Starting phenix.real_space_refine on Tue Jun 17 19:07:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tpl_26059/06_2025/7tpl_26059.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpl_26059/06_2025/7tpl_26059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tpl_26059/06_2025/7tpl_26059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpl_26059/06_2025/7tpl_26059.map" model { file = "/net/cci-nas-00/data/ceres_data/7tpl_26059/06_2025/7tpl_26059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpl_26059/06_2025/7tpl_26059.cif" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.006 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19992 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3250 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain breaks: 1 Chain: "B" Number of atoms: 8113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8113 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 48, 'TRANS': 991} Chain breaks: 6 Chain: "C" Number of atoms: 7985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7985 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 49, 'TRANS': 972} Chain breaks: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 11.00, per 1000 atoms: 0.55 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: 5.08 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.68 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: 7.67 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5720 1.34 - 1.46: 3585 1.46 - 1.58: 11000 1.58 - 1.70: 0 1.70 - 1.83: 110 Bond restraints: 20415 Sorted by residual: bond pdb=" C5 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.542 -0.025 6.70e-03 2.23e+04 1.43e+01 bond pdb=" C5 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C5 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C5 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.39e+01 ... (remaining 20410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 25502 3.13 - 6.26: 2206 6.26 - 9.39: 61 9.39 - 12.52: 2 12.52 - 15.65: 1 Bond angle restraints: 27772 Sorted by residual: angle pdb=" CA THR C 323 " pdb=" CB THR C 323 " pdb=" OG1 THR C 323 " ideal model delta sigma weight residual 109.60 125.25 -15.65 1.50e+00 4.44e-01 1.09e+02 angle pdb=" C LEU B 849 " pdb=" N ILE B 850 " pdb=" CA ILE B 850 " ideal model delta sigma weight residual 121.97 129.68 -7.71 1.00e+00 1.00e+00 5.94e+01 angle pdb=" N ASN C 540 " pdb=" CA ASN C 540 " pdb=" C ASN C 540 " ideal model delta sigma weight residual 108.86 118.49 -9.63 1.41e+00 5.03e-01 4.67e+01 angle pdb=" N PHE C 541 " pdb=" CA PHE C 541 " pdb=" C PHE C 541 " ideal model delta sigma weight residual 111.14 118.24 -7.10 1.08e+00 8.57e-01 4.32e+01 angle pdb=" C GLU B 619 " pdb=" N VAL B 620 " pdb=" CA VAL B 620 " ideal model delta sigma weight residual 120.24 124.33 -4.09 6.30e-01 2.52e+00 4.21e+01 ... (remaining 27767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 11735 17.87 - 35.73: 819 35.73 - 53.60: 155 53.60 - 71.47: 43 71.47 - 89.33: 29 Dihedral angle restraints: 12781 sinusoidal: 5555 harmonic: 7226 Sorted by residual: dihedral pdb=" CA GLY B 199 " pdb=" C GLY B 199 " pdb=" N TYR B 200 " pdb=" CA TYR B 200 " ideal model delta harmonic sigma weight residual 180.00 149.98 30.02 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA VAL B 90 " pdb=" C VAL B 90 " pdb=" N TYR B 91 " pdb=" CA TYR B 91 " ideal model delta harmonic sigma weight residual 180.00 149.99 30.01 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA GLN C 563 " pdb=" C GLN C 563 " pdb=" N GLN C 564 " pdb=" CA GLN C 564 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 12778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.264: 3285 0.264 - 0.528: 28 0.528 - 0.792: 0 0.792 - 1.056: 0 1.056 - 1.320: 1 Chirality restraints: 3314 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.86e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.37e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.40e+01 ... (remaining 3311 not shown) Planarity restraints: 3567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " 0.138 2.00e-02 2.50e+03 1.47e-01 2.70e+02 pdb=" CG ASN B1074 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " -0.227 2.00e-02 2.50e+03 pdb=" C1 NAG B1311 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " 0.135 2.00e-02 2.50e+03 1.44e-01 2.60e+02 pdb=" CG ASN B 603 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " -0.223 2.00e-02 2.50e+03 pdb=" C1 NAG B1303 " 0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " -0.137 2.00e-02 2.50e+03 1.44e-01 2.58e+02 pdb=" CG ASN B 61 " 0.087 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " 0.218 2.00e-02 2.50e+03 pdb=" C1 NAG B1304 " -0.171 2.00e-02 2.50e+03 ... (remaining 3564 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 10528 3.00 - 3.47: 20625 3.47 - 3.95: 33768 3.95 - 4.42: 36901 4.42 - 4.90: 61171 Nonbonded interactions: 162993 Sorted by model distance: nonbonded pdb=" OD1 ASP C 586 " pdb=" OG1 THR C 588 " model vdw 2.519 3.040 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.530 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.543 3.040 nonbonded pdb=" OE1 GLU C 324 " pdb=" OG1 THR C 549 " model vdw 2.546 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.550 3.040 ... (remaining 162988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 27 through 827 or resid 854 through 1147 or resid 1301 thr \ ough 1309)) selection = (chain 'C' and (resid 27 through 623 or resid 632 through 1147 or resid 1301 thr \ ough 1309)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 45.680 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.078 20492 Z= 0.768 Angle : 1.820 15.653 27972 Z= 1.183 Chirality : 0.104 1.320 3314 Planarity : 0.015 0.165 3533 Dihedral : 13.644 89.332 8032 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.40 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.114 0.027 TRP C 633 HIS 0.018 0.003 HIS C1048 PHE 0.083 0.012 PHE C 559 TYR 0.190 0.023 TYR B 266 ARG 0.015 0.002 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00849 ( 34) link_NAG-ASN : angle 4.61750 ( 102) link_BETA1-4 : bond 0.02402 ( 12) link_BETA1-4 : angle 4.79025 ( 36) hydrogen bonds : bond 0.16936 ( 824) hydrogen bonds : angle 8.60199 ( 2334) SS BOND : bond 0.01168 ( 31) SS BOND : angle 1.87414 ( 62) covalent geometry : bond 0.01348 (20415) covalent geometry : angle 1.79406 (27772) *********************** 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 : 2.090 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: 0.8032 (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: 0.8151 (mmp80) REVERT: C 731 MET cc_start: 0.9034 (ptm) cc_final: 0.8297 (ttp) outliers start: 42 outliers final: 10 residues processed: 90 average time/residue: 0.4203 time to fit residues: 56.9698 Evaluate side-chains 49 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 33 time to evaluate : 3.142 ------------------------------------------------------------------------------- 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 466 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 209 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 64 optimal weight: 0.0970 chunk 126 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 75 optimal weight: 0.0870 chunk 118 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN B 121 ASN B 493 GLN B 853 GLN B 907 ASN B 935 GLN C 207 HIS C 334 ASN C 751 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.049782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.036744 restraints weight = 167137.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.037578 restraints weight = 96307.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.038111 restraints weight = 67720.389| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20492 Z= 0.151 Angle : 0.755 12.325 27972 Z= 0.389 Chirality : 0.047 0.337 3314 Planarity : 0.004 0.041 3533 Dihedral : 8.309 83.994 3655 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.58 % Favored : 94.17 % Rotamer: Outliers : 1.34 % Allowed : 5.09 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.74 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2453 helix: 1.08 (0.20), residues: 648 sheet: -0.03 (0.25), residues: 380 loop : -1.35 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 104 HIS 0.006 0.001 HIS B1048 PHE 0.019 0.002 PHE B 192 TYR 0.020 0.002 TYR B 38 ARG 0.005 0.001 ARG C1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 34) link_NAG-ASN : angle 3.55332 ( 102) link_BETA1-4 : bond 0.00518 ( 12) link_BETA1-4 : angle 1.88133 ( 36) hydrogen bonds : bond 0.05775 ( 824) hydrogen bonds : angle 6.20232 ( 2334) SS BOND : bond 0.00428 ( 31) SS BOND : angle 1.32492 ( 62) covalent geometry : bond 0.00304 (20415) covalent geometry : angle 0.72011 (27772) *********************** 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 66 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 37 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 906 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8659 (m-80) REVERT: B 615 VAL cc_start: 0.7941 (OUTLIER) cc_final: 0.7720 (t) REVERT: B 634 ARG cc_start: 0.4329 (OUTLIER) cc_final: 0.3831 (tpp80) REVERT: C 1050 MET cc_start: 0.7898 (ttm) cc_final: 0.7440 (ttm) outliers start: 29 outliers final: 15 residues processed: 63 average time/residue: 0.4123 time to fit residues: 39.6928 Evaluate side-chains 50 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 32 time to evaluate : 2.063 ------------------------------------------------------------------------------- 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 A residue 988 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 ARG 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 948 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 120 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 179 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 95 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 225 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 675 GLN B 853 GLN C 360 ASN C 675 GLN C 913 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.048875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.035643 restraints weight = 167756.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.036464 restraints weight = 97614.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.036993 restraints weight = 69171.724| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20492 Z= 0.187 Angle : 0.692 12.636 27972 Z= 0.353 Chirality : 0.045 0.261 3314 Planarity : 0.004 0.047 3533 Dihedral : 7.339 59.846 3634 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.60 % Favored : 93.11 % Rotamer: Outliers : 1.06 % Allowed : 6.85 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2453 helix: 1.24 (0.20), residues: 653 sheet: -0.16 (0.23), residues: 434 loop : -1.24 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 64 HIS 0.005 0.001 HIS B1064 PHE 0.021 0.002 PHE B 201 TYR 0.019 0.002 TYR B1067 ARG 0.008 0.001 ARG C 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 34) link_NAG-ASN : angle 3.04810 ( 102) link_BETA1-4 : bond 0.00360 ( 12) link_BETA1-4 : angle 1.65636 ( 36) hydrogen bonds : bond 0.05174 ( 824) hydrogen bonds : angle 5.80864 ( 2334) SS BOND : bond 0.00454 ( 31) SS BOND : angle 1.12305 ( 62) covalent geometry : bond 0.00419 (20415) covalent geometry : angle 0.66449 (27772) *********************** 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 58 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 35 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 634 ARG cc_start: 0.4302 (OUTLIER) cc_final: 0.3786 (tpp80) REVERT: B 844 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7319 (mt) REVERT: C 613 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7876 (mp-120) outliers start: 23 outliers final: 13 residues processed: 55 average time/residue: 0.3553 time to fit residues: 31.5203 Evaluate side-chains 49 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 33 time to evaluate : 2.062 ------------------------------------------------------------------------------- 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 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 634 ARG Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 948 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 57 optimal weight: 30.0000 chunk 74 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 182 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 233 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN B 69 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN C 655 HIS ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.047588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.034170 restraints weight = 171668.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.034955 restraints weight = 99716.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.035456 restraints weight = 71020.977| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 20492 Z= 0.339 Angle : 0.812 12.714 27972 Z= 0.410 Chirality : 0.049 0.372 3314 Planarity : 0.005 0.051 3533 Dihedral : 7.830 59.722 3633 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.26 % Favored : 92.58 % Rotamer: Outliers : 1.80 % Allowed : 7.73 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2453 helix: 0.76 (0.20), residues: 650 sheet: -0.56 (0.23), residues: 430 loop : -1.36 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 64 HIS 0.007 0.001 HIS B1064 PHE 0.020 0.002 PHE C 194 TYR 0.023 0.002 TYR C 707 ARG 0.005 0.001 ARG B1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00834 ( 34) link_NAG-ASN : angle 3.14554 ( 102) link_BETA1-4 : bond 0.00448 ( 12) link_BETA1-4 : angle 1.73079 ( 36) hydrogen bonds : bond 0.05670 ( 824) hydrogen bonds : angle 6.18699 ( 2334) SS BOND : bond 0.00566 ( 31) SS BOND : angle 1.12956 ( 62) covalent geometry : bond 0.00769 (20415) covalent geometry : angle 0.78782 (27772) *********************** 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 72 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 33 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 634 ARG cc_start: 0.4349 (OUTLIER) cc_final: 0.3874 (tpp80) REVERT: B 844 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7542 (mt) REVERT: B 1050 MET cc_start: 0.8599 (mmm) cc_final: 0.8201 (mmt) REVERT: C 613 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8259 (mp-120) outliers start: 39 outliers final: 21 residues processed: 67 average time/residue: 0.3263 time to fit residues: 36.0134 Evaluate side-chains 56 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 32 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 1126 CYS 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 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 719 THR 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 201 optimal weight: 0.0470 chunk 221 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 49 optimal weight: 40.0000 chunk 75 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 230 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 183 optimal weight: 0.3980 overall best weight: 1.8884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS C1088 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.048818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.035594 restraints weight = 168975.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.036425 restraints weight = 97090.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.036978 restraints weight = 68504.483| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2875 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= 0.127 Angle : 0.618 12.652 27972 Z= 0.315 Chirality : 0.044 0.280 3314 Planarity : 0.004 0.049 3533 Dihedral : 6.999 59.247 3633 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.91 % Favored : 93.84 % Rotamer: Outliers : 1.39 % Allowed : 8.70 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2453 helix: 1.40 (0.20), residues: 654 sheet: -0.44 (0.23), residues: 456 loop : -1.22 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 633 HIS 0.009 0.001 HIS C 625 PHE 0.016 0.001 PHE B 456 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG C 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 34) link_NAG-ASN : angle 2.71657 ( 102) link_BETA1-4 : bond 0.00311 ( 12) link_BETA1-4 : angle 1.33174 ( 36) hydrogen bonds : bond 0.04586 ( 824) hydrogen bonds : angle 5.56202 ( 2334) SS BOND : bond 0.00338 ( 31) SS BOND : angle 0.87457 ( 62) covalent geometry : bond 0.00272 (20415) covalent geometry : angle 0.59474 (27772) *********************** 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 62 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 32 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 615 VAL cc_start: 0.7910 (OUTLIER) cc_final: 0.7667 (t) REVERT: B 634 ARG cc_start: 0.4427 (OUTLIER) cc_final: 0.4124 (tpp80) REVERT: C 613 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7712 (mp-120) outliers start: 30 outliers final: 20 residues processed: 58 average time/residue: 0.3186 time to fit residues: 31.5179 Evaluate side-chains 54 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 31 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 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 760 CYS Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 740 MET 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 73 optimal weight: 7.9990 chunk 207 optimal weight: 0.4980 chunk 62 optimal weight: 20.0000 chunk 217 optimal weight: 8.9990 chunk 247 optimal weight: 7.9990 chunk 157 optimal weight: 20.0000 chunk 230 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 overall best weight: 7.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.047714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.034290 restraints weight = 169406.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.035063 restraints weight = 99257.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.035585 restraints weight = 70511.667| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 20492 Z= 0.300 Angle : 0.723 12.550 27972 Z= 0.367 Chirality : 0.046 0.297 3314 Planarity : 0.004 0.052 3533 Dihedral : 7.283 59.535 3633 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.17 % Favored : 92.62 % Rotamer: Outliers : 1.99 % Allowed : 8.84 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.17), residues: 2453 helix: 1.04 (0.20), residues: 656 sheet: -0.50 (0.23), residues: 432 loop : -1.25 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 886 HIS 0.006 0.001 HIS C 625 PHE 0.015 0.002 PHE B 201 TYR 0.020 0.002 TYR C 707 ARG 0.004 0.001 ARG B1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00773 ( 34) link_NAG-ASN : angle 2.92775 ( 102) link_BETA1-4 : bond 0.00312 ( 12) link_BETA1-4 : angle 1.58309 ( 36) hydrogen bonds : bond 0.05164 ( 824) hydrogen bonds : angle 5.92723 ( 2334) SS BOND : bond 0.00565 ( 31) SS BOND : angle 1.05682 ( 62) covalent geometry : bond 0.00684 (20415) covalent geometry : angle 0.69943 (27772) *********************** 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 75 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 32 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 634 ARG cc_start: 0.4434 (OUTLIER) cc_final: 0.4177 (tpp80) REVERT: B 844 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7525 (mt) REVERT: C 309 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8498 (pm20) REVERT: C 613 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8075 (mp-120) outliers start: 43 outliers final: 29 residues processed: 70 average time/residue: 0.3252 time to fit residues: 37.5025 Evaluate side-chains 63 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 30 time to evaluate : 2.109 ------------------------------------------------------------------------------- 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 369 TYR 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 634 ARG Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 896 ILE 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 130 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 112 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 239 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 360 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.048668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.035453 restraints weight = 168964.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.036282 restraints weight = 97328.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.036809 restraints weight = 68921.261| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20492 Z= 0.120 Angle : 0.594 12.638 27972 Z= 0.303 Chirality : 0.044 0.292 3314 Planarity : 0.004 0.050 3533 Dihedral : 6.665 59.739 3633 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.07 % Favored : 93.72 % Rotamer: Outliers : 1.48 % Allowed : 9.44 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2453 helix: 1.60 (0.20), residues: 649 sheet: -0.45 (0.23), residues: 452 loop : -1.19 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.004 0.001 HIS B1048 PHE 0.015 0.001 PHE B 456 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.000 ARG C 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 34) link_NAG-ASN : angle 2.60346 ( 102) link_BETA1-4 : bond 0.00264 ( 12) link_BETA1-4 : angle 1.26911 ( 36) hydrogen bonds : bond 0.04338 ( 824) hydrogen bonds : angle 5.47382 ( 2334) SS BOND : bond 0.00328 ( 31) SS BOND : angle 0.84088 ( 62) covalent geometry : bond 0.00252 (20415) covalent geometry : angle 0.57217 (27772) *********************** 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 64 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 32 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 615 VAL cc_start: 0.7914 (OUTLIER) cc_final: 0.7612 (t) REVERT: C 613 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7738 (mp-120) outliers start: 32 outliers final: 25 residues processed: 59 average time/residue: 0.3247 time to fit residues: 32.1345 Evaluate side-chains 58 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 31 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 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 760 CYS 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 556 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 197 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 116 optimal weight: 0.0870 chunk 109 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 overall best weight: 3.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.048279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.035044 restraints weight = 170298.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.035850 restraints weight = 98783.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.036373 restraints weight = 70185.748| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20492 Z= 0.163 Angle : 0.601 12.628 27972 Z= 0.306 Chirality : 0.044 0.300 3314 Planarity : 0.004 0.050 3533 Dihedral : 6.455 55.620 3629 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.52 % Favored : 93.31 % Rotamer: Outliers : 1.43 % Allowed : 9.49 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2453 helix: 1.59 (0.20), residues: 653 sheet: -0.44 (0.23), residues: 458 loop : -1.14 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.004 0.001 HIS A1048 PHE 0.015 0.001 PHE B 456 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.000 ARG B 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 34) link_NAG-ASN : angle 2.60565 ( 102) link_BETA1-4 : bond 0.00217 ( 12) link_BETA1-4 : angle 1.36046 ( 36) hydrogen bonds : bond 0.04360 ( 824) hydrogen bonds : angle 5.45268 ( 2334) SS BOND : bond 0.00413 ( 31) SS BOND : angle 0.86980 ( 62) covalent geometry : bond 0.00364 (20415) covalent geometry : angle 0.57842 (27772) *********************** 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 62 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 31 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 844 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7658 (mt) REVERT: B 900 MET cc_start: 0.8237 (mtm) cc_final: 0.8021 (mtm) REVERT: C 613 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7774 (mp-120) outliers start: 31 outliers final: 27 residues processed: 59 average time/residue: 0.2864 time to fit residues: 29.7154 Evaluate side-chains 60 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 31 time to evaluate : 2.153 ------------------------------------------------------------------------------- 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 63 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 46 SER 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 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 247 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 192 optimal weight: 40.0000 chunk 162 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 235 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1064 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.047738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.034305 restraints weight = 170686.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.035102 restraints weight = 98973.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.035597 restraints weight = 70290.514| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 20492 Z= 0.244 Angle : 0.666 12.526 27972 Z= 0.339 Chirality : 0.045 0.302 3314 Planarity : 0.004 0.050 3533 Dihedral : 6.654 57.801 3629 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.58 % Favored : 92.25 % Rotamer: Outliers : 1.62 % Allowed : 9.49 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2453 helix: 1.32 (0.20), residues: 659 sheet: -0.51 (0.23), residues: 455 loop : -1.23 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 886 HIS 0.006 0.001 HIS A1048 PHE 0.014 0.002 PHE B 201 TYR 0.018 0.002 TYR A 904 ARG 0.005 0.000 ARG B 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00670 ( 34) link_NAG-ASN : angle 2.67295 ( 102) link_BETA1-4 : bond 0.00246 ( 12) link_BETA1-4 : angle 1.44633 ( 36) hydrogen bonds : bond 0.04785 ( 824) hydrogen bonds : angle 5.69868 ( 2334) SS BOND : bond 0.00493 ( 31) SS BOND : angle 1.07769 ( 62) covalent geometry : bond 0.00551 (20415) covalent geometry : angle 0.64450 (27772) *********************** 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 65 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 30 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 844 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7650 (mt) REVERT: C 613 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.7959 (mp-120) outliers start: 35 outliers final: 29 residues processed: 61 average time/residue: 0.2984 time to fit residues: 31.9370 Evaluate side-chains 61 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 30 time to evaluate : 2.215 ------------------------------------------------------------------------------- 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 A residue 1018 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 849 LEU 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 455 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 105 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 156 optimal weight: 0.0010 chunk 166 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 218 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 overall best weight: 2.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.048285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.035028 restraints weight = 169975.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.035832 restraints weight = 98524.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.036333 restraints weight = 70080.319| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20492 Z= 0.137 Angle : 0.584 12.596 27972 Z= 0.298 Chirality : 0.043 0.299 3314 Planarity : 0.004 0.051 3533 Dihedral : 6.272 59.556 3629 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.40 % Favored : 93.44 % Rotamer: Outliers : 1.39 % Allowed : 9.53 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2453 helix: 1.68 (0.20), residues: 651 sheet: -0.42 (0.23), residues: 459 loop : -1.17 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.004 0.001 HIS B1048 PHE 0.014 0.001 PHE B 456 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG B 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 34) link_NAG-ASN : angle 2.48274 ( 102) link_BETA1-4 : bond 0.00214 ( 12) link_BETA1-4 : angle 1.24712 ( 36) hydrogen bonds : bond 0.04284 ( 824) hydrogen bonds : angle 5.40592 ( 2334) SS BOND : bond 0.00349 ( 31) SS BOND : angle 1.02690 ( 62) covalent geometry : bond 0.00301 (20415) covalent geometry : angle 0.56258 (27772) ********************** 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 60 residues out of total 2161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 30 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 844 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7660 (mt) REVERT: C 309 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8358 (pm20) REVERT: C 613 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7781 (mp-120) outliers start: 30 outliers final: 24 residues processed: 57 average time/residue: 0.2798 time to fit residues: 27.7138 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 : 2.193 ------------------------------------------------------------------------------- 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 369 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 46 SER 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 613 GLN Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 148 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 241 optimal weight: 0.0770 chunk 27 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 126 optimal weight: 0.0570 overall best weight: 2.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.048241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.035024 restraints weight = 170102.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.035851 restraints weight = 97533.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.036390 restraints weight = 68613.123| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20492 Z= 0.148 Angle : 0.584 12.600 27972 Z= 0.298 Chirality : 0.043 0.302 3314 Planarity : 0.004 0.051 3533 Dihedral : 6.090 57.767 3628 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.73 % Favored : 93.11 % Rotamer: Outliers : 1.43 % Allowed : 9.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.17), residues: 2453 helix: 1.73 (0.20), residues: 654 sheet: -0.35 (0.23), residues: 459 loop : -1.15 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.003 0.001 HIS A1048 PHE 0.014 0.001 PHE B 456 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG B 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 34) link_NAG-ASN : angle 2.43016 ( 102) link_BETA1-4 : bond 0.00208 ( 12) link_BETA1-4 : angle 1.30111 ( 36) hydrogen bonds : bond 0.04235 ( 824) hydrogen bonds : angle 5.31332 ( 2334) SS BOND : bond 0.00356 ( 31) SS BOND : angle 0.97973 ( 62) covalent geometry : bond 0.00329 (20415) covalent geometry : angle 0.56372 (27772) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5658.57 seconds wall clock time: 99 minutes 49.02 seconds (5989.02 seconds total)