Starting phenix.real_space_refine on Sat Jul 4 10:45:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tpl_26059/07_2026/7tpl_26059.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpl_26059/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tpl_26059/07_2026/7tpl_26059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpl_26059/07_2026/7tpl_26059.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tpl_26059/07_2026/7tpl_26059.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tpl_26059/07_2026/7tpl_26059.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tpl_26059/07_2026/7tpl_26059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpl_26059/07_2026/7tpl_26059.map" } 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-6108/lib/python3.11/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 chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 chiralities: 9 Time building chain proxies: 3.67, per 1000 atoms: 0.18 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: 1.58 Conformation dependent library (CDL) restraints added in 800.6 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: 0.85 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: 4.43 Time building geometry restraints manager: 2.15 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: 10827 17.87 - 35.73: 769 35.73 - 53.60: 147 53.60 - 71.47: 43 71.47 - 89.33: 29 Dihedral angle restraints: 11815 sinusoidal: 4589 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 11812 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.900 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 14.153 89.332 7066 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/Z covalent geometry : bond 0.01348 / 0.77 (20415) covalent geometry : angle 1.79406 / 1.18 (27772) SS BOND : bond 0.01168 / 0.83 ( 31) SS BOND : angle 1.87414 / 1.24 ( 62) hydrogen bonds : bond 0.16936 / 11.38 ( 824) hydrogen bonds : angle 8.60199 / 6.14 ( 2334) link_BETA1-4 : bond 0.02402 / 1.70 ( 12) link_BETA1-4 : angle 4.79025 / 3.34 ( 36) link_NAG-ASN : bond 0.00849 / 0.58 ( 34) link_NAG-ASN : angle 4.61750 / 3.19 ( 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 : 0.700 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: 0.1418 time to fit residues: 19.4204 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 : 0.539 ------------------------------------------------------------------------------- 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... A 751 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.049384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.036290 restraints weight = 168719.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.037127 restraints weight = 97079.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.037650 restraints weight = 68305.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.037985 restraints weight = 55076.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.038148 restraints weight = 48430.292| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20492 Z= 0.172 Angle : 0.768 14.390 27972 Z= 0.396 Chirality : 0.048 0.341 3314 Planarity : 0.004 0.042 3533 Dihedral : 7.911 83.049 2685 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.71 % 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: -0.07 (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 0.018 0.002 TYR C1067 PHE 0.018 0.002 PHE B 192 TRP 0.019 0.002 TRP B 104 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (20415) covalent geometry : angle 0.73538 / 0.39 (27772) SS BOND : bond 0.00413 / 0.29 ( 31) SS BOND : angle 1.32296 / 0.96 ( 62) hydrogen bonds : bond 0.05814 / 3.84 ( 824) hydrogen bonds : angle 6.27128 / 4.55 ( 2334) link_BETA1-4 : bond 0.00299 / 0.21 ( 12) link_BETA1-4 : angle 1.72931 / 1.10 ( 36) link_NAG-ASN : bond 0.00515 / 0.42 ( 34) link_NAG-ASN : angle 3.54727 / 2.68 ( 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 : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 906 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8728 (m-80) REVERT: B 615 VAL cc_start: 0.7933 (OUTLIER) cc_final: 0.7692 (t) REVERT: B 634 ARG cc_start: 0.4420 (OUTLIER) cc_final: 0.3852 (tpp80) REVERT: B 1050 MET cc_start: 0.8444 (tpp) cc_final: 0.8106 (mtp) REVERT: C 613 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7712 (mp-120) outliers start: 31 outliers final: 13 residues processed: 63 average time/residue: 0.1671 time to fit residues: 16.0463 Evaluate side-chains 49 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 32 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 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: 2.9990 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: 7.9990 chunk 55 optimal weight: 50.0000 chunk 216 optimal weight: 5.9990 chunk 174 optimal weight: 30.0000 chunk 113 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 926 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN C 360 ASN C 556 ASN C 655 HIS C 675 GLN C 913 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.048349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.034982 restraints weight = 170559.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.035796 restraints weight = 99830.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.036312 restraints weight = 70949.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.036569 restraints weight = 57488.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.036786 restraints weight = 50988.024| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20492 Z= 0.228 Angle : 0.724 12.148 27972 Z= 0.371 Chirality : 0.046 0.243 3314 Planarity : 0.004 0.048 3533 Dihedral : 7.061 79.118 2671 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.01 % Favored : 92.70 % Rotamer: Outliers : 1.25 % Allowed : 7.22 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.87 % 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: -0.71 (0.16), residues: 2453 helix: 1.03 (0.20), residues: 652 sheet: -0.29 (0.23), residues: 430 loop : -1.31 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 634 TYR 0.019 0.002 TYR B1067 PHE 0.022 0.002 PHE B 201 TRP 0.013 0.002 TRP B 64 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 (20415) covalent geometry : angle 0.70231 / 0.37 (27772) SS BOND : bond 0.00553 / 0.42 ( 31) SS BOND : angle 1.16573 / 0.83 ( 62) hydrogen bonds : bond 0.05371 / 3.53 ( 824) hydrogen bonds : angle 5.97554 / 4.33 ( 2334) link_BETA1-4 : bond 0.00285 / 0.20 ( 12) link_BETA1-4 : angle 1.50621 / 0.98 ( 36) link_NAG-ASN : bond 0.00649 / 0.52 ( 34) link_NAG-ASN : angle 2.82145 / 2.08 ( 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 63 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 36 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 634 ARG cc_start: 0.4318 (OUTLIER) cc_final: 0.3814 (tpp80) REVERT: B 844 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7383 (mt) outliers start: 27 outliers final: 18 residues processed: 59 average time/residue: 0.1736 time to fit residues: 16.0653 Evaluate side-chains 54 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 34 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 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 556 ASN 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: 5.9990 chunk 23 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 187 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 69 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.048276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.035016 restraints weight = 170509.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.035812 restraints weight = 98666.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.036331 restraints weight = 70094.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.036621 restraints weight = 56787.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.036819 restraints weight = 50330.438| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2593 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= 0.216 Angle : 0.683 12.407 27972 Z= 0.348 Chirality : 0.046 0.437 3314 Planarity : 0.004 0.048 3533 Dihedral : 6.887 80.339 2670 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.36 % Favored : 93.48 % Rotamer: Outliers : 1.57 % Allowed : 7.54 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.87 % 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: -0.68 (0.16), residues: 2453 helix: 1.11 (0.20), residues: 657 sheet: -0.42 (0.23), residues: 427 loop : -1.27 (0.16), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.018 0.002 TYR C1067 PHE 0.016 0.001 PHE B 456 TRP 0.011 0.002 TRP C 886 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 (20415) covalent geometry : angle 0.66025 / 0.34 (27772) SS BOND : bond 0.00459 / 0.35 ( 31) SS BOND : angle 0.99557 / 0.69 ( 62) hydrogen bonds : bond 0.05050 / 3.32 ( 824) hydrogen bonds : angle 5.84553 / 4.24 ( 2334) link_BETA1-4 : bond 0.00240 / 0.15 ( 12) link_BETA1-4 : angle 1.42077 / 0.92 ( 36) link_NAG-ASN : bond 0.00560 / 0.43 ( 34) link_NAG-ASN : angle 2.79099 / 1.98 ( 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 67 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 33 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 634 ARG cc_start: 0.4385 (OUTLIER) cc_final: 0.3914 (tpp80) REVERT: B 844 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7325 (mt) REVERT: C 740 MET cc_start: 0.8474 (ttt) cc_final: 0.8197 (tmm) outliers start: 34 outliers final: 19 residues processed: 63 average time/residue: 0.1560 time to fit residues: 15.6847 Evaluate side-chains 53 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 32 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 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 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 C residue 62 VAL 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 620 VAL 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: 1.9990 chunk 176 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 48 optimal weight: 50.0000 chunk 3 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.048733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.035510 restraints weight = 168604.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.036336 restraints weight = 97673.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.036876 restraints weight = 69020.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.037158 restraints weight = 55741.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.037365 restraints weight = 49356.500| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20492 Z= 0.151 Angle : 0.615 12.469 27972 Z= 0.314 Chirality : 0.044 0.332 3314 Planarity : 0.004 0.048 3533 Dihedral : 6.311 59.467 2667 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.36 % Favored : 93.36 % Rotamer: Outliers : 1.62 % Allowed : 8.24 % Favored : 90.14 % 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: -0.47 (0.17), residues: 2453 helix: 1.48 (0.20), residues: 651 sheet: -0.29 (0.24), residues: 427 loop : -1.24 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 634 TYR 0.018 0.001 TYR C1067 PHE 0.015 0.001 PHE B 456 TRP 0.012 0.001 TRP C 633 HIS 0.007 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (20415) covalent geometry : angle 0.59465 / 0.31 (27772) SS BOND : bond 0.00362 / 0.28 ( 31) SS BOND : angle 0.90067 / 0.62 ( 62) hydrogen bonds : bond 0.04545 / 2.98 ( 824) hydrogen bonds : angle 5.54690 / 4.03 ( 2334) link_BETA1-4 : bond 0.00246 / 0.18 ( 12) link_BETA1-4 : angle 1.30222 / 0.87 ( 36) link_NAG-ASN : bond 0.00518 / 0.42 ( 34) link_NAG-ASN : angle 2.50316 / 1.76 ( 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 67 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 32 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 615 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7650 (t) REVERT: B 634 ARG cc_start: 0.4438 (OUTLIER) cc_final: 0.4121 (tpp80) REVERT: B 844 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7307 (mt) outliers start: 35 outliers final: 22 residues processed: 63 average time/residue: 0.1616 time to fit residues: 16.3968 Evaluate side-chains 57 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 32 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 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 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 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 578 ASP Chi-restraints excluded: chain C residue 581 THR 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: 8.9990 chunk 51 optimal weight: 40.0000 chunk 237 optimal weight: 0.4980 chunk 95 optimal weight: 20.0000 chunk 184 optimal weight: 40.0000 chunk 13 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 17 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 154 optimal weight: 3.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 613 GLN C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.048420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.035214 restraints weight = 169217.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.036027 restraints weight = 98058.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.036557 restraints weight = 69501.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.036811 restraints weight = 56141.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.037021 restraints weight = 49892.318| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20492 Z= 0.170 Angle : 0.620 12.460 27972 Z= 0.315 Chirality : 0.044 0.304 3314 Planarity : 0.004 0.049 3533 Dihedral : 6.174 59.905 2667 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.20 % Favored : 93.60 % Rotamer: Outliers : 1.80 % Allowed : 8.93 % Favored : 89.26 % 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: -0.42 (0.17), residues: 2453 helix: 1.55 (0.20), residues: 644 sheet: -0.36 (0.23), residues: 450 loop : -1.19 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.018 0.001 TYR C1067 PHE 0.015 0.001 PHE B 456 TRP 0.009 0.001 TRP C 886 HIS 0.006 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (20415) covalent geometry : angle 0.60128 / 0.31 (27772) SS BOND : bond 0.00397 / 0.30 ( 31) SS BOND : angle 0.89463 / 0.62 ( 62) hydrogen bonds : bond 0.04529 / 2.97 ( 824) hydrogen bonds : angle 5.50959 / 4.00 ( 2334) link_BETA1-4 : bond 0.00230 / 0.16 ( 12) link_BETA1-4 : angle 1.33150 / 0.88 ( 36) link_NAG-ASN : bond 0.00519 / 0.41 ( 34) link_NAG-ASN : angle 2.44812 / 1.72 ( 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 72 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 33 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 615 VAL cc_start: 0.7905 (OUTLIER) cc_final: 0.7656 (t) REVERT: B 634 ARG cc_start: 0.4432 (OUTLIER) cc_final: 0.4206 (tpp80) REVERT: B 844 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7418 (mt) outliers start: 39 outliers final: 27 residues processed: 68 average time/residue: 0.1591 time to fit residues: 17.2111 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 : 0.688 ------------------------------------------------------------------------------- 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 243 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.048456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035258 restraints weight = 169829.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.036059 restraints weight = 97806.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.036593 restraints weight = 69915.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.036879 restraints weight = 56225.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.037093 restraints weight = 49700.998| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20492 Z= 0.153 Angle : 0.600 12.481 27972 Z= 0.304 Chirality : 0.044 0.304 3314 Planarity : 0.004 0.049 3533 Dihedral : 6.033 59.538 2667 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.20 % Favored : 93.60 % Rotamer: Outliers : 1.71 % Allowed : 9.07 % Favored : 89.22 % 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: -0.31 (0.17), residues: 2453 helix: 1.68 (0.20), residues: 644 sheet: -0.29 (0.23), residues: 460 loop : -1.15 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 577 TYR 0.018 0.001 TYR C1067 PHE 0.014 0.001 PHE B 456 TRP 0.009 0.001 TRP C 886 HIS 0.003 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (20415) covalent geometry : angle 0.58056 / 0.30 (27772) SS BOND : bond 0.00351 / 0.27 ( 31) SS BOND : angle 0.99435 / 0.69 ( 62) hydrogen bonds : bond 0.04359 / 2.86 ( 824) hydrogen bonds : angle 5.42514 / 3.94 ( 2334) link_BETA1-4 : bond 0.00234 / 0.18 ( 12) link_BETA1-4 : angle 1.27141 / 0.85 ( 36) link_NAG-ASN : bond 0.00489 / 0.40 ( 34) link_NAG-ASN : angle 2.37249 / 1.66 ( 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 70 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 33 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 615 VAL cc_start: 0.7905 (OUTLIER) cc_final: 0.7642 (t) REVERT: B 844 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7417 (mt) REVERT: C 309 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8359 (pm20) outliers start: 37 outliers final: 26 residues processed: 67 average time/residue: 0.1594 time to fit residues: 16.9960 Evaluate side-chains 61 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 32 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 40 ASP 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 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 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 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 578 ASP Chi-restraints excluded: chain C residue 581 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 68 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 170 optimal weight: 50.0000 chunk 74 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.048173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.034939 restraints weight = 169665.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.035750 restraints weight = 98797.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.036273 restraints weight = 70261.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.036590 restraints weight = 56753.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.036741 restraints weight = 49984.555| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20492 Z= 0.182 Angle : 0.617 12.429 27972 Z= 0.313 Chirality : 0.044 0.311 3314 Planarity : 0.004 0.049 3533 Dihedral : 5.912 55.691 2663 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.69 % Favored : 93.11 % Rotamer: Outliers : 1.67 % Allowed : 9.21 % Favored : 89.13 % 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: -0.39 (0.17), residues: 2453 helix: 1.56 (0.20), residues: 644 sheet: -0.30 (0.23), residues: 462 loop : -1.17 (0.17), residues: 1347 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 0.009 0.001 TRP C 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (20415) covalent geometry : angle 0.59879 / 0.31 (27772) SS BOND : bond 0.00375 / 0.29 ( 31) SS BOND : angle 0.98925 / 0.69 ( 62) hydrogen bonds : bond 0.04466 / 2.93 ( 824) hydrogen bonds : angle 5.47033 / 3.96 ( 2334) link_BETA1-4 : bond 0.00193 / 0.14 ( 12) link_BETA1-4 : angle 1.31410 / 0.87 ( 36) link_NAG-ASN : bond 0.00529 / 0.42 ( 34) link_NAG-ASN : angle 2.38052 / 1.66 ( 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 67 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 31 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 615 VAL cc_start: 0.7905 (OUTLIER) cc_final: 0.7621 (t) REVERT: B 844 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7601 (mt) REVERT: C 309 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8389 (pm20) outliers start: 36 outliers final: 31 residues processed: 65 average time/residue: 0.1177 time to fit residues: 13.0211 Evaluate side-chains 64 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 30 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 B residue 40 ASP 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 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 615 VAL 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 578 ASP Chi-restraints excluded: chain C residue 581 THR 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=1.50 ------------------------------------------------------------------------------- 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: 6.9990 chunk 211 optimal weight: 9.9990 chunk 110 optimal weight: 0.4980 chunk 142 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 180 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 460 ASN C 556 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.048020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.034800 restraints weight = 168958.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.035570 restraints weight = 99338.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.036087 restraints weight = 71139.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.036328 restraints weight = 57815.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.036575 restraints weight = 51579.237| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20492 Z= 0.191 Angle : 0.621 12.377 27972 Z= 0.316 Chirality : 0.044 0.313 3314 Planarity : 0.004 0.049 3533 Dihedral : 5.908 59.320 2663 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.05 % Favored : 92.78 % Rotamer: Outliers : 1.85 % Allowed : 9.21 % Favored : 88.94 % 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: -0.41 (0.17), residues: 2453 helix: 1.55 (0.20), residues: 644 sheet: -0.36 (0.23), residues: 461 loop : -1.17 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 983 TYR 0.017 0.001 TYR C1067 PHE 0.014 0.001 PHE B 456 TRP 0.008 0.001 TRP C 886 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (20415) covalent geometry : angle 0.60376 / 0.31 (27772) SS BOND : bond 0.00384 / 0.29 ( 31) SS BOND : angle 0.95234 / 0.65 ( 62) hydrogen bonds : bond 0.04485 / 2.94 ( 824) hydrogen bonds : angle 5.50079 / 3.97 ( 2334) link_BETA1-4 : bond 0.00198 / 0.15 ( 12) link_BETA1-4 : angle 1.28987 / 0.87 ( 36) link_NAG-ASN : bond 0.00525 / 0.42 ( 34) link_NAG-ASN : angle 2.34919 / 1.64 ( 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 70 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 30 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 615 VAL cc_start: 0.7875 (OUTLIER) cc_final: 0.7566 (t) REVERT: B 844 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7572 (mt) outliers start: 40 outliers final: 33 residues processed: 68 average time/residue: 0.1351 time to fit residues: 15.3411 Evaluate side-chains 64 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 29 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 63 THR 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 615 VAL 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 859 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 46 SER 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 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: 30.0000 chunk 86 optimal weight: 6.9990 chunk 213 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 955 ASN B 901 GLN C 540 ASN C1083 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.048422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.035298 restraints weight = 169090.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.036093 restraints weight = 97914.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.036632 restraints weight = 69217.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.036943 restraints weight = 55822.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.037065 restraints weight = 49178.934| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3554 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= 0.128 Angle : 0.581 12.290 27972 Z= 0.295 Chirality : 0.044 0.306 3314 Planarity : 0.004 0.050 3533 Dihedral : 5.724 58.552 2663 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.40 % Favored : 93.44 % Rotamer: Outliers : 1.34 % Allowed : 9.72 % Favored : 88.94 % 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: -0.24 (0.17), residues: 2453 helix: 1.78 (0.21), residues: 643 sheet: -0.30 (0.23), residues: 465 loop : -1.10 (0.17), residues: 1345 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 456 TRP 0.011 0.001 TRP C 886 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (20415) covalent geometry : angle 0.56400 / 0.29 (27772) SS BOND : bond 0.00332 / 0.26 ( 31) SS BOND : angle 0.89959 / 0.61 ( 62) hydrogen bonds : bond 0.04198 / 2.74 ( 824) hydrogen bonds : angle 5.28354 / 3.82 ( 2334) link_BETA1-4 : bond 0.00252 / 0.17 ( 12) link_BETA1-4 : angle 1.17925 / 0.80 ( 36) link_NAG-ASN : bond 0.00457 / 0.38 ( 34) link_NAG-ASN : angle 2.22598 / 1.55 ( 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 58 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 29 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 615 VAL cc_start: 0.7873 (OUTLIER) cc_final: 0.7587 (t) REVERT: B 844 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7450 (mt) outliers start: 29 outliers final: 25 residues processed: 57 average time/residue: 0.1471 time to fit residues: 14.0914 Evaluate side-chains 56 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 29 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 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 615 VAL 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 859 THR 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 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: 7.9990 chunk 27 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 205 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 152 optimal weight: 20.0000 chunk 228 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.048069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.034848 restraints weight = 169983.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.035631 restraints weight = 99787.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.036151 restraints weight = 71430.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.036432 restraints weight = 57936.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.036639 restraints weight = 51416.500| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20492 Z= 0.179 Angle : 0.609 12.261 27972 Z= 0.309 Chirality : 0.044 0.314 3314 Planarity : 0.004 0.049 3533 Dihedral : 5.724 57.488 2662 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.93 % Favored : 92.91 % Rotamer: Outliers : 1.39 % Allowed : 9.63 % Favored : 88.99 % 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: -0.28 (0.17), residues: 2453 helix: 1.70 (0.21), residues: 644 sheet: -0.29 (0.23), residues: 460 loop : -1.12 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 634 TYR 0.019 0.001 TYR C1067 PHE 0.013 0.001 PHE B 456 TRP 0.008 0.001 TRP C 886 HIS 0.004 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (20415) covalent geometry : angle 0.59136 / 0.31 (27772) SS BOND : bond 0.00378 / 0.29 ( 31) SS BOND : angle 0.93332 / 0.63 ( 62) hydrogen bonds : bond 0.04377 / 2.86 ( 824) hydrogen bonds : angle 5.35141 / 3.86 ( 2334) link_BETA1-4 : bond 0.00198 / 0.15 ( 12) link_BETA1-4 : angle 1.28569 / 0.86 ( 36) link_NAG-ASN : bond 0.00514 / 0.41 ( 34) link_NAG-ASN : angle 2.29618 / 1.60 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2926.98 seconds wall clock time: 51 minutes 45.01 seconds (3105.01 seconds total)