Starting phenix.real_space_refine on Thu Mar 5 07:18:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tpl_26059/03_2026/7tpl_26059.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpl_26059/03_2026/7tpl_26059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tpl_26059/03_2026/7tpl_26059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpl_26059/03_2026/7tpl_26059.map" model { file = "/net/cci-nas-00/data/ceres_data/7tpl_26059/03_2026/7tpl_26059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpl_26059/03_2026/7tpl_26059.cif" } resolution = 3.87 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= -0.006 sd= 0.120 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 87 5.16 5 C 12704 2.51 5 N 3280 2.21 5 O 3921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19992 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3250 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain breaks: 1 Chain: "B" Number of atoms: 8113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8113 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 48, 'TRANS': 991} Chain breaks: 6 Chain: "C" Number of atoms: 7985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7985 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 49, 'TRANS': 972} Chain breaks: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 3.90, per 1000 atoms: 0.20 Number of scatterers: 19992 At special positions: 0 Unit cell: (99.36, 137.16, 178.2, 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 87 16.00 O 3921 8.00 N 3280 7.00 C 12704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.00 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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 K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A1074 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 61 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 165 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 122 " " 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 234 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 801 " Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 851.7 milliseconds 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4656 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 32 sheets defined 31.5% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.967A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.992A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 removed outlier: 4.321A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 4.235A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) 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 removed outlier: 3.546A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.549A pdb=" N ALA A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.667A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.897A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.973A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.540A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (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 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.932A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.517A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.669A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.721A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 844 removed outlier: 3.570A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.979A 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 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 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: 4.355A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.623A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.673A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.619A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.081A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.657A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.120A 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 Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 621 through 625 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 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 758 through 783 removed outlier: 3.717A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.622A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.527A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.542A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.555A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (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: 3.767A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.945A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.562A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 702 through 704 removed outlier: 6.371A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.529A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.587A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AA5, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.701A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.500A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.742A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.888A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.942A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.435A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.552A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AB4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.796A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 653 through 655 removed outlier: 6.536A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AB7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.560A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.560A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.690A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.395A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.429A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.365A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.975A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 315 removed outlier: 3.838A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 334 through 335 removed outlier: 6.614A pdb=" N ASN C 334 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.792A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'C' and resid 565 through 567 removed outlier: 6.578A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.244A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.631A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.631A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.893A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 850 hydrogen bonds defined for protein. 2334 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: 4.63 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5720 1.34 - 1.46: 3585 1.46 - 1.58: 11000 1.58 - 1.70: 0 1.70 - 1.83: 110 Bond restraints: 20415 Sorted by residual: bond pdb=" C5 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.542 -0.025 6.70e-03 2.23e+04 1.43e+01 bond pdb=" C5 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C5 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C5 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.39e+01 ... (remaining 20410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 25502 3.13 - 6.26: 2206 6.26 - 9.39: 61 9.39 - 12.52: 2 12.52 - 15.65: 1 Bond angle restraints: 27772 Sorted by residual: angle pdb=" CA THR C 323 " pdb=" CB THR C 323 " pdb=" OG1 THR C 323 " ideal model delta sigma weight residual 109.60 125.25 -15.65 1.50e+00 4.44e-01 1.09e+02 angle pdb=" C LEU B 849 " pdb=" N ILE B 850 " pdb=" CA ILE B 850 " ideal model delta sigma weight residual 121.97 129.68 -7.71 1.00e+00 1.00e+00 5.94e+01 angle pdb=" N ASN C 540 " pdb=" CA ASN C 540 " pdb=" C ASN C 540 " ideal model delta sigma weight residual 108.86 118.49 -9.63 1.41e+00 5.03e-01 4.67e+01 angle pdb=" N PHE C 541 " pdb=" CA PHE C 541 " pdb=" C PHE C 541 " ideal model delta sigma weight residual 111.14 118.24 -7.10 1.08e+00 8.57e-01 4.32e+01 angle pdb=" C GLU B 619 " pdb=" N VAL B 620 " pdb=" CA VAL B 620 " ideal model delta sigma weight residual 120.24 124.33 -4.09 6.30e-01 2.52e+00 4.21e+01 ... (remaining 27767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 11735 17.87 - 35.73: 819 35.73 - 53.60: 155 53.60 - 71.47: 43 71.47 - 89.33: 29 Dihedral angle restraints: 12781 sinusoidal: 5555 harmonic: 7226 Sorted by residual: dihedral pdb=" CA GLY B 199 " pdb=" C GLY B 199 " pdb=" N TYR B 200 " pdb=" CA TYR B 200 " ideal model delta harmonic sigma weight residual 180.00 149.98 30.02 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA VAL B 90 " pdb=" C VAL B 90 " pdb=" N TYR B 91 " pdb=" CA TYR B 91 " ideal model delta harmonic sigma weight residual 180.00 149.99 30.01 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA GLN C 563 " pdb=" C GLN C 563 " pdb=" N GLN C 564 " pdb=" CA GLN C 564 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 12778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.264: 3285 0.264 - 0.528: 28 0.528 - 0.792: 0 0.792 - 1.056: 0 1.056 - 1.320: 1 Chirality restraints: 3314 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.86e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.37e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.40e+01 ... (remaining 3311 not shown) Planarity restraints: 3567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " 0.138 2.00e-02 2.50e+03 1.47e-01 2.70e+02 pdb=" CG ASN B1074 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " -0.227 2.00e-02 2.50e+03 pdb=" C1 NAG B1311 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " 0.135 2.00e-02 2.50e+03 1.44e-01 2.60e+02 pdb=" CG ASN B 603 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " -0.223 2.00e-02 2.50e+03 pdb=" C1 NAG B1303 " 0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " -0.137 2.00e-02 2.50e+03 1.44e-01 2.58e+02 pdb=" CG ASN B 61 " 0.087 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " 0.218 2.00e-02 2.50e+03 pdb=" C1 NAG B1304 " -0.171 2.00e-02 2.50e+03 ... (remaining 3564 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 10528 3.00 - 3.47: 20625 3.47 - 3.95: 33768 3.95 - 4.42: 36901 4.42 - 4.90: 61171 Nonbonded interactions: 162993 Sorted by model distance: nonbonded pdb=" OD1 ASP C 586 " pdb=" OG1 THR C 588 " model vdw 2.519 3.040 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.530 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.543 3.040 nonbonded pdb=" OE1 GLU C 324 " pdb=" OG1 THR C 549 " model vdw 2.546 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.550 3.040 ... (remaining 162988 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 'B' and (resid 27 through 827 or resid 854 through 1309)) selection = (chain 'C' and (resid 27 through 623 or resid 632 through 1309)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } 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: 1.550 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.480 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.013 0.078 20492 Z= 0.768 Angle : 1.820 15.653 27972 Z= 1.183 Chirality : 0.104 1.320 3314 Planarity : 0.015 0.165 3533 Dihedral : 13.644 89.332 8032 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 1.10 % Allowed : 8.60 % Favored : 90.30 % Rotamer: Outliers : 1.94 % Allowed : 3.98 % Favored : 94.08 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.79 (0.15), residues: 2453 helix: -1.06 (0.17), residues: 658 sheet: 0.14 (0.27), residues: 330 loop : -1.62 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG C 457 TYR 0.190 0.023 TYR B 266 PHE 0.083 0.012 PHE C 559 TRP 0.114 0.027 TRP C 633 HIS 0.018 0.003 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.01348 (20415) covalent geometry : angle 1.79406 (27772) SS BOND : bond 0.01168 ( 31) SS BOND : angle 1.87414 ( 62) hydrogen bonds : bond 0.16936 ( 824) hydrogen bonds : angle 8.60199 ( 2334) link_BETA1-4 : bond 0.02402 ( 12) link_BETA1-4 : angle 4.79025 ( 36) link_NAG-ASN : bond 0.00849 ( 34) link_NAG-ASN : angle 4.61750 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 49 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.9063 (mmm) cc_final: 0.8768 (tpt) REVERT: A 1029 MET cc_start: 0.9495 (tpp) cc_final: 0.9125 (tpt) REVERT: B 428 ASP cc_start: 0.8172 (p0) cc_final: 0.7810 (p0) REVERT: B 453 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6351 (p90) REVERT: B 615 VAL cc_start: 0.7929 (OUTLIER) cc_final: 0.7661 (t) REVERT: B 634 ARG cc_start: 0.4619 (OUTLIER) cc_final: 0.3905 (tpp80) REVERT: B 1050 MET cc_start: 0.8447 (tpp) cc_final: 0.8036 (mmm) REVERT: C 613 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8033 (mp-120) REVERT: C 619 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7902 (tm-30) REVERT: C 634 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8516 (mmp80) REVERT: C 731 MET cc_start: 0.9034 (ptm) cc_final: 0.8297 (ttp) outliers start: 42 outliers final: 9 residues processed: 90 average time/residue: 0.1762 time to fit residues: 23.7769 Evaluate side-chains 48 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 948 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 360 ASN B 493 GLN B 907 ASN B 935 GLN C 207 HIS C 334 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.049402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.036187 restraints weight = 167694.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.037019 restraints weight = 96621.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.037533 restraints weight = 68121.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.037882 restraints weight = 55150.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.038069 restraints weight = 48377.909| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20492 Z= 0.174 Angle : 0.764 12.180 27972 Z= 0.394 Chirality : 0.048 0.341 3314 Planarity : 0.004 0.042 3533 Dihedral : 8.397 83.102 3651 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.75 % Favored : 94.01 % Rotamer: Outliers : 1.43 % Allowed : 5.23 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.74 % Twisted General : 0.13 % 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: -0.77 (0.16), residues: 2453 helix: 0.96 (0.20), residues: 650 sheet: -0.08 (0.25), residues: 379 loop : -1.39 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1091 TYR 0.019 0.002 TYR C1067 PHE 0.018 0.002 PHE B 201 TRP 0.020 0.002 TRP B 104 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00366 (20415) covalent geometry : angle 0.72966 (27772) SS BOND : bond 0.00686 ( 31) SS BOND : angle 1.33176 ( 62) hydrogen bonds : bond 0.05865 ( 824) hydrogen bonds : angle 6.27633 ( 2334) link_BETA1-4 : bond 0.00519 ( 12) link_BETA1-4 : angle 1.95494 ( 36) link_NAG-ASN : bond 0.00672 ( 34) link_NAG-ASN : angle 3.54171 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 36 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 906 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8730 (m-80) REVERT: B 615 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7653 (t) REVERT: B 634 ARG cc_start: 0.4421 (OUTLIER) cc_final: 0.3855 (tpp80) REVERT: B 1050 MET cc_start: 0.8390 (tpp) cc_final: 0.8106 (mtp) REVERT: C 613 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7710 (mp-120) outliers start: 31 outliers final: 14 residues processed: 63 average time/residue: 0.1682 time to fit residues: 16.3387 Evaluate side-chains 50 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 32 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 948 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 155 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 229 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 chunk 55 optimal weight: 50.0000 chunk 216 optimal weight: 5.9990 chunk 174 optimal weight: 30.0000 chunk 113 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN C 360 ASN C 655 HIS C 675 GLN C 913 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.048489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.035044 restraints weight = 169458.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.035843 restraints weight = 99102.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.036367 restraints weight = 70664.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.036645 restraints weight = 57336.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.036869 restraints weight = 50811.738| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20492 Z= 0.237 Angle : 0.733 12.417 27972 Z= 0.374 Chirality : 0.047 0.268 3314 Planarity : 0.004 0.052 3533 Dihedral : 7.757 79.709 3637 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.01 % Favored : 92.78 % Rotamer: Outliers : 1.25 % Allowed : 7.08 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.16), residues: 2453 helix: 1.03 (0.20), residues: 652 sheet: -0.28 (0.23), residues: 427 loop : -1.31 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 634 TYR 0.019 0.002 TYR B1067 PHE 0.020 0.002 PHE B 201 TRP 0.013 0.002 TRP B 64 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00535 (20415) covalent geometry : angle 0.70670 (27772) SS BOND : bond 0.00666 ( 31) SS BOND : angle 1.15855 ( 62) hydrogen bonds : bond 0.05425 ( 824) hydrogen bonds : angle 6.02989 ( 2334) link_BETA1-4 : bond 0.00299 ( 12) link_BETA1-4 : angle 1.70415 ( 36) link_NAG-ASN : bond 0.00685 ( 34) link_NAG-ASN : angle 3.11797 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 34 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 634 ARG cc_start: 0.4322 (OUTLIER) cc_final: 0.3812 (tpp80) REVERT: B 844 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7390 (mt) outliers start: 27 outliers final: 18 residues processed: 57 average time/residue: 0.1774 time to fit residues: 15.8146 Evaluate side-chains 52 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 32 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 948 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 179 optimal weight: 0.0770 chunk 23 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 234 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 187 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.049059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.035831 restraints weight = 169169.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.036671 restraints weight = 97299.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.037215 restraints weight = 68382.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.037550 restraints weight = 54913.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.037763 restraints weight = 48328.386| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20492 Z= 0.134 Angle : 0.641 12.814 27972 Z= 0.324 Chirality : 0.045 0.432 3314 Planarity : 0.004 0.048 3533 Dihedral : 7.391 82.436 3636 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.67 % Favored : 94.17 % Rotamer: Outliers : 1.39 % Allowed : 7.31 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.17), residues: 2453 helix: 1.45 (0.20), residues: 651 sheet: -0.24 (0.23), residues: 437 loop : -1.22 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 634 TYR 0.019 0.001 TYR C1067 PHE 0.018 0.001 PHE B 456 TRP 0.011 0.001 TRP C 633 HIS 0.003 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00287 (20415) covalent geometry : angle 0.61425 (27772) SS BOND : bond 0.00363 ( 31) SS BOND : angle 0.92975 ( 62) hydrogen bonds : bond 0.04663 ( 824) hydrogen bonds : angle 5.59898 ( 2334) link_BETA1-4 : bond 0.00244 ( 12) link_BETA1-4 : angle 1.44157 ( 36) link_NAG-ASN : bond 0.00466 ( 34) link_NAG-ASN : angle 2.97224 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 33 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.8841 (tpp) cc_final: 0.8622 (tpt) REVERT: B 615 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7645 (t) REVERT: B 634 ARG cc_start: 0.4363 (OUTLIER) cc_final: 0.3891 (tpp80) REVERT: B 844 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7195 (mt) REVERT: C 613 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7860 (mp-120) outliers start: 30 outliers final: 19 residues processed: 59 average time/residue: 0.1491 time to fit residues: 13.9921 Evaluate side-chains 55 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 32 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 948 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 137 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 48 optimal weight: 50.0000 chunk 3 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 228 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 57 optimal weight: 30.0000 chunk 159 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 69 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.048701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.035372 restraints weight = 168006.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.036201 restraints weight = 97354.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.036742 restraints weight = 68999.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.037026 restraints weight = 55586.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.037242 restraints weight = 49070.992| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20492 Z= 0.158 Angle : 0.624 12.791 27972 Z= 0.317 Chirality : 0.044 0.374 3314 Planarity : 0.004 0.048 3533 Dihedral : 7.017 80.531 3636 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.40 % Favored : 93.36 % Rotamer: Outliers : 1.71 % Allowed : 7.77 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.43 (0.17), residues: 2453 helix: 1.49 (0.20), residues: 651 sheet: -0.35 (0.23), residues: 455 loop : -1.19 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 634 TYR 0.017 0.001 TYR C1067 PHE 0.016 0.001 PHE B 456 TRP 0.009 0.001 TRP C 633 HIS 0.004 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00346 (20415) covalent geometry : angle 0.59756 (27772) SS BOND : bond 0.00368 ( 31) SS BOND : angle 0.93111 ( 62) hydrogen bonds : bond 0.04534 ( 824) hydrogen bonds : angle 5.50975 ( 2334) link_BETA1-4 : bond 0.00314 ( 12) link_BETA1-4 : angle 1.44807 ( 36) link_NAG-ASN : bond 0.00585 ( 34) link_NAG-ASN : angle 2.85264 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 32 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 634 ARG cc_start: 0.4299 (OUTLIER) cc_final: 0.3948 (tpp80) REVERT: B 844 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7335 (mt) REVERT: C 613 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8280 (mp-120) outliers start: 37 outliers final: 25 residues processed: 66 average time/residue: 0.1515 time to fit residues: 15.6883 Evaluate side-chains 60 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 32 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 948 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 247 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 237 optimal weight: 0.5980 chunk 95 optimal weight: 30.0000 chunk 184 optimal weight: 40.0000 chunk 13 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 105 optimal weight: 0.0470 chunk 17 optimal weight: 9.9990 chunk 157 optimal weight: 20.0000 chunk 154 optimal weight: 4.9990 overall best weight: 3.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS C 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.048623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.035384 restraints weight = 169022.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.036215 restraints weight = 97829.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.036739 restraints weight = 69085.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.037013 restraints weight = 56225.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.037223 restraints weight = 49900.309| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20492 Z= 0.157 Angle : 0.602 12.691 27972 Z= 0.307 Chirality : 0.044 0.298 3314 Planarity : 0.004 0.049 3533 Dihedral : 6.792 81.569 3636 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.99 % Favored : 93.80 % Rotamer: Outliers : 1.67 % Allowed : 8.47 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.33 (0.17), residues: 2453 helix: 1.61 (0.20), residues: 646 sheet: -0.33 (0.23), residues: 462 loop : -1.12 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.017 0.001 TYR C1067 PHE 0.015 0.001 PHE B 456 TRP 0.009 0.001 TRP C 886 HIS 0.007 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00348 (20415) covalent geometry : angle 0.57939 (27772) SS BOND : bond 0.00378 ( 31) SS BOND : angle 0.86201 ( 62) hydrogen bonds : bond 0.04368 ( 824) hydrogen bonds : angle 5.41434 ( 2334) link_BETA1-4 : bond 0.00224 ( 12) link_BETA1-4 : angle 1.33929 ( 36) link_NAG-ASN : bond 0.00471 ( 34) link_NAG-ASN : angle 2.64130 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 34 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 634 ARG cc_start: 0.4483 (OUTLIER) cc_final: 0.4242 (tpp80) REVERT: B 844 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7399 (mt) REVERT: B 900 MET cc_start: 0.8149 (mtm) cc_final: 0.7882 (mtm) REVERT: C 613 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7983 (mp-120) outliers start: 36 outliers final: 23 residues processed: 68 average time/residue: 0.1613 time to fit residues: 17.3692 Evaluate side-chains 58 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 32 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 948 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 243 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 246 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.047931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.034571 restraints weight = 170908.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.035387 restraints weight = 98735.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.035910 restraints weight = 69960.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.036173 restraints weight = 56466.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.036394 restraints weight = 49999.354| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 20492 Z= 0.247 Angle : 0.673 12.580 27972 Z= 0.342 Chirality : 0.045 0.343 3314 Planarity : 0.004 0.050 3533 Dihedral : 7.003 78.807 3635 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.13 % Favored : 92.66 % Rotamer: Outliers : 1.57 % Allowed : 8.88 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.17), residues: 2453 helix: 1.35 (0.20), residues: 652 sheet: -0.40 (0.23), residues: 461 loop : -1.18 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 577 TYR 0.017 0.002 TYR B1067 PHE 0.016 0.002 PHE B 429 TRP 0.009 0.002 TRP A 886 HIS 0.005 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00560 (20415) covalent geometry : angle 0.65101 (27772) SS BOND : bond 0.00501 ( 31) SS BOND : angle 1.05409 ( 62) hydrogen bonds : bond 0.04770 ( 824) hydrogen bonds : angle 5.65311 ( 2334) link_BETA1-4 : bond 0.00272 ( 12) link_BETA1-4 : angle 1.46687 ( 36) link_NAG-ASN : bond 0.00671 ( 34) link_NAG-ASN : angle 2.74600 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 32 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 844 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7401 (mt) outliers start: 34 outliers final: 28 residues processed: 63 average time/residue: 0.1575 time to fit residues: 15.8066 Evaluate side-chains 60 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 31 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 948 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 68 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 170 optimal weight: 40.0000 chunk 74 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 214 optimal weight: 0.7980 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 ASN C 556 ASN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.047931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.034479 restraints weight = 168986.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.035265 restraints weight = 99249.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.035764 restraints weight = 71209.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.036041 restraints weight = 57988.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.036241 restraints weight = 51587.681| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20492 Z= 0.231 Angle : 0.657 12.507 27972 Z= 0.335 Chirality : 0.045 0.324 3314 Planarity : 0.004 0.050 3533 Dihedral : 6.979 79.288 3631 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.97 % Favored : 92.83 % Rotamer: Outliers : 1.76 % Allowed : 9.21 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.52 (0.17), residues: 2453 helix: 1.34 (0.20), residues: 652 sheet: -0.44 (0.23), residues: 463 loop : -1.19 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 634 TYR 0.017 0.002 TYR C1067 PHE 0.014 0.002 PHE B 201 TRP 0.009 0.002 TRP B 104 HIS 0.006 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00520 (20415) covalent geometry : angle 0.63541 (27772) SS BOND : bond 0.00443 ( 31) SS BOND : angle 1.04785 ( 62) hydrogen bonds : bond 0.04718 ( 824) hydrogen bonds : angle 5.65527 ( 2334) link_BETA1-4 : bond 0.00229 ( 12) link_BETA1-4 : angle 1.39136 ( 36) link_NAG-ASN : bond 0.00620 ( 34) link_NAG-ASN : angle 2.67078 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 31 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 844 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7526 (mt) REVERT: C 309 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8413 (pm20) outliers start: 38 outliers final: 32 residues processed: 67 average time/residue: 0.1549 time to fit residues: 16.8017 Evaluate side-chains 65 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 31 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 948 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 66 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 211 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 180 optimal weight: 30.0000 chunk 116 optimal weight: 8.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.047742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.034342 restraints weight = 169398.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.035129 restraints weight = 99381.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.035627 restraints weight = 71296.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.035895 restraints weight = 58124.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.036050 restraints weight = 51670.369| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 20492 Z= 0.242 Angle : 0.668 12.485 27972 Z= 0.340 Chirality : 0.045 0.328 3314 Planarity : 0.004 0.050 3533 Dihedral : 6.950 78.830 3631 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.70 % Favored : 92.13 % Rotamer: Outliers : 1.67 % Allowed : 9.49 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.54 (0.17), residues: 2453 helix: 1.32 (0.20), residues: 650 sheet: -0.42 (0.23), residues: 452 loop : -1.21 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 634 TYR 0.018 0.002 TYR C1067 PHE 0.014 0.002 PHE B 201 TRP 0.010 0.002 TRP B 104 HIS 0.005 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00548 (20415) covalent geometry : angle 0.64609 (27772) SS BOND : bond 0.00428 ( 31) SS BOND : angle 1.00312 ( 62) hydrogen bonds : bond 0.04771 ( 824) hydrogen bonds : angle 5.69011 ( 2334) link_BETA1-4 : bond 0.00234 ( 12) link_BETA1-4 : angle 1.41922 ( 36) link_NAG-ASN : bond 0.00647 ( 34) link_NAG-ASN : angle 2.69957 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 30 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 844 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7627 (mt) REVERT: C 309 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8415 (pm20) outliers start: 36 outliers final: 33 residues processed: 64 average time/residue: 0.1502 time to fit residues: 15.9344 Evaluate side-chains 65 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 30 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 948 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 56 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 213 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS C 556 ASN C1083 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.048329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.035009 restraints weight = 168291.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.035833 restraints weight = 97443.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.036360 restraints weight = 69004.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.036660 restraints weight = 55830.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.036814 restraints weight = 49426.881| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20492 Z= 0.140 Angle : 0.590 12.551 27972 Z= 0.300 Chirality : 0.044 0.321 3314 Planarity : 0.004 0.051 3533 Dihedral : 6.525 81.293 3631 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.48 % Favored : 93.36 % Rotamer: Outliers : 1.39 % Allowed : 9.81 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.33 (0.17), residues: 2453 helix: 1.62 (0.20), residues: 656 sheet: -0.31 (0.23), residues: 456 loop : -1.16 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 634 TYR 0.018 0.001 TYR C1067 PHE 0.014 0.001 PHE B 456 TRP 0.012 0.001 TRP C 886 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00309 (20415) covalent geometry : angle 0.56880 (27772) SS BOND : bond 0.00349 ( 31) SS BOND : angle 0.90613 ( 62) hydrogen bonds : bond 0.04284 ( 824) hydrogen bonds : angle 5.36860 ( 2334) link_BETA1-4 : bond 0.00191 ( 12) link_BETA1-4 : angle 1.22904 ( 36) link_NAG-ASN : bond 0.00487 ( 34) link_NAG-ASN : angle 2.50710 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 31 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 613 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8024 (mp-120) outliers start: 30 outliers final: 25 residues processed: 59 average time/residue: 0.1409 time to fit residues: 14.2567 Evaluate side-chains 56 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 30 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 948 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 193 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 210 optimal weight: 0.4980 chunk 205 optimal weight: 10.0000 chunk 13 optimal weight: 0.0270 chunk 79 optimal weight: 0.5980 chunk 152 optimal weight: 20.0000 chunk 228 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN C 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.048733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.035526 restraints weight = 169033.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.036370 restraints weight = 97299.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.036910 restraints weight = 68369.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.037194 restraints weight = 55188.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.037403 restraints weight = 48813.154| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20492 Z= 0.108 Angle : 0.561 12.646 27972 Z= 0.286 Chirality : 0.043 0.326 3314 Planarity : 0.004 0.050 3533 Dihedral : 6.076 82.848 3631 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.91 % Favored : 93.93 % Rotamer: Outliers : 1.02 % Allowed : 10.18 % Favored : 88.80 % 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: -0.14 (0.17), residues: 2453 helix: 1.86 (0.21), residues: 651 sheet: -0.22 (0.23), residues: 470 loop : -1.07 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 634 TYR 0.019 0.001 TYR C1067 PHE 0.014 0.001 PHE B 392 TRP 0.015 0.001 TRP C 633 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00227 (20415) covalent geometry : angle 0.54103 (27772) SS BOND : bond 0.00319 ( 31) SS BOND : angle 0.85713 ( 62) hydrogen bonds : bond 0.03927 ( 824) hydrogen bonds : angle 5.08938 ( 2334) link_BETA1-4 : bond 0.00273 ( 12) link_BETA1-4 : angle 1.19745 ( 36) link_NAG-ASN : bond 0.00453 ( 34) link_NAG-ASN : angle 2.36520 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3146.76 seconds wall clock time: 55 minutes 30.93 seconds (3330.93 seconds total)