (m) REVERT: A 281 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.5816 (tt0) REVERT: A 359 SER cc_start: 0.7485 (p) cc_final: 0.7279 (m) REVERT: A 528 LYS cc_start: 0.7879 (ttmm) cc_final: 0.7279 (ttpt) REVERT: A 779 GLN cc_start: 0.8704 (tt0) cc_final: 0.8442 (tp40) REVERT: A 933 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8429 (mtmt) REVERT: A 987 PRO cc_start: 0.7843 (Cg_exo) cc_final: 0.7600 (Cg_endo) REVERT: A 1119 ASN cc_start: 0.8101 (m-40) cc_final: 0.7869 (m-40) REVERT: B 53 ASP cc_start: 0.7537 (t0) cc_final: 0.7194 (t0) REVERT: B 68 ILE cc_start: 0.3679 (OUTLIER) cc_final: 0.3380 (pp) REVERT: B 153 MET cc_start: 0.0715 (tpp) cc_final: -0.1637 (mtt) REVERT: B 338 PHE cc_start: 0.4595 (OUTLIER) cc_final: 0.3783 (m-10) REVERT: B 468 ILE cc_start: 0.3125 (OUTLIER) cc_final: 0.2830 (pp) REVERT: B 654 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: B 814 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6683 (pptt) REVERT: B 990 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7612 (tm-30) REVERT: B 1010 GLN cc_start: 0.8545 (mm110) cc_final: 0.8312 (pt0) REVERT: C 82 MET cc_start: 0.0428 (mmm) cc_final: -0.1355 (ptp) REVERT: D 28 TYR cc_start: 0.7144 (OUTLIER) cc_final: 0.5217 (m-80) REVERT: D 153 MET cc_start: -0.0325 (mtm) cc_final: -0.1062 (mmp) REVERT: D 211 ASN cc_start: 0.2671 (OUTLIER) cc_final: 0.2384 (m-40) REVERT: D 237 ARG cc_start: 0.7567 (mtt180) cc_final: 0.7225 (mtm180) REVERT: D 304 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7755 (mmtm) REVERT: D 361 CYS cc_start: 0.6276 (OUTLIER) cc_final: 0.5136 (p) REVERT: D 565 PHE cc_start: 0.5985 (m-80) cc_final: 0.5767 (m-10) REVERT: D 583 GLU cc_start: 0.5888 (mp0) cc_final: 0.5575 (tp30) REVERT: D 661 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7683 (tt0) REVERT: D 703 ASN cc_start: 0.8285 (t0) cc_final: 0.8049 (t0) REVERT: D 854 LYS cc_start: 0.5315 (ptpt) cc_final: 0.4872 (tptt) REVERT: D 978 ASN cc_start: 0.8008 (t0) cc_final: 0.7246 (m-40) outliers start: 104 outliers final: 57 residues processed: 270 average time/residue: 1.1208 time to fit residues: 371.1584 Evaluate side-chains 246 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 176 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain A residue 70 VAL 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 316 SER 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 654 GLU Chi-restraints excluded: chain A residue 933 LYS 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 48 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 468 ILE 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 616 ASN 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 32 ASN 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 126 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 267 VAL 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 740 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 162 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 303 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 115 optimal weight: 0.3980 chunk 280 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 ASN D 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.226203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.165900 restraints weight = 33338.821| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.05 r_work: 0.3381 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3900 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= 0.158 Angle : 0.621 11.829 38560 Z= 0.311 Chirality : 0.046 0.259 4469 Planarity : 0.005 0.057 4917 Dihedral : 5.335 58.571 4689 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.66 % Favored : 96.25 % Rotamer: Outliers : 3.26 % Allowed : 15.56 % Favored : 81.18 % 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: -0.35 (0.14), residues: 3413 helix: 1.80 (0.20), residues: 688 sheet: -0.04 (0.16), residues: 911 loop : -1.16 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 436 HIS 0.004 0.001 HIS A1064 PHE 0.035 0.002 PHE D 541 TYR 0.025 0.001 TYR A1067 ARG 0.007 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 36) link_NAG-ASN : angle 2.87225 ( 108) link_BETA1-4 : bond 0.00315 ( 11) link_BETA1-4 : angle 1.52227 ( 33) hydrogen bonds : bond 0.04862 ( 1091) hydrogen bonds : angle 5.53133 ( 3003) SS BOND : bond 0.00647 ( 41) SS BOND : angle 1.56285 ( 82) covalent geometry : bond 0.00371 (28167) covalent geometry : angle 0.59831 (38337) Misc. bond : bond 0.00020 ( 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 280 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 182 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.1018 (tmt) cc_final: 0.0259 (mpt) REVERT: E 44 GLN cc_start: 0.1379 (OUTLIER) cc_final: 0.1178 (tm130) REVERT: E 51 ILE cc_start: 0.4288 (OUTLIER) cc_final: 0.3873 (tt) REVERT: A 70 VAL cc_start: 0.1632 (OUTLIER) cc_final: 0.1412 (m) REVERT: A 127 VAL cc_start: 0.7035 (OUTLIER) cc_final: 0.6658 (m) REVERT: A 281 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.5806 (tt0) REVERT: A 359 SER cc_start: 0.7483 (p) cc_final: 0.7279 (m) REVERT: A 528 LYS cc_start: 0.7880 (ttmm) cc_final: 0.7271 (ttpt) REVERT: A 740 MET cc_start: 0.8591 (mtp) cc_final: 0.8221 (ttm) REVERT: A 779 GLN cc_start: 0.8702 (tt0) cc_final: 0.8440 (tp40) REVERT: A 933 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8393 (mtmt) REVERT: A 987 PRO cc_start: 0.7823 (Cg_exo) cc_final: 0.7537 (Cg_endo) REVERT: A 1119 ASN cc_start: 0.8122 (m-40) cc_final: 0.7577 (m110) REVERT: B 53 ASP cc_start: 0.7489 (t0) cc_final: 0.7102 (t0) REVERT: B 68 ILE cc_start: 0.3733 (OUTLIER) cc_final: 0.3486 (pp) REVERT: B 153 MET cc_start: 0.0749 (tpp) cc_final: -0.1625 (mtt) REVERT: B 338 PHE cc_start: 0.4662 (OUTLIER) cc_final: 0.3854 (m-10) REVERT: B 468 ILE cc_start: 0.3013 (OUTLIER) cc_final: 0.2741 (pp) REVERT: B 654 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: B 814 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6633 (pptt) REVERT: B 990 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7615 (tm-30) REVERT: B 1005 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8506 (mt0) REVERT: B 1010 GLN cc_start: 0.8575 (mm110) cc_final: 0.8300 (pt0) REVERT: C 82 MET cc_start: 0.0592 (mmm) cc_final: -0.1273 (ptp) REVERT: D 52 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7448 (mm-40) REVERT: D 153 MET cc_start: -0.0364 (mtm) cc_final: -0.0947 (mmp) REVERT: D 200 TYR cc_start: 0.6975 (m-80) cc_final: 0.6406 (m-80) REVERT: D 211 ASN cc_start: 0.2750 (OUTLIER) cc_final: 0.2383 (m-40) REVERT: D 237 ARG cc_start: 0.7581 (mtt180) cc_final: 0.7214 (mtm180) REVERT: D 304 LYS cc_start: 0.8244 (mtpt) cc_final: 0.7732 (mmtm) REVERT: D 361 CYS cc_start: 0.6348 (OUTLIER) cc_final: 0.5314 (p) REVERT: D 583 GLU cc_start: 0.5891 (mp0) cc_final: 0.5486 (tp30) REVERT: D 703 ASN cc_start: 0.8278 (t0) cc_final: 0.8050 (t0) REVERT: D 854 LYS cc_start: 0.5364 (ptpt) cc_final: 0.4872 (tptt) REVERT: D 978 ASN cc_start: 0.8092 (t0) cc_final: 0.7369 (m-40) outliers start: 98 outliers final: 59 residues processed: 260 average time/residue: 1.0926 time to fit residues: 346.2467 Evaluate side-chains 250 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 176 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain A residue 70 VAL 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 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 654 GLU Chi-restraints excluded: chain A residue 933 LYS 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 48 LEU Chi-restraints excluded: chain B residue 51 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 468 ILE 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 1005 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 32 ASN 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 51 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 63 THR 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 740 MET 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 974 SER Chi-restraints excluded: chain D residue 985 ASP 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: 20.0000 chunk 313 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 309 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 158 optimal weight: 9.9990 chunk 285 optimal weight: 7.9990 chunk 93 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 493 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.227899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.166424 restraints weight = 33434.395| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.00 r_work: 0.3420 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28256 Z= 0.111 Angle : 0.574 9.801 38560 Z= 0.289 Chirality : 0.045 0.278 4469 Planarity : 0.004 0.062 4917 Dihedral : 4.979 56.372 4689 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.99 % Favored : 96.92 % Rotamer: Outliers : 2.39 % Allowed : 16.29 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3413 helix: 2.01 (0.20), residues: 688 sheet: -0.02 (0.16), residues: 915 loop : -1.08 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 436 HIS 0.003 0.001 HIS B 69 PHE 0.036 0.001 PHE D 541 TYR 0.016 0.001 TYR B1067 ARG 0.006 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 36) link_NAG-ASN : angle 2.62494 ( 108) link_BETA1-4 : bond 0.00368 ( 11) link_BETA1-4 : angle 1.38810 ( 33) hydrogen bonds : bond 0.04158 ( 1091) hydrogen bonds : angle 5.40875 ( 3003) SS BOND : bond 0.00380 ( 41) SS BOND : angle 1.61984 ( 82) covalent geometry : bond 0.00251 (28167) covalent geometry : angle 0.55235 (38337) Misc. bond : bond 0.00011 ( 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 264 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 192 time to evaluate : 2.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 MET cc_start: 0.0995 (tmt) cc_final: 0.0250 (mpt) REVERT: E 51 ILE cc_start: 0.4345 (OUTLIER) cc_final: 0.3914 (tt) REVERT: A 70 VAL cc_start: 0.1645 (OUTLIER) cc_final: 0.1435 (m) REVERT: A 127 VAL cc_start: 0.7038 (OUTLIER) cc_final: 0.6667 (m) REVERT: A 281 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5799 (tt0) REVERT: A 528 LYS cc_start: 0.7858 (ttmm) cc_final: 0.7257 (ttpt) REVERT: A 779 GLN cc_start: 0.8599 (tt0) cc_final: 0.8371 (tp-100) REVERT: A 987 PRO cc_start: 0.7752 (Cg_exo) cc_final: 0.7449 (Cg_endo) REVERT: A 1119 ASN cc_start: 0.7911 (m-40) cc_final: 0.7360 (m110) REVERT: B 53 ASP cc_start: 0.7459 (t0) cc_final: 0.7013 (t0) REVERT: B 68 ILE cc_start: 0.3866 (OUTLIER) cc_final: 0.3625 (pp) REVERT: B 153 MET cc_start: 0.0921 (tpp) cc_final: -0.1406 (mtt) REVERT: B 338 PHE cc_start: 0.4561 (OUTLIER) cc_final: 0.3781 (m-10) REVERT: B 468 ILE cc_start: 0.2963 (OUTLIER) cc_final: 0.2707 (pt) REVERT: B 587 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7377 (mt) REVERT: B 654 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: B 814 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.7063 (mmtp) REVERT: B 990 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7579 (tm-30) REVERT: B 1010 GLN cc_start: 0.8548 (mm110) cc_final: 0.8297 (pt0) REVERT: C 82 MET cc_start: 0.0403 (mmm) cc_final: -0.1383 (ptp) REVERT: D 51 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8148 (t) REVERT: D 126 VAL cc_start: 0.6936 (OUTLIER) cc_final: 0.6508 (t) REVERT: D 153 MET cc_start: -0.0222 (mtm) cc_final: -0.0853 (mmp) REVERT: D 200 TYR cc_start: 0.6936 (m-80) cc_final: 0.6440 (m-80) REVERT: D 211 ASN cc_start: 0.2946 (OUTLIER) cc_final: 0.2684 (m-40) REVERT: D 237 ARG cc_start: 0.7584 (mtt180) cc_final: 0.7187 (mtm180) REVERT: D 304 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7706 (mmtm) REVERT: D 361 CYS cc_start: 0.6233 (OUTLIER) cc_final: 0.5401 (p) REVERT: D 583 GLU cc_start: 0.5822 (mp0) cc_final: 0.5517 (tp30) REVERT: D 854 LYS cc_start: 0.5383 (ptpt) cc_final: 0.4921 (tptt) REVERT: D 978 ASN cc_start: 0.8035 (t0) cc_final: 0.7328 (m-40) outliers start: 72 outliers final: 44 residues processed: 252 average time/residue: 1.1212 time to fit residues: 349.5148 Evaluate side-chains 235 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 177 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain A residue 70 VAL 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 281 GLU 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 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 549 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 68 ILE 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 338 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL 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 654 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain C residue 32 ASN 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 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 941 THR Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 985 ASP 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: 6.9990 chunk 60 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 294 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 238 optimal weight: 0.8980 chunk 201 optimal weight: 0.7980 chunk 259 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 87 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 ASN D 703 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 = 0.4525 r_free = 0.4525 target = 0.223763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.163063 restraints weight = 33108.594| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.13 r_work: 0.3330 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 28256 Z= 0.269 Angle : 0.736 13.399 38560 Z= 0.369 Chirality : 0.051 0.268 4469 Planarity : 0.005 0.077 4917 Dihedral : 5.817 59.114 4687 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 2.89 % Allowed : 15.96 % Favored : 81.15 % 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: -0.50 (0.14), residues: 3413 helix: 1.54 (0.20), residues: 684 sheet: -0.15 (0.17), residues: 891 loop : -1.17 (0.13), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 436 HIS 0.008 0.002 HIS B1088 PHE 0.033 0.002 PHE D 541 TYR 0.034 0.002 TYR A1067 ARG 0.007 0.001 ARG D 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 36) link_NAG-ASN : angle 3.17612 ( 108) link_BETA1-4 : bond 0.00328 ( 11) link_BETA1-4 : angle 1.78967 ( 33) hydrogen bonds : bond 0.06021 ( 1091) hydrogen bonds : angle 5.75623 ( 3003) SS BOND : bond 0.01162 ( 41) SS BOND : angle 2.29888 ( 82) covalent geometry : bond 0.00645 (28167) covalent geometry : angle 0.70839 (38337) Misc. bond : bond 0.00014 ( 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 264 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 177 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 32 ASN cc_start: 0.5702 (OUTLIER) cc_final: 0.5303 (m-40) REVERT: E 34 MET cc_start: 0.1258 (tmt) cc_final: 0.0537 (mpt) REVERT: E 51 ILE cc_start: 0.4409 (OUTLIER) cc_final: 0.4101 (tt) REVERT: A 127 VAL cc_start: 0.7052 (OUTLIER) cc_final: 0.6665 (m) REVERT: A 281 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5798 (tt0) REVERT: A 528 LYS cc_start: 0.7852 (ttmm) cc_final: 0.7248 (ttpt) REVERT: A 740 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8430 (ttp) REVERT: A 779 GLN cc_start: 0.8781 (tt0) cc_final: 0.8465 (tp40) REVERT: A 987 PRO cc_start: 0.7872 (Cg_exo) cc_final: 0.7622 (Cg_endo) REVERT: B 53 ASP cc_start: 0.7592 (t0) cc_final: 0.7116 (t0) REVERT: B 68 ILE cc_start: 0.3787 (OUTLIER) cc_final: 0.3526 (pp) REVERT: B 153 MET cc_start: 0.0856 (tpp) cc_final: -0.1496 (mtt) REVERT: B 338 PHE cc_start: 0.4878 (OUTLIER) cc_final: 0.4038 (m-10) REVERT: B 468 ILE cc_start: 0.3081 (OUTLIER) cc_final: 0.2808 (pp) REVERT: B 654 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: B 814 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7204 (mmtp) REVERT: B 1005 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8541 (mt0) REVERT: B 1010 GLN cc_start: 0.8620 (mm110) cc_final: 0.8341 (pt0) REVERT: C 82 MET cc_start: 0.0661 (mmm) cc_final: -0.1316 (ptp) REVERT: D 28 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.5936 (m-80) REVERT: D 153 MET cc_start: -0.0283 (mtm) cc_final: -0.0901 (mmp) REVERT: D 200 TYR cc_start: 0.7004 (m-80) cc_final: 0.6443 (m-80) REVERT: D 211 ASN cc_start: 0.3020 (OUTLIER) cc_final: 0.2744 (m-40) REVERT: D 237 ARG cc_start: 0.7715 (mtt180) cc_final: 0.7203 (mtm180) REVERT: D 304 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7737 (mmtm) REVERT: D 361 CYS cc_start: 0.6354 (OUTLIER) cc_final: 0.5078 (p) REVERT: D 583 GLU cc_start: 0.5940 (mp0) cc_final: 0.5481 (tp30) REVERT: D 586 ASP cc_start: 0.5417 (p0) cc_final: 0.4471 (m-30) REVERT: D 854 LYS cc_start: 0.5463 (ptpt) cc_final: 0.4978 (tptt) REVERT: D 978 ASN cc_start: 0.8151 (t0) cc_final: 0.7440 (m-40) outliers start: 87 outliers final: 55 residues processed: 247 average time/residue: 1.0309 time to fit residues: 314.3997 Evaluate side-chains 235 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 166 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 51 ILE 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 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 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 991 VAL 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 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 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 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 126 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 211 ASN 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 941 THR Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 979 ASP 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: 4.9990 chunk 186 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 309 optimal weight: 0.5980 chunk 329 optimal weight: 0.2980 chunk 12 optimal weight: 8.9990 chunk 153 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 ASN E 44 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 52 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS ** 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 = 0.4542 r_free = 0.4542 target = 0.225645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153033 restraints weight = 33129.334| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 4.58 r_work: 0.3311 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 28256 Z= 0.145 Angle : 0.635 15.254 38560 Z= 0.319 Chirality : 0.050 1.258 4469 Planarity : 0.005 0.057 4917 Dihedral : 5.480 59.692 4687 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.43 % Favored : 96.48 % Rotamer: Outliers : 2.39 % Allowed : 16.72 % Favored : 80.88 % 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: -0.37 (0.14), residues: 3413 helix: 1.90 (0.20), residues: 666 sheet: -0.09 (0.16), residues: 901 loop : -1.16 (0.13), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 436 HIS 0.004 0.001 HIS A1064 PHE 0.036 0.001 PHE D 541 TYR 0.023 0.001 TYR A1067 ARG 0.005 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 36) link_NAG-ASN : angle 3.06963 ( 108) link_BETA1-4 : bond 0.00380 ( 11) link_BETA1-4 : angle 1.47792 ( 33) hydrogen bonds : bond 0.04846 ( 1091) hydrogen bonds : angle 5.59427 ( 3003) SS BOND : bond 0.00597 ( 41) SS BOND : angle 1.84775 ( 82) covalent geometry : bond 0.00336 (28167) covalent geometry : angle 0.60805 (38337) Misc. bond : bond 0.00011 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32101.73 seconds wall clock time: 557 minutes 52.39 seconds (33472.39 seconds total)