Starting phenix.real_space_refine on Sat Jul 4 21:38:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kj5_22894/07_2026/7kj5_22894.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kj5_22894/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7kj5_22894/07_2026/7kj5_22894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kj5_22894/07_2026/7kj5_22894.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kj5_22894/07_2026/7kj5_22894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kj5_22894/07_2026/7kj5_22894.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7kj5_22894/07_2026/7kj5_22894.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kj5_22894/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 12 Time building chain proxies: 4.85, per 1000 atoms: 0.21 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: 1.45 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.56 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: 5.32 Time building geometry restraints manager: 2.04 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: 12761 17.65 - 35.30: 815 35.30 - 52.95: 189 52.95 - 70.61: 63 70.61 - 88.26: 38 Dihedral angle restraints: 13866 sinusoidal: 5400 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 13863 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: 9.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.260 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 33.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 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 : 13.843 88.257 8289 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/Z covalent geometry : bond 0.01558 / 0.90 (24062) covalent geometry : angle 1.94758 / 1.29 (32728) SS BOND : bond 0.34335 / 23.32 ( 37) SS BOND : angle 13.12755 / 8.38 ( 74) hydrogen bonds : bond 0.16260 / 10.35 ( 980) hydrogen bonds : angle 9.15606 / 6.24 ( 2676) link_BETA1-4 : bond 0.05813 / 3.87 ( 12) link_BETA1-4 : angle 3.39574 / 2.12 ( 36) link_NAG-ASN : bond 0.14105 / 9.46 ( 44) link_NAG-ASN : angle 12.64574 / 7.68 ( 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 : 0.821 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: 0.1548 time to fit residues: 126.8430 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 : 0.800 ------------------------------------------------------------------------------- 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... 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 = 0.135317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.100767 restraints weight = 51179.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.100959 restraints weight = 36004.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.101735 restraints weight = 32764.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.101693 restraints weight = 25086.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.101912 restraints weight = 22957.674| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 24155 Z= 0.160 Angle : 0.781 17.277 32970 Z= 0.398 Chirality : 0.050 0.447 3914 Planarity : 0.005 0.042 4147 Dihedral : 6.554 56.213 3117 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.52 % Favored : 96.34 % Rotamer: Outliers : 1.92 % Allowed : 9.49 % Favored : 88.59 % 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: -1.12 (0.14), residues: 2841 helix: -0.44 (0.19), residues: 695 sheet: -0.05 (0.19), residues: 609 loop : -1.15 (0.14), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 44 TYR 0.025 0.002 TYR C1067 PHE 0.028 0.002 PHE B 168 TRP 0.022 0.002 TRP C 353 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (24062) covalent geometry : angle 0.72992 / 0.39 (32728) SS BOND : bond 0.00460 / 0.27 ( 37) SS BOND : angle 2.05892 / 1.50 ( 74) hydrogen bonds : bond 0.04580 / 2.98 ( 980) hydrogen bonds : angle 6.65305 / 4.48 ( 2676) link_BETA1-4 : bond 0.00742 / 0.40 ( 12) link_BETA1-4 : angle 1.73952 / 1.07 ( 36) link_NAG-ASN : bond 0.00678 / 0.44 ( 44) link_NAG-ASN : angle 4.14550 / 2.84 ( 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 326 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 277 time to evaluate : 0.960 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: symmetry clash REVERT: A 987 PRO cc_start: 0.8671 (Cg_exo) cc_final: 0.8400 (Cg_endo) REVERT: B 460 ASN cc_start: 0.2575 (OUTLIER) cc_final: 0.2235 (p0) REVERT: B 489 TYR cc_start: 0.4815 (OUTLIER) cc_final: 0.4004 (t80) REVERT: B 1017 GLU cc_start: 0.7147 (tp30) cc_final: 0.6871 (tm-30) REVERT: B 1139 ASP cc_start: 0.8237 (t0) cc_final: 0.7528 (t0) REVERT: C 453 TYR cc_start: 0.7409 (p90) cc_final: 0.7207 (p90) REVERT: C 1006 THR cc_start: 0.8505 (m) cc_final: 0.8166 (p) outliers start: 49 outliers final: 22 residues processed: 314 average time/residue: 0.1651 time to fit residues: 83.3703 Evaluate side-chains 220 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 961 THR 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 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 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: 6.9990 chunk 91 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 227 optimal weight: 30.0000 chunk 1 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 764 ASN B 784 GLN C 49 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.131642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.096881 restraints weight = 51413.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.095229 restraints weight = 37144.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.096057 restraints weight = 34100.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.096288 restraints weight = 27764.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.096415 restraints weight = 25292.514| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 24155 Z= 0.204 Angle : 0.716 14.368 32970 Z= 0.360 Chirality : 0.047 0.339 3914 Planarity : 0.005 0.058 4147 Dihedral : 5.855 55.115 3104 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.51 % Favored : 95.39 % Rotamer: Outliers : 3.06 % Allowed : 10.66 % Favored : 86.28 % 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: -0.82 (0.15), residues: 2841 helix: -0.14 (0.19), residues: 693 sheet: 0.10 (0.19), residues: 613 loop : -0.98 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1000 TYR 0.026 0.002 TYR B 453 PHE 0.022 0.002 PHE B 168 TRP 0.022 0.002 TRP C 353 HIS 0.008 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (24062) covalent geometry : angle 0.68410 / 0.35 (32728) SS BOND : bond 0.00471 / 0.31 ( 37) SS BOND : angle 2.05103 / 1.50 ( 74) hydrogen bonds : bond 0.04219 / 2.73 ( 980) hydrogen bonds : angle 6.25643 / 4.22 ( 2676) link_BETA1-4 : bond 0.00349 / 0.24 ( 12) link_BETA1-4 : angle 1.33417 / 0.82 ( 36) link_NAG-ASN : bond 0.00421 / 0.28 ( 44) link_NAG-ASN : angle 3.04000 / 2.13 ( 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 299 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 221 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.7816 (p90) cc_final: 0.7509 (p90) REVERT: A 558 LYS cc_start: 0.7537 (mttt) cc_final: 0.7315 (mttt) REVERT: B 460 ASN cc_start: 0.2667 (OUTLIER) cc_final: 0.2162 (p0) REVERT: B 900 MET cc_start: 0.7974 (mtp) cc_final: 0.7739 (mtm) REVERT: B 990 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: B 1017 GLU cc_start: 0.7140 (tp30) cc_final: 0.6856 (tm-30) REVERT: B 1139 ASP cc_start: 0.8233 (t0) cc_final: 0.7960 (t0) REVERT: C 115 GLN cc_start: 0.6952 (mt0) cc_final: 0.6308 (mm110) REVERT: C 796 ASP cc_start: 0.6770 (t0) cc_final: 0.6418 (t0) REVERT: C 1006 THR cc_start: 0.8528 (m) cc_final: 0.8184 (p) outliers start: 78 outliers final: 57 residues processed: 277 average time/residue: 0.1579 time to fit residues: 71.0257 Evaluate side-chains 230 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 171 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 374 PHE 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 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 1081 ILE 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 597 VAL Chi-restraints excluded: chain B residue 720 ILE 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 376 THR 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 645 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 1041 ASP 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: 1.9990 chunk 39 optimal weight: 10.0000 chunk 109 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 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: 3.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 B1071 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.133290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.098691 restraints weight = 51480.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.097645 restraints weight = 38667.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.098639 restraints weight = 31911.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.098808 restraints weight = 25665.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.098960 restraints weight = 23843.749| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24155 Z= 0.128 Angle : 0.623 13.715 32970 Z= 0.313 Chirality : 0.045 0.262 3914 Planarity : 0.004 0.048 4147 Dihedral : 5.459 55.812 3104 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.52 % Favored : 96.37 % Rotamer: Outliers : 2.70 % Allowed : 12.19 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.56 (0.15), residues: 2841 helix: 0.36 (0.20), residues: 702 sheet: 0.04 (0.19), residues: 615 loop : -0.87 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 346 TYR 0.024 0.001 TYR B 453 PHE 0.019 0.001 PHE C 135 TRP 0.018 0.002 TRP C 353 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (24062) covalent geometry : angle 0.59386 / 0.31 (32728) SS BOND : bond 0.00456 / 0.30 ( 37) SS BOND : angle 1.89366 / 1.39 ( 74) hydrogen bonds : bond 0.03580 / 2.32 ( 980) hydrogen bonds : angle 5.93574 / 4.03 ( 2676) link_BETA1-4 : bond 0.00437 / 0.29 ( 12) link_BETA1-4 : angle 1.25400 / 0.78 ( 36) link_NAG-ASN : bond 0.00405 / 0.26 ( 44) link_NAG-ASN : angle 2.64627 / 1.90 ( 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 287 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 218 time to evaluate : 0.913 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: 0.7587 (p90) cc_final: 0.7084 (p90) REVERT: A 558 LYS cc_start: 0.7488 (mttt) cc_final: 0.7003 (mtpt) REVERT: A 902 MET cc_start: 0.8533 (tpt) cc_final: 0.8050 (tpt) REVERT: A 1135 ASN cc_start: 0.7130 (t0) cc_final: 0.6927 (t0) REVERT: B 460 ASN cc_start: 0.2642 (OUTLIER) cc_final: 0.1799 (p0) REVERT: B 990 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: B 1017 GLU cc_start: 0.6985 (tp30) cc_final: 0.6702 (tm-30) REVERT: B 1139 ASP cc_start: 0.8089 (t0) cc_final: 0.7819 (t0) REVERT: C 115 GLN cc_start: 0.6972 (mt0) cc_final: 0.6344 (mm110) REVERT: C 195 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7990 (ptpp) REVERT: C 796 ASP cc_start: 0.6707 (t0) cc_final: 0.6404 (t0) REVERT: C 1006 THR cc_start: 0.8534 (m) cc_final: 0.8267 (p) outliers start: 69 outliers final: 45 residues processed: 270 average time/residue: 0.1529 time to fit residues: 68.1533 Evaluate side-chains 232 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 323 THR 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 931 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1127 ASP 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 705 VAL 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 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 195 LYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 376 THR 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 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: 0.7980 chunk 53 optimal weight: 8.9990 chunk 229 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 258 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 235 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN B 907 ASN C 957 GLN C1036 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.129708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.094996 restraints weight = 51419.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.093886 restraints weight = 38429.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.094525 restraints weight = 35208.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.094954 restraints weight = 27054.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.095076 restraints weight = 24719.832| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24155 Z= 0.222 Angle : 0.670 13.407 32970 Z= 0.339 Chirality : 0.047 0.263 3914 Planarity : 0.005 0.045 4147 Dihedral : 5.432 55.902 3100 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.89 % Favored : 95.00 % Rotamer: Outliers : 3.25 % Allowed : 13.56 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.83 (0.15), residues: 2841 helix: 0.04 (0.19), residues: 705 sheet: -0.04 (0.18), residues: 651 loop : -1.04 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 346 TYR 0.024 0.002 TYR C 453 PHE 0.022 0.002 PHE B 168 TRP 0.013 0.002 TRP C 353 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 (24062) covalent geometry : angle 0.64677 / 0.33 (32728) SS BOND : bond 0.00528 / 0.39 ( 37) SS BOND : angle 1.40864 / 0.97 ( 74) hydrogen bonds : bond 0.03973 / 2.56 ( 980) hydrogen bonds : angle 6.02487 / 4.08 ( 2676) link_BETA1-4 : bond 0.00245 / 0.16 ( 12) link_BETA1-4 : angle 1.15230 / 0.73 ( 36) link_NAG-ASN : bond 0.00398 / 0.26 ( 44) link_NAG-ASN : angle 2.62546 / 1.89 ( 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 287 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 204 time to evaluate : 0.915 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: 0.7686 (p90) cc_final: 0.7411 (p90) REVERT: A 558 LYS cc_start: 0.7595 (mttt) cc_final: 0.7015 (mtpt) REVERT: A 740 MET cc_start: 0.7692 (tpt) cc_final: 0.7462 (tpt) REVERT: A 902 MET cc_start: 0.8518 (tpt) cc_final: 0.8166 (tpt) REVERT: A 964 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8146 (mtpt) REVERT: B 588 THR cc_start: 0.8810 (m) cc_final: 0.8580 (p) REVERT: B 900 MET cc_start: 0.7977 (mtp) cc_final: 0.7636 (mtm) REVERT: B 990 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: B 1017 GLU cc_start: 0.7197 (tp30) cc_final: 0.6935 (tm-30) REVERT: B 1139 ASP cc_start: 0.8102 (t0) cc_final: 0.7902 (t0) REVERT: C 104 TRP cc_start: 0.7014 (m-90) cc_final: 0.6744 (m-90) REVERT: C 115 GLN cc_start: 0.7015 (mt0) cc_final: 0.6341 (mm-40) REVERT: C 195 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8002 (pttm) REVERT: C 796 ASP cc_start: 0.6708 (t0) cc_final: 0.6464 (t0) REVERT: C 955 ASN cc_start: 0.7900 (m-40) cc_final: 0.7434 (m110) REVERT: C 1006 THR cc_start: 0.8504 (m) cc_final: 0.8196 (p) outliers start: 83 outliers final: 64 residues processed: 269 average time/residue: 0.1493 time to fit residues: 66.4143 Evaluate side-chains 252 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 185 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 289 VAL 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 881 THR 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 1081 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL 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 203 ILE 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 587 ILE 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 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 195 LYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 376 THR 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 738 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 806 LEU 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 1001 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 186 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 273 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 11 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 251 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.131617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.097234 restraints weight = 51525.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.096132 restraints weight = 39817.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.096964 restraints weight = 35625.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.097217 restraints weight = 27033.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.097540 restraints weight = 25362.779| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24155 Z= 0.125 Angle : 0.584 13.137 32970 Z= 0.295 Chirality : 0.044 0.251 3914 Planarity : 0.004 0.042 4147 Dihedral : 4.957 52.785 3098 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.55 % Rotamer: Outliers : 2.47 % Allowed : 15.01 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.59 (0.15), residues: 2841 helix: 0.45 (0.20), residues: 705 sheet: 0.01 (0.19), residues: 664 loop : -0.97 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 346 TYR 0.027 0.001 TYR C 495 PHE 0.021 0.001 PHE B 135 TRP 0.013 0.001 TRP A 104 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (24062) covalent geometry : angle 0.56227 / 0.29 (32728) SS BOND : bond 0.00250 / 0.16 ( 37) SS BOND : angle 1.16971 / 0.84 ( 74) hydrogen bonds : bond 0.03458 / 2.25 ( 980) hydrogen bonds : angle 5.79151 / 3.93 ( 2676) link_BETA1-4 : bond 0.00389 / 0.25 ( 12) link_BETA1-4 : angle 1.07672 / 0.68 ( 36) link_NAG-ASN : bond 0.00342 / 0.23 ( 44) link_NAG-ASN : angle 2.42123 / 1.76 ( 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 270 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 207 time to evaluate : 0.841 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: 0.7586 (p90) cc_final: 0.7039 (p90) REVERT: A 902 MET cc_start: 0.8398 (tpt) cc_final: 0.8135 (tpt) REVERT: B 900 MET cc_start: 0.7698 (mtp) cc_final: 0.7390 (mtm) REVERT: B 990 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: B 1017 GLU cc_start: 0.7049 (tp30) cc_final: 0.6778 (tm-30) REVERT: B 1139 ASP cc_start: 0.8007 (t0) cc_final: 0.7675 (t0) REVERT: C 104 TRP cc_start: 0.6892 (m-90) cc_final: 0.6603 (m-90) REVERT: C 115 GLN cc_start: 0.6752 (mt0) cc_final: 0.6245 (mm-40) REVERT: C 129 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8341 (mtpp) REVERT: C 195 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7818 (ptpp) REVERT: C 796 ASP cc_start: 0.6709 (t0) cc_final: 0.6461 (t0) REVERT: C 955 ASN cc_start: 0.7862 (m-40) cc_final: 0.7531 (m110) REVERT: C 1006 THR cc_start: 0.8548 (m) cc_final: 0.8285 (p) outliers start: 63 outliers final: 47 residues processed: 255 average time/residue: 0.1454 time to fit residues: 61.1933 Evaluate side-chains 227 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 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 1122 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 203 ILE 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 705 VAL Chi-restraints excluded: chain B residue 720 ILE 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 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 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 129 LYS Chi-restraints excluded: chain C residue 195 LYS 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 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: 0.3980 chunk 215 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 269 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B1119 ASN ** 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 = 0.4083 r_free = 0.4083 target = 0.130839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.096246 restraints weight = 51244.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.095645 restraints weight = 40724.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.096294 restraints weight = 34893.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.096675 restraints weight = 26969.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.096999 restraints weight = 24813.250| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24155 Z= 0.150 Angle : 0.600 13.053 32970 Z= 0.303 Chirality : 0.045 0.260 3914 Planarity : 0.004 0.042 4147 Dihedral : 4.901 53.744 3098 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.15 % Favored : 95.74 % Rotamer: Outliers : 2.74 % Allowed : 15.17 % Favored : 82.09 % 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: 708 sheet: 0.03 (0.19), residues: 663 loop : -0.99 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1019 TYR 0.036 0.001 TYR B 904 PHE 0.020 0.001 PHE B 168 TRP 0.011 0.001 TRP C 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (24062) covalent geometry : angle 0.57926 / 0.30 (32728) SS BOND : bond 0.00254 / 0.16 ( 37) SS BOND : angle 1.19155 / 0.86 ( 74) hydrogen bonds : bond 0.03472 / 2.24 ( 980) hydrogen bonds : angle 5.72483 / 3.89 ( 2676) link_BETA1-4 : bond 0.00333 / 0.22 ( 12) link_BETA1-4 : angle 1.03470 / 0.68 ( 36) link_NAG-ASN : bond 0.00344 / 0.23 ( 44) link_NAG-ASN : angle 2.37189 / 1.73 ( 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 260 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 190 time to evaluate : 0.780 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: 0.7651 (p90) cc_final: 0.7339 (p90) REVERT: A 558 LYS cc_start: 0.7297 (mtpt) cc_final: 0.6841 (mtpt) REVERT: A 902 MET cc_start: 0.8441 (tpt) cc_final: 0.8207 (tpt) REVERT: B 900 MET cc_start: 0.7783 (mtp) cc_final: 0.7528 (mtm) REVERT: B 990 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: B 1017 GLU cc_start: 0.7127 (tp30) cc_final: 0.6904 (tm-30) REVERT: B 1139 ASP cc_start: 0.8041 (t0) cc_final: 0.7723 (t0) REVERT: C 104 TRP cc_start: 0.6912 (m-90) cc_final: 0.6686 (m-90) REVERT: C 115 GLN cc_start: 0.6860 (mt0) cc_final: 0.6295 (mm-40) REVERT: C 195 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7810 (ptpp) REVERT: C 555 SER cc_start: 0.7588 (OUTLIER) cc_final: 0.7136 (p) REVERT: C 796 ASP cc_start: 0.6702 (t0) cc_final: 0.6437 (t0) REVERT: C 955 ASN cc_start: 0.7901 (m-40) cc_final: 0.7523 (m110) REVERT: C 1006 THR cc_start: 0.8524 (m) cc_final: 0.8249 (p) outliers start: 70 outliers final: 57 residues processed: 244 average time/residue: 0.1377 time to fit residues: 55.9318 Evaluate side-chains 243 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 183 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 1027 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 118 LEU 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 203 ILE 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 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 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 195 LYS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 376 THR 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 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 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: 1.9990 chunk 154 optimal weight: 0.7980 chunk 252 optimal weight: 2.9990 chunk 230 optimal weight: 0.4980 chunk 19 optimal weight: 7.9990 chunk 269 optimal weight: 4.9990 chunk 130 optimal weight: 30.0000 chunk 127 optimal weight: 0.0670 chunk 244 optimal weight: 5.9990 chunk 238 optimal weight: 0.0970 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A1106 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.132593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.098082 restraints weight = 50947.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.098207 restraints weight = 39529.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.098830 restraints weight = 32170.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.099214 restraints weight = 25179.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.099439 restraints weight = 23340.019| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24155 Z= 0.109 Angle : 0.566 12.966 32970 Z= 0.286 Chirality : 0.044 0.249 3914 Planarity : 0.004 0.042 4147 Dihedral : 4.723 55.164 3098 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.41 % Favored : 96.48 % Rotamer: Outliers : 2.04 % Allowed : 16.31 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.75 (0.20), residues: 712 sheet: 0.21 (0.19), residues: 649 loop : -0.94 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.025 0.001 TYR B 904 PHE 0.017 0.001 PHE C 135 TRP 0.016 0.001 TRP C 436 HIS 0.004 0.001 HIS C1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (24062) covalent geometry : angle 0.54592 / 0.28 (32728) SS BOND : bond 0.00207 / 0.12 ( 37) SS BOND : angle 1.11728 / 0.82 ( 74) hydrogen bonds : bond 0.03189 / 2.06 ( 980) hydrogen bonds : angle 5.58906 / 3.81 ( 2676) link_BETA1-4 : bond 0.00357 / 0.23 ( 12) link_BETA1-4 : angle 1.02894 / 0.66 ( 36) link_NAG-ASN : bond 0.00338 / 0.23 ( 44) link_NAG-ASN : angle 2.23524 / 1.65 ( 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 257 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 0.970 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: 0.7604 (p90) cc_final: 0.7037 (p90) REVERT: A 902 MET cc_start: 0.8375 (tpt) cc_final: 0.8170 (tpt) REVERT: B 740 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7239 (ttt) REVERT: B 900 MET cc_start: 0.7711 (mtp) cc_final: 0.7388 (mtm) REVERT: B 990 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: B 1047 TYR cc_start: 0.8496 (m-80) cc_final: 0.8257 (m-80) REVERT: C 104 TRP cc_start: 0.6834 (m-90) cc_final: 0.6604 (m-90) REVERT: C 115 GLN cc_start: 0.6764 (mt0) cc_final: 0.6223 (mm-40) REVERT: C 555 SER cc_start: 0.7417 (OUTLIER) cc_final: 0.6997 (p) REVERT: C 955 ASN cc_start: 0.7901 (m-40) cc_final: 0.7509 (m110) outliers start: 52 outliers final: 39 residues processed: 245 average time/residue: 0.1549 time to fit residues: 62.6158 Evaluate side-chains 224 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 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 1027 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 118 LEU 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 203 ILE Chi-restraints excluded: chain B residue 296 LEU 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 740 MET 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 B residue 1114 ILE 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 170 optimal weight: 0.9980 chunk 188 optimal weight: 0.5980 chunk 185 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 155 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 226 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN B 907 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.132010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.097430 restraints weight = 51300.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.097034 restraints weight = 40292.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.097569 restraints weight = 34163.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.097983 restraints weight = 26740.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.098247 restraints weight = 24431.677| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24155 Z= 0.125 Angle : 0.581 12.818 32970 Z= 0.293 Chirality : 0.044 0.254 3914 Planarity : 0.004 0.050 4147 Dihedral : 4.676 55.406 3098 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.63 % Favored : 96.23 % Rotamer: Outliers : 2.35 % Allowed : 16.50 % Favored : 81.14 % 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: -0.36 (0.15), residues: 2841 helix: 0.78 (0.20), residues: 705 sheet: 0.17 (0.19), residues: 664 loop : -0.92 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 214 TYR 0.022 0.001 TYR B 904 PHE 0.024 0.001 PHE B 135 TRP 0.017 0.001 TRP C 436 HIS 0.004 0.001 HIS C1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (24062) covalent geometry : angle 0.56108 / 0.29 (32728) SS BOND : bond 0.00230 / 0.14 ( 37) SS BOND : angle 1.37576 / 1.04 ( 74) hydrogen bonds : bond 0.03263 / 2.10 ( 980) hydrogen bonds : angle 5.57168 / 3.80 ( 2676) link_BETA1-4 : bond 0.00343 / 0.22 ( 12) link_BETA1-4 : angle 1.01222 / 0.65 ( 36) link_NAG-ASN : bond 0.00329 / 0.23 ( 44) link_NAG-ASN : angle 2.21367 / 1.64 ( 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 244 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 184 time to evaluate : 0.923 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 400 PHE cc_start: 0.7584 (p90) cc_final: 0.7043 (p90) REVERT: B 740 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7127 (ttt) REVERT: B 900 MET cc_start: 0.7794 (mtp) cc_final: 0.7446 (mtm) REVERT: B 990 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: C 104 TRP cc_start: 0.6880 (m-90) cc_final: 0.6656 (m-90) REVERT: C 115 GLN cc_start: 0.6808 (mt0) cc_final: 0.6257 (mm-40) REVERT: C 555 SER cc_start: 0.7429 (OUTLIER) cc_final: 0.6999 (p) REVERT: C 955 ASN cc_start: 0.7913 (m-40) cc_final: 0.7522 (m110) outliers start: 60 outliers final: 48 residues processed: 228 average time/residue: 0.1575 time to fit residues: 58.7698 Evaluate side-chains 222 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS 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 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 1018 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 118 LEU 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 203 ILE Chi-restraints excluded: chain B residue 296 LEU 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 731 MET 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 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 950 ASP 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 338 PHE Chi-restraints excluded: chain C residue 401 VAL 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 716 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 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: 0.9990 chunk 61 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 263 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 965 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.131218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.096517 restraints weight = 51344.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.095586 restraints weight = 38470.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.096392 restraints weight = 33360.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.096722 restraints weight = 25824.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.096928 restraints weight = 24031.482| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4847 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= 0.143 Angle : 0.591 12.848 32970 Z= 0.299 Chirality : 0.045 0.308 3914 Planarity : 0.004 0.067 4147 Dihedral : 4.729 56.064 3098 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.77 % Favored : 96.13 % Rotamer: Outliers : 2.08 % Allowed : 16.78 % Favored : 81.14 % 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: -0.40 (0.15), residues: 2841 helix: 0.70 (0.20), residues: 705 sheet: 0.16 (0.19), residues: 654 loop : -0.91 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 765 TYR 0.022 0.001 TYR B 904 PHE 0.029 0.001 PHE B 168 TRP 0.018 0.001 TRP C 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (24062) covalent geometry : angle 0.57154 / 0.29 (32728) SS BOND : bond 0.00223 / 0.14 ( 37) SS BOND : angle 1.49613 / 1.09 ( 74) hydrogen bonds : bond 0.03383 / 2.17 ( 980) hydrogen bonds : angle 5.60763 / 3.83 ( 2676) link_BETA1-4 : bond 0.00382 / 0.24 ( 12) link_BETA1-4 : angle 1.00716 / 0.66 ( 36) link_NAG-ASN : bond 0.00340 / 0.23 ( 44) link_NAG-ASN : angle 2.19631 / 1.63 ( 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 232 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 179 time to evaluate : 0.946 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 386 LYS cc_start: 0.6632 (mttp) cc_final: 0.6426 (ttmt) REVERT: A 400 PHE cc_start: 0.7786 (p90) cc_final: 0.7142 (p90) REVERT: B 740 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7213 (ttt) REVERT: B 900 MET cc_start: 0.7946 (mtp) cc_final: 0.7611 (mtm) REVERT: B 990 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: C 104 TRP cc_start: 0.6992 (m-90) cc_final: 0.6746 (m-90) REVERT: C 115 GLN cc_start: 0.6908 (mt0) cc_final: 0.6307 (mm-40) REVERT: C 555 SER cc_start: 0.7595 (OUTLIER) cc_final: 0.7168 (p) REVERT: C 955 ASN cc_start: 0.7957 (m-40) cc_final: 0.7573 (m110) outliers start: 53 outliers final: 44 residues processed: 219 average time/residue: 0.1542 time to fit residues: 55.7294 Evaluate side-chains 220 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS 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 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 1018 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 203 ILE 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 740 MET 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 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 338 PHE Chi-restraints excluded: chain C residue 401 VAL 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 716 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 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: 6.9990 chunk 20 optimal weight: 0.9980 chunk 176 optimal weight: 0.6980 chunk 192 optimal weight: 9.9990 chunk 173 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN A 493 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.128957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.094906 restraints weight = 51841.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.093781 restraints weight = 40293.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.094331 restraints weight = 40494.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.094989 restraints weight = 28854.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.095287 restraints weight = 26198.584| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24155 Z= 0.222 Angle : 0.660 12.742 32970 Z= 0.334 Chirality : 0.047 0.294 3914 Planarity : 0.005 0.046 4147 Dihedral : 5.019 58.485 3098 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.65 % Favored : 95.25 % Rotamer: Outliers : 2.04 % Allowed : 17.21 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.71 (0.15), residues: 2841 helix: 0.30 (0.19), residues: 700 sheet: -0.00 (0.20), residues: 623 loop : -1.03 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 190 TYR 0.026 0.002 TYR B 904 PHE 0.015 0.002 PHE C 135 TRP 0.020 0.002 TRP C 436 HIS 0.009 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 (24062) covalent geometry : angle 0.63881 / 0.33 (32728) SS BOND : bond 0.00433 / 0.25 ( 37) SS BOND : angle 1.70858 / 1.22 ( 74) hydrogen bonds : bond 0.03792 / 2.44 ( 980) hydrogen bonds : angle 5.82940 / 3.98 ( 2676) link_BETA1-4 : bond 0.00308 / 0.19 ( 12) link_BETA1-4 : angle 1.04324 / 0.68 ( 36) link_NAG-ASN : bond 0.00378 / 0.24 ( 44) link_NAG-ASN : angle 2.35702 / 1.72 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3996.89 seconds wall clock time: 70 minutes 21.01 seconds (4221.01 seconds total)