Starting phenix.real_space_refine on Thu Mar 5 16:04:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kj5_22894/03_2026/7kj5_22894.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kj5_22894/03_2026/7kj5_22894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kj5_22894/03_2026/7kj5_22894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kj5_22894/03_2026/7kj5_22894.map" model { file = "/net/cci-nas-00/data/ceres_data/7kj5_22894/03_2026/7kj5_22894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kj5_22894/03_2026/7kj5_22894.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 14999 2.51 5 N 3830 2.21 5 O 4632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 172 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23562 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7569 Classifications: {'peptide': 967} Link IDs: {'PTRANS': 48, 'TRANS': 918} Chain breaks: 11 Chain: "B" Number of atoms: 7662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7662 Classifications: {'peptide': 981} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 932} Chain breaks: 10 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 7505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 7505 Classifications: {'peptide': 961} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 912} Chain breaks: 10 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: "A" 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: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.71, per 1000 atoms: 0.24 Number of scatterers: 23562 At special positions: 0 Unit cell: (129.525, 137.775, 193.05, 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 101 16.00 O 4632 8.00 N 3830 7.00 C 14999 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.84 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.97 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.06 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.95 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.00 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.14 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.24 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=2.46 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 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=2.51 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.06 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.01 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.95 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.84 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.01 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.05 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 Atom "HETATM22776 O5 NAG E 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 717 " " NAG B1312 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " 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 B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 904.6 milliseconds 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5466 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 42 sheets defined 27.7% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.543A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.986A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.598A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.644A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.071A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.577A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) 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 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.231A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.621A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.302A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.753A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.622A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.222A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.991A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.563A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.422A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.610A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 3.653A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.659A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.952A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 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: 4.485A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.625A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.109A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.731A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.914A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.615A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.631A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.604A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.269A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.768A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.094A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.713A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.771A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.878A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.346A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.102A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.173A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.633A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.613A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.545A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.510A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.875A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.768A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.768A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.041A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.098A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.397A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.149A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.197A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.663A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.819A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.205A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.628A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.129A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.706A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.450A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.573A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.635A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD1, first strand: chain 'B' and resid 721 through 728 removed outlier: 6.197A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.742A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.795A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.034A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.990A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.767A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.642A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.644A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.791A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.333A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.658A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 980 hydrogen bonds defined for protein. 2676 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: 5.49 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5701 1.33 - 1.46: 5446 1.46 - 1.58: 12784 1.58 - 1.71: 6 1.71 - 1.83: 125 Bond restraints: 24062 Sorted by residual: bond pdb=" C5 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.413 1.504 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" N ILE B 402 " pdb=" CA ILE B 402 " ideal model delta sigma weight residual 1.457 1.506 -0.049 1.11e-02 8.12e+03 1.98e+01 bond pdb=" C5 NAG C1311 " pdb=" O5 NAG C1311 " ideal model delta sigma weight residual 1.413 1.501 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C5 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.413 1.499 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.497 -0.084 2.00e-02 2.50e+03 1.78e+01 ... (remaining 24057 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 26589 2.50 - 5.01: 5639 5.01 - 7.51: 465 7.51 - 10.01: 30 10.01 - 12.52: 5 Bond angle restraints: 32728 Sorted by residual: angle pdb=" N ARG C 328 " pdb=" CA ARG C 328 " pdb=" C ARG C 328 " ideal model delta sigma weight residual 109.54 122.06 -12.52 1.37e+00 5.33e-01 8.35e+01 angle pdb=" N LEU C 390 " pdb=" CA LEU C 390 " pdb=" C LEU C 390 " ideal model delta sigma weight residual 110.53 121.99 -11.46 1.32e+00 5.74e-01 7.53e+01 angle pdb=" N ARG A 214 " pdb=" CA ARG A 214 " pdb=" C ARG A 214 " ideal model delta sigma weight residual 112.12 122.85 -10.73 1.34e+00 5.57e-01 6.41e+01 angle pdb=" CA PHE B 643 " pdb=" CB PHE B 643 " pdb=" CG PHE B 643 " ideal model delta sigma weight residual 113.80 120.63 -6.83 1.00e+00 1.00e+00 4.67e+01 angle pdb=" N ASN B 121 " pdb=" CA ASN B 121 " pdb=" C ASN B 121 " ideal model delta sigma weight residual 108.67 98.20 10.47 1.55e+00 4.16e-01 4.56e+01 ... (remaining 32723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 13924 17.65 - 35.30: 885 35.30 - 52.95: 195 52.95 - 70.61: 63 70.61 - 88.26: 38 Dihedral angle restraints: 15105 sinusoidal: 6639 harmonic: 8466 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual 93.00 12.72 80.28 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -165.59 79.59 1 1.00e+01 1.00e-02 7.86e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 17.11 75.89 1 1.00e+01 1.00e-02 7.26e+01 ... (remaining 15102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 3870 0.338 - 0.676: 37 0.676 - 1.014: 2 1.014 - 1.353: 2 1.353 - 1.691: 3 Chirality restraints: 3914 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -0.71 -1.69 2.00e-01 2.50e+01 7.15e+01 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -0.74 -1.66 2.00e-01 2.50e+01 6.86e+01 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN C 717 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.94 -1.46 2.00e-01 2.50e+01 5.34e+01 ... (remaining 3911 not shown) Planarity restraints: 4191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C1134 " 0.226 2.00e-02 2.50e+03 3.12e-01 1.21e+03 pdb=" CG ASN C1134 " -0.133 2.00e-02 2.50e+03 pdb=" OD1 ASN C1134 " -0.081 2.00e-02 2.50e+03 pdb=" ND2 ASN C1134 " -0.459 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.447 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.088 2.00e-02 2.50e+03 2.15e-01 5.77e+02 pdb=" CG ASN A 331 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.068 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.397 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 616 " 0.184 2.00e-02 2.50e+03 1.86e-01 4.34e+02 pdb=" CG ASN C 616 " -0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN C 616 " -0.063 2.00e-02 2.50e+03 pdb=" ND2 ASN C 616 " -0.274 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " 0.233 2.00e-02 2.50e+03 ... (remaining 4188 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 7 2.08 - 2.79: 2524 2.79 - 3.49: 32772 3.49 - 4.20: 56504 4.20 - 4.90: 96716 Nonbonded interactions: 188523 Sorted by model distance: nonbonded pdb=" OD1 ASN C 125 " pdb=" OG SER C 172 " model vdw 1.376 3.040 nonbonded pdb=" ND2 ASN C1134 " pdb=" N2 NAG O 1 " model vdw 1.829 2.560 nonbonded pdb=" CE1 PHE C 559 " pdb=" CB GLN C 563 " model vdw 1.923 3.740 nonbonded pdb=" ND2 ASN A 125 " pdb=" O SER A 172 " model vdw 1.997 3.120 nonbonded pdb=" N CYS B 617 " pdb=" OE1 GLN B 644 " model vdw 2.028 3.120 ... (remaining 188518 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 140 or resi \ d 166 through 196 or resid 200 through 211 or resid 215 through 263 or resid 265 \ through 442 or resid 450 through 451 or resid 453 or resid 455 or resid 457 or \ (resid 458 and (name N or name CA or name C or name O or name CB )) or resid 463 \ through 470 or resid 491 through 515 or resid 522 through 827 or resid 856 thro \ ugh 1310)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 113 or resid 116 through \ 140 or resid 166 through 263 or resid 265 through 442 or resid 450 through 451 \ or resid 453 or resid 455 or resid 457 or (resid 458 and (name N or name CA or n \ ame C or name O or name CB )) or resid 463 through 470 or resid 491 through 501 \ or resid 503 through 676 or resid 690 through 827 or resid 856 through 1310)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 113 or resi \ d 116 through 140 or resid 166 through 196 or resid 200 through 211 or resid 215 \ through 442 or resid 448 through 449 or resid 451 through 452 or resid 454 thro \ ugh 501 or resid 503 through 515 or resid 522 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = 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' } 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 group one per residue 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: 10.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 23.690 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 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 : 0.021 0.943 24155 Z= 1.162 Angle : 2.192 51.065 32970 Z= 1.351 Chirality : 0.133 1.691 3914 Planarity : 0.013 0.118 4147 Dihedral : 13.266 88.257 9528 Min Nonbonded Distance : 1.376 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.95 % Favored : 91.62 % Rotamer: Outliers : 2.00 % Allowed : 3.57 % Favored : 94.43 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.14), residues: 2841 helix: -2.59 (0.15), residues: 670 sheet: -0.24 (0.22), residues: 465 loop : -1.48 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.002 ARG A 577 TYR 0.116 0.020 TYR B 707 PHE 0.082 0.017 PHE A 464 TRP 0.103 0.026 TRP C 436 HIS 0.026 0.007 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.01558 (24062) covalent geometry : angle 1.94758 (32728) SS BOND : bond 0.34335 ( 37) SS BOND : angle 13.12755 ( 74) hydrogen bonds : bond 0.16260 ( 980) hydrogen bonds : angle 9.15606 ( 2676) link_BETA1-4 : bond 0.05813 ( 12) link_BETA1-4 : angle 3.39574 ( 36) link_NAG-ASN : bond 0.14105 ( 44) link_NAG-ASN : angle 12.64574 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 489 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7375 (ttm) cc_final: 0.7131 (ttp) REVERT: A 987 PRO cc_start: 0.8240 (Cg_exo) cc_final: 0.8030 (Cg_endo) REVERT: B 460 ASN cc_start: 0.2418 (OUTLIER) cc_final: 0.2123 (p0) REVERT: B 480 CYS cc_start: 0.1907 (OUTLIER) cc_final: 0.1182 (p) REVERT: B 904 TYR cc_start: 0.6394 (m-10) cc_final: 0.6076 (m-10) REVERT: C 453 TYR cc_start: 0.6945 (p90) cc_final: 0.6467 (p90) REVERT: C 1006 THR cc_start: 0.8444 (m) cc_final: 0.8128 (p) outliers start: 51 outliers final: 13 residues processed: 531 average time/residue: 0.1633 time to fit residues: 133.0698 Evaluate side-chains 250 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 235 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 239 GLN B 764 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 207 HIS C 314 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 901 GLN C 955 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.135330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.100303 restraints weight = 51073.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.099935 restraints weight = 37528.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.100677 restraints weight = 30970.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.100872 restraints weight = 26383.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.101062 restraints weight = 23995.674| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24155 Z= 0.157 Angle : 0.771 17.297 32970 Z= 0.394 Chirality : 0.050 0.504 3914 Planarity : 0.005 0.043 4147 Dihedral : 6.604 55.276 4356 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.45 % Favored : 96.41 % Rotamer: Outliers : 1.92 % Allowed : 9.45 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 2841 helix: -0.40 (0.19), residues: 692 sheet: -0.05 (0.19), residues: 609 loop : -1.14 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 44 TYR 0.026 0.002 TYR C1067 PHE 0.029 0.002 PHE B 168 TRP 0.023 0.003 TRP A 886 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00338 (24062) covalent geometry : angle 0.71956 (32728) SS BOND : bond 0.00511 ( 37) SS BOND : angle 2.13262 ( 74) hydrogen bonds : bond 0.04510 ( 980) hydrogen bonds : angle 6.62920 ( 2676) link_BETA1-4 : bond 0.00443 ( 12) link_BETA1-4 : angle 1.88979 ( 36) link_NAG-ASN : bond 0.00590 ( 44) link_NAG-ASN : angle 4.06463 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 278 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 987 PRO cc_start: 0.8695 (Cg_exo) cc_final: 0.8414 (Cg_endo) REVERT: B 460 ASN cc_start: 0.2583 (OUTLIER) cc_final: 0.2239 (p0) REVERT: B 489 TYR cc_start: 0.4802 (OUTLIER) cc_final: 0.4004 (t80) REVERT: B 900 MET cc_start: 0.7964 (mtp) cc_final: 0.7701 (mtm) REVERT: B 990 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: B 1017 GLU cc_start: 0.7096 (tp30) cc_final: 0.6827 (tm-30) REVERT: B 1139 ASP cc_start: 0.8249 (t0) cc_final: 0.7523 (t0) REVERT: C 453 TYR cc_start: 0.7452 (p90) cc_final: 0.7185 (p90) REVERT: C 796 ASP cc_start: 0.6637 (t0) cc_final: 0.6365 (t0) REVERT: C 1006 THR cc_start: 0.8494 (m) cc_final: 0.8158 (p) outliers start: 49 outliers final: 23 residues processed: 315 average time/residue: 0.1414 time to fit residues: 71.6488 Evaluate side-chains 217 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 761 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 227 optimal weight: 30.0000 chunk 1 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 784 GLN C 49 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.132380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.097859 restraints weight = 51199.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.096456 restraints weight = 38183.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.097186 restraints weight = 34449.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.097556 restraints weight = 27255.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.097846 restraints weight = 24574.071| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 : 0.004 0.090 24155 Z= 0.180 Angle : 0.688 14.525 32970 Z= 0.347 Chirality : 0.047 0.358 3914 Planarity : 0.004 0.058 4147 Dihedral : 5.867 55.251 4343 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 2.74 % Allowed : 10.82 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.15), residues: 2841 helix: -0.01 (0.19), residues: 692 sheet: 0.13 (0.19), residues: 603 loop : -0.92 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 237 TYR 0.025 0.002 TYR B 453 PHE 0.024 0.002 PHE B 168 TRP 0.022 0.002 TRP C 353 HIS 0.006 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00413 (24062) covalent geometry : angle 0.65487 (32728) SS BOND : bond 0.00868 ( 37) SS BOND : angle 1.91080 ( 74) hydrogen bonds : bond 0.04101 ( 980) hydrogen bonds : angle 6.20257 ( 2676) link_BETA1-4 : bond 0.00460 ( 12) link_BETA1-4 : angle 1.48671 ( 36) link_NAG-ASN : bond 0.00566 ( 44) link_NAG-ASN : angle 3.05123 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 225 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.7698 (p90) cc_final: 0.7441 (p90) REVERT: A 558 LYS cc_start: 0.7553 (mttt) cc_final: 0.7071 (mtpt) REVERT: B 460 ASN cc_start: 0.2789 (OUTLIER) cc_final: 0.2155 (p0) REVERT: B 900 MET cc_start: 0.7911 (mtp) cc_final: 0.7652 (mtm) REVERT: B 990 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: B 1017 GLU cc_start: 0.7035 (tp30) cc_final: 0.6714 (tm-30) REVERT: B 1139 ASP cc_start: 0.8236 (t0) cc_final: 0.7947 (t0) REVERT: C 115 GLN cc_start: 0.6916 (mt0) cc_final: 0.6290 (mm110) REVERT: C 796 ASP cc_start: 0.6724 (t0) cc_final: 0.6386 (t0) REVERT: C 955 ASN cc_start: 0.7749 (m-40) cc_final: 0.7287 (m110) REVERT: C 1006 THR cc_start: 0.8554 (m) cc_final: 0.8207 (p) outliers start: 70 outliers final: 49 residues processed: 274 average time/residue: 0.1364 time to fit residues: 61.8284 Evaluate side-chains 233 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 146 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 252 optimal weight: 0.8980 chunk 133 optimal weight: 30.0000 chunk 149 optimal weight: 0.9980 chunk 279 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 872 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.132542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.098159 restraints weight = 51582.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.097643 restraints weight = 38725.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.098625 restraints weight = 36166.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.098462 restraints weight = 28133.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.098658 restraints weight = 25131.780| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24155 Z= 0.151 Angle : 0.634 13.823 32970 Z= 0.320 Chirality : 0.045 0.301 3914 Planarity : 0.004 0.048 4147 Dihedral : 5.551 55.715 4342 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.84 % Favored : 96.06 % Rotamer: Outliers : 2.98 % Allowed : 12.15 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.15), residues: 2841 helix: 0.29 (0.20), residues: 694 sheet: 0.02 (0.19), residues: 615 loop : -0.90 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 346 TYR 0.025 0.002 TYR B 453 PHE 0.016 0.001 PHE C 135 TRP 0.018 0.002 TRP C 353 HIS 0.005 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00344 (24062) covalent geometry : angle 0.60141 (32728) SS BOND : bond 0.00481 ( 37) SS BOND : angle 2.18603 ( 74) hydrogen bonds : bond 0.03689 ( 980) hydrogen bonds : angle 5.97211 ( 2676) link_BETA1-4 : bond 0.00398 ( 12) link_BETA1-4 : angle 1.33876 ( 36) link_NAG-ASN : bond 0.00399 ( 44) link_NAG-ASN : angle 2.73877 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 212 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.7603 (p90) cc_final: 0.7077 (p90) REVERT: A 402 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7748 (pt) REVERT: A 558 LYS cc_start: 0.7535 (mttt) cc_final: 0.7281 (mttt) REVERT: A 732 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8803 (p) REVERT: A 902 MET cc_start: 0.8537 (tpt) cc_final: 0.8015 (tpt) REVERT: B 460 ASN cc_start: 0.2645 (OUTLIER) cc_final: 0.1789 (p0) REVERT: B 990 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: B 1017 GLU cc_start: 0.7032 (tp30) cc_final: 0.6765 (tm-30) REVERT: B 1139 ASP cc_start: 0.8110 (t0) cc_final: 0.7868 (t0) REVERT: C 115 GLN cc_start: 0.6949 (mt0) cc_final: 0.6339 (mm110) REVERT: C 353 TRP cc_start: 0.5364 (p-90) cc_final: 0.5137 (p-90) REVERT: C 796 ASP cc_start: 0.6800 (t0) cc_final: 0.6488 (t0) REVERT: C 955 ASN cc_start: 0.7766 (m-40) cc_final: 0.7413 (m110) REVERT: C 1006 THR cc_start: 0.8572 (m) cc_final: 0.8280 (p) outliers start: 76 outliers final: 52 residues processed: 268 average time/residue: 0.1328 time to fit residues: 58.6204 Evaluate side-chains 244 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 51 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 chunk 233 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN B1119 ASN C 784 GLN C1036 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.129922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.095803 restraints weight = 51544.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.093986 restraints weight = 39593.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.094756 restraints weight = 36352.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.095192 restraints weight = 27902.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.095399 restraints weight = 25685.363| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 24155 Z= 0.214 Angle : 0.670 13.284 32970 Z= 0.339 Chirality : 0.047 0.285 3914 Planarity : 0.005 0.057 4147 Dihedral : 5.673 55.545 4341 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.82 % Favored : 95.07 % Rotamer: Outliers : 3.10 % Allowed : 13.68 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.15), residues: 2841 helix: -0.01 (0.19), residues: 693 sheet: -0.13 (0.19), residues: 646 loop : -1.05 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1107 TYR 0.022 0.002 TYR B 904 PHE 0.024 0.002 PHE B 168 TRP 0.011 0.002 TRP A 104 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00494 (24062) covalent geometry : angle 0.64400 (32728) SS BOND : bond 0.00433 ( 37) SS BOND : angle 1.77553 ( 74) hydrogen bonds : bond 0.03989 ( 980) hydrogen bonds : angle 6.06383 ( 2676) link_BETA1-4 : bond 0.00319 ( 12) link_BETA1-4 : angle 1.22224 ( 36) link_NAG-ASN : bond 0.00407 ( 44) link_NAG-ASN : angle 2.65056 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 211 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 SER cc_start: 0.7728 (OUTLIER) cc_final: 0.7507 (p) REVERT: A 400 PHE cc_start: 0.7789 (p90) cc_final: 0.7232 (p90) REVERT: A 558 LYS cc_start: 0.7603 (mttt) cc_final: 0.7333 (mttt) REVERT: A 902 MET cc_start: 0.8478 (tpt) cc_final: 0.8161 (tpt) REVERT: A 964 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8163 (mtpt) REVERT: B 588 THR cc_start: 0.8790 (m) cc_final: 0.8543 (p) REVERT: B 900 MET cc_start: 0.7912 (mtp) cc_final: 0.7564 (mtm) REVERT: B 990 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: B 1017 GLU cc_start: 0.7148 (tp30) cc_final: 0.6904 (tm-30) REVERT: B 1139 ASP cc_start: 0.8122 (t0) cc_final: 0.7896 (t0) REVERT: C 115 GLN cc_start: 0.7071 (mt0) cc_final: 0.6363 (mm-40) REVERT: C 353 TRP cc_start: 0.5522 (p-90) cc_final: 0.5172 (p-90) REVERT: C 796 ASP cc_start: 0.6678 (t0) cc_final: 0.6451 (t0) REVERT: C 955 ASN cc_start: 0.7749 (m-40) cc_final: 0.7365 (m110) REVERT: C 1006 THR cc_start: 0.8491 (m) cc_final: 0.8185 (p) outliers start: 79 outliers final: 60 residues processed: 271 average time/residue: 0.1359 time to fit residues: 60.3243 Evaluate side-chains 245 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 182 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 186 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 273 optimal weight: 5.9990 chunk 230 optimal weight: 9.9990 chunk 83 optimal weight: 0.5980 chunk 11 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 251 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.132101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.097654 restraints weight = 51549.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.096971 restraints weight = 41294.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.097694 restraints weight = 35381.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.098094 restraints weight = 27147.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.098421 restraints weight = 25046.756| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24155 Z= 0.121 Angle : 0.587 13.009 32970 Z= 0.296 Chirality : 0.044 0.253 3914 Planarity : 0.004 0.042 4147 Dihedral : 5.069 55.543 4339 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.41 % Favored : 96.48 % Rotamer: Outliers : 2.04 % Allowed : 15.33 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.15), residues: 2841 helix: 0.46 (0.20), residues: 693 sheet: -0.04 (0.19), residues: 662 loop : -0.95 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 346 TYR 0.029 0.001 TYR B 904 PHE 0.022 0.001 PHE B 802 TRP 0.016 0.001 TRP C 104 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00276 (24062) covalent geometry : angle 0.56310 (32728) SS BOND : bond 0.00361 ( 37) SS BOND : angle 1.42654 ( 74) hydrogen bonds : bond 0.03397 ( 980) hydrogen bonds : angle 5.77874 ( 2676) link_BETA1-4 : bond 0.00379 ( 12) link_BETA1-4 : angle 1.18618 ( 36) link_NAG-ASN : bond 0.00354 ( 44) link_NAG-ASN : angle 2.42926 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.7621 (p90) cc_final: 0.7119 (p90) REVERT: A 902 MET cc_start: 0.8362 (tpt) cc_final: 0.8128 (tpt) REVERT: B 588 THR cc_start: 0.8731 (m) cc_final: 0.8529 (p) REVERT: B 900 MET cc_start: 0.7641 (mtp) cc_final: 0.7391 (mtm) REVERT: B 904 TYR cc_start: 0.6879 (m-10) cc_final: 0.6218 (m-80) REVERT: B 990 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: B 1017 GLU cc_start: 0.7129 (tp30) cc_final: 0.6863 (tm-30) REVERT: B 1139 ASP cc_start: 0.8004 (t0) cc_final: 0.7686 (t0) REVERT: C 115 GLN cc_start: 0.6783 (mt0) cc_final: 0.6246 (mm-40) REVERT: C 353 TRP cc_start: 0.5412 (p-90) cc_final: 0.5201 (p-90) REVERT: C 796 ASP cc_start: 0.6716 (t0) cc_final: 0.6457 (t0) REVERT: C 955 ASN cc_start: 0.7672 (m-40) cc_final: 0.7278 (m110) REVERT: C 1006 THR cc_start: 0.8536 (m) cc_final: 0.8283 (p) outliers start: 52 outliers final: 40 residues processed: 253 average time/residue: 0.1369 time to fit residues: 56.6813 Evaluate side-chains 225 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 260 optimal weight: 1.9990 chunk 215 optimal weight: 0.0060 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 269 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.131163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.096709 restraints weight = 51501.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.095808 restraints weight = 38728.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.096778 restraints weight = 36596.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.096783 restraints weight = 28349.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.096978 restraints weight = 25194.473| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24155 Z= 0.146 Angle : 0.597 13.122 32970 Z= 0.302 Chirality : 0.045 0.289 3914 Planarity : 0.004 0.047 4147 Dihedral : 4.976 56.870 4339 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.36 % Favored : 95.53 % Rotamer: Outliers : 2.59 % Allowed : 15.72 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.15), residues: 2841 helix: 0.48 (0.20), residues: 701 sheet: 0.04 (0.19), residues: 659 loop : -0.98 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 905 TYR 0.027 0.001 TYR C 453 PHE 0.020 0.001 PHE B 168 TRP 0.012 0.001 TRP C 104 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00337 (24062) covalent geometry : angle 0.57418 (32728) SS BOND : bond 0.00349 ( 37) SS BOND : angle 1.38763 ( 74) hydrogen bonds : bond 0.03462 ( 980) hydrogen bonds : angle 5.74592 ( 2676) link_BETA1-4 : bond 0.00346 ( 12) link_BETA1-4 : angle 1.15341 ( 36) link_NAG-ASN : bond 0.00350 ( 44) link_NAG-ASN : angle 2.39015 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 190 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LYS cc_start: 0.6983 (mmtm) cc_final: 0.6563 (mptt) REVERT: A 400 PHE cc_start: 0.7737 (p90) cc_final: 0.7165 (p90) REVERT: A 740 MET cc_start: 0.7637 (tpt) cc_final: 0.7381 (tpt) REVERT: A 902 MET cc_start: 0.8456 (tpt) cc_final: 0.8219 (tpt) REVERT: B 588 THR cc_start: 0.8744 (m) cc_final: 0.8517 (p) REVERT: B 900 MET cc_start: 0.7860 (mtp) cc_final: 0.7651 (mtm) REVERT: B 990 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: B 1017 GLU cc_start: 0.7151 (tp30) cc_final: 0.6931 (tm-30) REVERT: B 1139 ASP cc_start: 0.8042 (t0) cc_final: 0.7716 (t0) REVERT: C 115 GLN cc_start: 0.6881 (mt0) cc_final: 0.6295 (mm-40) REVERT: C 555 SER cc_start: 0.7637 (OUTLIER) cc_final: 0.7189 (p) REVERT: C 796 ASP cc_start: 0.6725 (t0) cc_final: 0.6486 (t0) REVERT: C 955 ASN cc_start: 0.7784 (m-40) cc_final: 0.7345 (m110) REVERT: C 1006 THR cc_start: 0.8484 (m) cc_final: 0.8186 (p) outliers start: 66 outliers final: 52 residues processed: 239 average time/residue: 0.1367 time to fit residues: 53.6378 Evaluate side-chains 235 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 181 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 228 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 252 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 269 optimal weight: 7.9990 chunk 130 optimal weight: 30.0000 chunk 127 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 238 optimal weight: 0.4980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.131004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.096838 restraints weight = 51316.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.095872 restraints weight = 38671.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.096525 restraints weight = 37396.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.096928 restraints weight = 27329.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.097521 restraints weight = 25077.149| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24155 Z= 0.147 Angle : 0.590 12.985 32970 Z= 0.298 Chirality : 0.045 0.265 3914 Planarity : 0.004 0.042 4147 Dihedral : 4.917 57.906 4339 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.84 % Favored : 96.06 % Rotamer: Outliers : 2.47 % Allowed : 16.15 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.15), residues: 2841 helix: 0.50 (0.20), residues: 701 sheet: 0.07 (0.19), residues: 661 loop : -0.96 (0.15), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 765 TYR 0.022 0.001 TYR C 453 PHE 0.028 0.001 PHE C 374 TRP 0.018 0.001 TRP C 353 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00340 (24062) covalent geometry : angle 0.56795 (32728) SS BOND : bond 0.00333 ( 37) SS BOND : angle 1.30375 ( 74) hydrogen bonds : bond 0.03436 ( 980) hydrogen bonds : angle 5.69782 ( 2676) link_BETA1-4 : bond 0.00343 ( 12) link_BETA1-4 : angle 1.12919 ( 36) link_NAG-ASN : bond 0.00340 ( 44) link_NAG-ASN : angle 2.34976 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 195 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.7658 (p90) cc_final: 0.7131 (p90) REVERT: A 740 MET cc_start: 0.7616 (tpt) cc_final: 0.7342 (tpt) REVERT: A 902 MET cc_start: 0.8424 (tpt) cc_final: 0.8210 (tpt) REVERT: B 588 THR cc_start: 0.8717 (m) cc_final: 0.8510 (p) REVERT: B 900 MET cc_start: 0.7750 (mtp) cc_final: 0.7488 (mtm) REVERT: B 990 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: B 1017 GLU cc_start: 0.7079 (tp30) cc_final: 0.6856 (tm-30) REVERT: B 1139 ASP cc_start: 0.8013 (t0) cc_final: 0.7800 (t0) REVERT: C 115 GLN cc_start: 0.6854 (mt0) cc_final: 0.6271 (mm-40) REVERT: C 955 ASN cc_start: 0.7778 (m-40) cc_final: 0.7345 (m110) REVERT: C 1006 THR cc_start: 0.8465 (m) cc_final: 0.8187 (p) outliers start: 63 outliers final: 53 residues processed: 241 average time/residue: 0.1351 time to fit residues: 53.7138 Evaluate side-chains 234 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 180 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 170 optimal weight: 0.9990 chunk 188 optimal weight: 0.5980 chunk 185 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 226 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.132534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.098554 restraints weight = 51454.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.097350 restraints weight = 37894.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.098030 restraints weight = 36864.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.098532 restraints weight = 26852.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.098816 restraints weight = 24509.954| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24155 Z= 0.111 Angle : 0.565 12.945 32970 Z= 0.285 Chirality : 0.044 0.259 3914 Planarity : 0.004 0.046 4147 Dihedral : 4.686 58.220 4339 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.92 % Rotamer: Outliers : 2.04 % Allowed : 16.86 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 2841 helix: 0.72 (0.20), residues: 698 sheet: 0.13 (0.19), residues: 646 loop : -0.86 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1019 TYR 0.022 0.001 TYR C 453 PHE 0.021 0.001 PHE B 135 TRP 0.018 0.001 TRP C 353 HIS 0.004 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00251 (24062) covalent geometry : angle 0.54474 (32728) SS BOND : bond 0.00303 ( 37) SS BOND : angle 1.11982 ( 74) hydrogen bonds : bond 0.03237 ( 980) hydrogen bonds : angle 5.57997 ( 2676) link_BETA1-4 : bond 0.00392 ( 12) link_BETA1-4 : angle 1.11632 ( 36) link_NAG-ASN : bond 0.00343 ( 44) link_NAG-ASN : angle 2.27038 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 200 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.7602 (p90) cc_final: 0.7099 (p90) REVERT: B 588 THR cc_start: 0.8752 (m) cc_final: 0.8548 (p) REVERT: B 900 MET cc_start: 0.7728 (mtp) cc_final: 0.7391 (mtm) REVERT: B 990 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: B 1139 ASP cc_start: 0.7959 (t0) cc_final: 0.7747 (t0) REVERT: C 115 GLN cc_start: 0.6833 (mt0) cc_final: 0.6267 (mm-40) REVERT: C 555 SER cc_start: 0.7426 (OUTLIER) cc_final: 0.7025 (p) REVERT: C 955 ASN cc_start: 0.7830 (m-40) cc_final: 0.7377 (m110) outliers start: 52 outliers final: 42 residues processed: 241 average time/residue: 0.1376 time to fit residues: 54.8900 Evaluate side-chains 231 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 215 optimal weight: 0.0270 chunk 61 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 90 optimal weight: 0.3980 chunk 6 optimal weight: 5.9990 chunk 240 optimal weight: 8.9990 chunk 257 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 263 optimal weight: 0.8980 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 957 GLN C 965 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.131366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.097185 restraints weight = 51542.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.095927 restraints weight = 38074.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.096653 restraints weight = 36619.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.097039 restraints weight = 27182.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.097314 restraints weight = 25277.953| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24155 Z= 0.138 Angle : 0.589 12.852 32970 Z= 0.297 Chirality : 0.045 0.269 3914 Planarity : 0.004 0.044 4147 Dihedral : 4.718 58.831 4339 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.05 % Favored : 95.85 % Rotamer: Outliers : 2.00 % Allowed : 16.97 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.15), residues: 2841 helix: 0.63 (0.20), residues: 698 sheet: 0.04 (0.19), residues: 662 loop : -0.88 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 646 TYR 0.025 0.001 TYR B 904 PHE 0.028 0.001 PHE C 377 TRP 0.014 0.001 TRP C 353 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00320 (24062) covalent geometry : angle 0.56857 (32728) SS BOND : bond 0.00352 ( 37) SS BOND : angle 1.46703 ( 74) hydrogen bonds : bond 0.03399 ( 980) hydrogen bonds : angle 5.59458 ( 2676) link_BETA1-4 : bond 0.00349 ( 12) link_BETA1-4 : angle 1.11524 ( 36) link_NAG-ASN : bond 0.00350 ( 44) link_NAG-ASN : angle 2.25116 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 184 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.7717 (p90) cc_final: 0.7162 (p90) REVERT: B 135 PHE cc_start: 0.5350 (OUTLIER) cc_final: 0.5127 (m-80) REVERT: B 588 THR cc_start: 0.8805 (m) cc_final: 0.8583 (p) REVERT: B 900 MET cc_start: 0.7900 (mtp) cc_final: 0.7580 (mtm) REVERT: B 990 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: B 1139 ASP cc_start: 0.8042 (t0) cc_final: 0.7780 (t0) REVERT: C 115 GLN cc_start: 0.6869 (mt0) cc_final: 0.6279 (mm-40) REVERT: C 555 SER cc_start: 0.7544 (OUTLIER) cc_final: 0.7118 (p) REVERT: C 955 ASN cc_start: 0.7769 (m-40) cc_final: 0.7320 (m110) outliers start: 51 outliers final: 45 residues processed: 225 average time/residue: 0.1349 time to fit residues: 49.8744 Evaluate side-chains 225 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 127 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 66 optimal weight: 0.0970 chunk 94 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.130533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.096622 restraints weight = 51489.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.095184 restraints weight = 39113.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.096026 restraints weight = 37349.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.096385 restraints weight = 27879.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.096653 restraints weight = 26082.984| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24155 Z= 0.157 Angle : 0.598 12.765 32970 Z= 0.301 Chirality : 0.045 0.282 3914 Planarity : 0.004 0.043 4147 Dihedral : 4.812 59.438 4339 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.29 % Favored : 95.60 % Rotamer: Outliers : 1.96 % Allowed : 17.33 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 2841 helix: 0.55 (0.20), residues: 698 sheet: -0.02 (0.19), residues: 636 loop : -0.87 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 328 TYR 0.019 0.001 TYR C1067 PHE 0.018 0.001 PHE C 377 TRP 0.013 0.001 TRP C 353 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00365 (24062) covalent geometry : angle 0.57745 (32728) SS BOND : bond 0.00328 ( 37) SS BOND : angle 1.47885 ( 74) hydrogen bonds : bond 0.03454 ( 980) hydrogen bonds : angle 5.62549 ( 2676) link_BETA1-4 : bond 0.00318 ( 12) link_BETA1-4 : angle 1.11770 ( 36) link_NAG-ASN : bond 0.00351 ( 44) link_NAG-ASN : angle 2.28437 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3680.20 seconds wall clock time: 64 minutes 37.79 seconds (3877.79 seconds total)