Starting phenix.real_space_refine on Mon Aug 25 05:51:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqw_34037/08_2025/7yqw_34037.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqw_34037/08_2025/7yqw_34037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yqw_34037/08_2025/7yqw_34037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqw_34037/08_2025/7yqw_34037.map" model { file = "/net/cci-nas-00/data/ceres_data/7yqw_34037/08_2025/7yqw_34037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqw_34037/08_2025/7yqw_34037.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.068 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 111 5.16 5 C 16215 2.51 5 N 4137 2.21 5 O 4959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25422 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8158 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 985} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 8158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8158 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 985} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 8158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8158 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 985} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" 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: 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: "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: 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 Time building chain proxies: 6.36, per 1000 atoms: 0.25 Number of scatterers: 25422 At special positions: 0 Unit cell: (143.38, 157.29, 175.48, 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 111 16.00 O 4959 8.00 N 4137 7.00 C 16215 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 657 " " NAG C1311 " - " ASN C 709 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1074 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1074 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 901.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5862 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 54 sheets defined 22.6% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.551A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.618A pdb=" N ASN A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.284A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.963A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 removed outlier: 3.711A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 783 removed outlier: 4.023A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 850 through 855 removed outlier: 4.022A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 850 through 855' Processing helix chain 'A' and resid 869 through 884 removed outlier: 3.650A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.639A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 941 removed outlier: 3.526A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.922A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 989 removed outlier: 3.951A pdb=" N GLU A 988 " --> pdb=" O ASP A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1033 removed outlier: 3.555A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.551A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.618A pdb=" N ASN B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.284A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.963A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 removed outlier: 3.711A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 783 removed outlier: 4.023A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 850 through 855 removed outlier: 4.022A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 850 through 855' Processing helix chain 'B' and resid 869 through 884 removed outlier: 3.650A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.639A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 941 removed outlier: 3.525A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.922A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP B 950 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 989 removed outlier: 3.951A pdb=" N GLU B 988 " --> pdb=" O ASP B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1033 removed outlier: 3.555A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.551A pdb=" N LEU C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.617A pdb=" N ASN C 343 " --> pdb=" O HIS C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.284A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.963A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 removed outlier: 3.711A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 783 removed outlier: 4.024A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 850 through 855 removed outlier: 4.023A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE C 855 " --> pdb=" O CYS C 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 850 through 855' Processing helix chain 'C' and resid 869 through 884 removed outlier: 3.650A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 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: 3.639A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 941 removed outlier: 3.526A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.922A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP C 950 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 989 removed outlier: 3.950A pdb=" N GLU C 988 " --> pdb=" O ASP C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1033 removed outlier: 3.554A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 3.723A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.343A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 55 removed outlier: 4.003A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.598A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.839A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.806A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.838A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 610 through 613 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.831A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.576A pdb=" N HIS A1064 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.933A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AC3, first strand: chain 'B' and resid 26 through 30 removed outlier: 3.723A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.342A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.004A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.598A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.839A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.806A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AD4, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.878A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 610 through 613 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.831A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD8, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.576A pdb=" N HIS B1064 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE2, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AE3, first strand: chain 'C' and resid 26 through 30 removed outlier: 3.723A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.342A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.418A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 50 through 55 removed outlier: 4.003A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.598A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.839A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.806A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF3, first strand: chain 'C' and resid 553 through 554 Processing sheet with id=AF4, first strand: chain 'C' and resid 610 through 613 Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.831A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AF7, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.577A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF9, first strand: chain 'C' and resid 1089 through 1090 755 hydrogen bonds defined for protein. 2013 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.91 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4469 1.33 - 1.45: 7079 1.45 - 1.57: 14321 1.57 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 26007 Sorted by residual: bond pdb=" CA SER B 591 " pdb=" CB SER B 591 " ideal model delta sigma weight residual 1.530 1.480 0.050 1.57e-02 4.06e+03 1.00e+01 bond pdb=" CA SER A 591 " pdb=" CB SER A 591 " ideal model delta sigma weight residual 1.530 1.481 0.049 1.57e-02 4.06e+03 9.94e+00 bond pdb=" CA SER C 591 " pdb=" CB SER C 591 " ideal model delta sigma weight residual 1.530 1.481 0.049 1.57e-02 4.06e+03 9.61e+00 bond pdb=" C PRO B 589 " pdb=" O PRO B 589 " ideal model delta sigma weight residual 1.235 1.202 0.033 1.30e-02 5.92e+03 6.53e+00 bond pdb=" C PRO A 589 " pdb=" O PRO A 589 " ideal model delta sigma weight residual 1.235 1.203 0.033 1.30e-02 5.92e+03 6.27e+00 ... (remaining 26002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 34297 1.68 - 3.36: 960 3.36 - 5.03: 106 5.03 - 6.71: 28 6.71 - 8.39: 6 Bond angle restraints: 35397 Sorted by residual: angle pdb=" C PRO A 589 " pdb=" CA PRO A 589 " pdb=" CB PRO A 589 " ideal model delta sigma weight residual 111.56 106.15 5.41 1.65e+00 3.67e-01 1.07e+01 angle pdb=" CA SER A 591 " pdb=" C SER A 591 " pdb=" O SER A 591 " ideal model delta sigma weight residual 120.96 117.78 3.18 1.09e+00 8.42e-01 8.53e+00 angle pdb=" CA SER C 591 " pdb=" C SER C 591 " pdb=" O SER C 591 " ideal model delta sigma weight residual 120.96 117.80 3.16 1.09e+00 8.42e-01 8.42e+00 angle pdb=" CA SER B 591 " pdb=" C SER B 591 " pdb=" O SER B 591 " ideal model delta sigma weight residual 120.96 117.85 3.11 1.09e+00 8.42e-01 8.16e+00 angle pdb=" C PRO B 589 " pdb=" CA PRO B 589 " pdb=" CB PRO B 589 " ideal model delta sigma weight residual 111.56 107.00 4.56 1.65e+00 3.67e-01 7.65e+00 ... (remaining 35392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 15138 21.80 - 43.59: 1032 43.59 - 65.39: 117 65.39 - 87.19: 57 87.19 - 108.99: 27 Dihedral angle restraints: 16371 sinusoidal: 7263 harmonic: 9108 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -22.89 -63.11 1 1.00e+01 1.00e-02 5.26e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -22.89 -63.11 1 1.00e+01 1.00e-02 5.26e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -22.91 -63.09 1 1.00e+01 1.00e-02 5.26e+01 ... (remaining 16368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3375 0.055 - 0.111: 729 0.111 - 0.166: 82 0.166 - 0.221: 14 0.221 - 0.276: 9 Chirality restraints: 4209 Sorted by residual: chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 4206 not shown) Planarity restraints: 4530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 586 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.59e+00 pdb=" C ASP C 586 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP C 586 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE C 587 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 586 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C ASP B 586 " 0.038 2.00e-02 2.50e+03 pdb=" O ASP B 586 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE B 587 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO C 986 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.019 5.00e-02 4.00e+02 ... (remaining 4527 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 77 2.44 - 3.05: 16330 3.05 - 3.67: 33892 3.67 - 4.28: 48906 4.28 - 4.90: 85027 Nonbonded interactions: 184232 Sorted by model distance: nonbonded pdb=" CG1 VAL B1094 " pdb=" OH TYR C 904 " model vdw 1.820 3.460 nonbonded pdb=" OH TYR A 904 " pdb=" CG1 VAL C1094 " model vdw 1.830 3.460 nonbonded pdb=" CG1 VAL A1094 " pdb=" OH TYR B 904 " model vdw 1.837 3.460 nonbonded pdb=" OE1 GLN A 957 " pdb=" NH2 ARG B 765 " model vdw 1.953 3.120 nonbonded pdb=" OE1 GLN B 957 " pdb=" NH2 ARG C 765 " model vdw 1.953 3.120 ... (remaining 184227 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'I' selection = chain 'L' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.890 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 0.004 0.073 26112 Z= 0.207 Angle : 0.655 8.390 35676 Z= 0.326 Chirality : 0.048 0.276 4209 Planarity : 0.004 0.035 4482 Dihedral : 15.071 108.986 10401 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.75 % Favored : 92.22 % Rotamer: Outliers : 0.18 % Allowed : 0.33 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.15), residues: 3084 helix: 0.73 (0.22), residues: 636 sheet: -0.85 (0.19), residues: 714 loop : -1.71 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 214 TYR 0.016 0.001 TYR B 265 PHE 0.017 0.001 PHE A 906 TRP 0.017 0.001 TRP B 633 HIS 0.008 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00436 (26007) covalent geometry : angle 0.64134 (35397) SS BOND : bond 0.00293 ( 36) SS BOND : angle 1.12981 ( 72) hydrogen bonds : bond 0.16122 ( 755) hydrogen bonds : angle 6.52208 ( 2013) link_BETA1-4 : bond 0.00581 ( 21) link_BETA1-4 : angle 1.34757 ( 63) link_NAG-ASN : bond 0.00249 ( 48) link_NAG-ASN : angle 1.97422 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 0.873 Fit side-chains REVERT: B 200 TYR cc_start: 0.7314 (m-80) cc_final: 0.6986 (m-10) REVERT: B 421 TYR cc_start: 0.8775 (m-80) cc_final: 0.8396 (m-80) REVERT: B 780 GLU cc_start: 0.8250 (tt0) cc_final: 0.8007 (tt0) REVERT: C 985 ASP cc_start: 0.7564 (p0) cc_final: 0.7245 (p0) outliers start: 5 outliers final: 5 residues processed: 192 average time/residue: 0.1314 time to fit residues: 44.1682 Evaluate side-chains 146 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.0040 chunk 248 optimal weight: 0.0470 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 overall best weight: 1.2094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN A 965 GLN B 913 GLN B 965 GLN C 913 GLN C 965 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.111468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.082899 restraints weight = 53546.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.085124 restraints weight = 39225.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.085774 restraints weight = 25383.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.086813 restraints weight = 24260.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.086970 restraints weight = 22004.728| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26112 Z= 0.126 Angle : 0.598 11.338 35676 Z= 0.298 Chirality : 0.044 0.172 4209 Planarity : 0.004 0.038 4482 Dihedral : 9.146 67.965 4790 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.84 % Allowed : 6.83 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.15), residues: 3084 helix: 0.82 (0.22), residues: 627 sheet: -0.49 (0.20), residues: 657 loop : -1.75 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.015 0.001 TYR B 265 PHE 0.019 0.001 PHE A 375 TRP 0.004 0.001 TRP B 436 HIS 0.002 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00296 (26007) covalent geometry : angle 0.58045 (35397) SS BOND : bond 0.00294 ( 36) SS BOND : angle 1.09998 ( 72) hydrogen bonds : bond 0.04399 ( 755) hydrogen bonds : angle 5.25959 ( 2013) link_BETA1-4 : bond 0.00645 ( 21) link_BETA1-4 : angle 1.71076 ( 63) link_NAG-ASN : bond 0.00314 ( 48) link_NAG-ASN : angle 1.99831 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.600 Fit side-chains REVERT: A 633 TRP cc_start: 0.6946 (p90) cc_final: 0.6680 (p90) REVERT: A 990 GLU cc_start: 0.7649 (pm20) cc_final: 0.7383 (pm20) REVERT: B 168 PHE cc_start: 0.7962 (t80) cc_final: 0.7716 (t80) REVERT: B 421 TYR cc_start: 0.8666 (m-80) cc_final: 0.8201 (m-80) REVERT: B 633 TRP cc_start: 0.7251 (p90) cc_final: 0.6952 (p90) REVERT: B 780 GLU cc_start: 0.8297 (tt0) cc_final: 0.8070 (tt0) REVERT: C 168 PHE cc_start: 0.7746 (t80) cc_final: 0.7469 (t80) REVERT: C 633 TRP cc_start: 0.6894 (p90) cc_final: 0.6641 (p90) outliers start: 23 outliers final: 15 residues processed: 164 average time/residue: 0.1299 time to fit residues: 36.6663 Evaluate side-chains 157 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 269 optimal weight: 0.9980 chunk 184 optimal weight: 0.7980 chunk 158 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 233 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 255 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.111707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.083186 restraints weight = 53559.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.085933 restraints weight = 38166.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.086215 restraints weight = 24402.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.086610 restraints weight = 23654.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.086806 restraints weight = 22343.724| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26112 Z= 0.111 Angle : 0.557 8.637 35676 Z= 0.277 Chirality : 0.044 0.169 4209 Planarity : 0.004 0.039 4482 Dihedral : 6.656 44.924 4789 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.54 % Allowed : 9.72 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.15), residues: 3084 helix: 0.80 (0.22), residues: 651 sheet: -0.45 (0.20), residues: 672 loop : -1.72 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.026 0.001 TYR B 170 PHE 0.022 0.001 PHE B 855 TRP 0.004 0.001 TRP B 436 HIS 0.002 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00261 (26007) covalent geometry : angle 0.53948 (35397) SS BOND : bond 0.00232 ( 36) SS BOND : angle 0.92317 ( 72) hydrogen bonds : bond 0.03938 ( 755) hydrogen bonds : angle 4.93412 ( 2013) link_BETA1-4 : bond 0.00577 ( 21) link_BETA1-4 : angle 1.63340 ( 63) link_NAG-ASN : bond 0.00282 ( 48) link_NAG-ASN : angle 1.90873 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 904 TYR cc_start: 0.7937 (m-10) cc_final: 0.7643 (m-10) REVERT: A 1002 GLN cc_start: 0.8252 (mp10) cc_final: 0.7938 (mp10) REVERT: B 421 TYR cc_start: 0.8603 (m-80) cc_final: 0.7649 (m-80) REVERT: B 780 GLU cc_start: 0.8321 (tt0) cc_final: 0.8090 (tt0) REVERT: B 904 TYR cc_start: 0.7823 (m-10) cc_final: 0.7606 (m-10) outliers start: 42 outliers final: 20 residues processed: 181 average time/residue: 0.1317 time to fit residues: 41.2705 Evaluate side-chains 158 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 68 optimal weight: 0.0070 chunk 192 optimal weight: 0.9980 chunk 269 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 232 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 0.0270 chunk 204 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.113414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.087684 restraints weight = 53302.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.088650 restraints weight = 39688.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.088668 restraints weight = 39304.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.090121 restraints weight = 31025.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.090197 restraints weight = 25150.720| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26112 Z= 0.091 Angle : 0.520 7.668 35676 Z= 0.261 Chirality : 0.043 0.209 4209 Planarity : 0.004 0.036 4482 Dihedral : 5.154 41.870 4788 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.61 % Allowed : 11.26 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.15), residues: 3084 helix: 0.92 (0.22), residues: 648 sheet: -0.34 (0.20), residues: 657 loop : -1.65 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.014 0.001 TYR B 160 PHE 0.025 0.001 PHE B 375 TRP 0.012 0.001 TRP C 633 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00202 (26007) covalent geometry : angle 0.50528 (35397) SS BOND : bond 0.00175 ( 36) SS BOND : angle 0.73100 ( 72) hydrogen bonds : bond 0.03276 ( 755) hydrogen bonds : angle 4.65010 ( 2013) link_BETA1-4 : bond 0.00596 ( 21) link_BETA1-4 : angle 1.38057 ( 63) link_NAG-ASN : bond 0.00286 ( 48) link_NAG-ASN : angle 1.76163 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8595 (m-80) cc_final: 0.7823 (m-80) REVERT: B 780 GLU cc_start: 0.8186 (tt0) cc_final: 0.7956 (tt0) REVERT: B 904 TYR cc_start: 0.7866 (m-10) cc_final: 0.7596 (m-10) REVERT: C 740 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7805 (ttp) outliers start: 44 outliers final: 19 residues processed: 192 average time/residue: 0.1470 time to fit residues: 49.2105 Evaluate side-chains 163 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 252 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 173 optimal weight: 0.6980 chunk 229 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** C 422 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 = 0.3605 r_free = 0.3605 target = 0.111783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.085974 restraints weight = 53295.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.086619 restraints weight = 40551.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.086864 restraints weight = 39639.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.087576 restraints weight = 31709.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.087769 restraints weight = 28330.527| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26112 Z= 0.122 Angle : 0.551 12.468 35676 Z= 0.275 Chirality : 0.043 0.168 4209 Planarity : 0.004 0.036 4482 Dihedral : 5.063 42.988 4787 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.90 % Allowed : 11.73 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.15), residues: 3084 helix: 0.91 (0.22), residues: 654 sheet: -0.32 (0.20), residues: 657 loop : -1.65 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.015 0.001 TYR B 265 PHE 0.024 0.001 PHE C 375 TRP 0.010 0.001 TRP C 633 HIS 0.002 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00298 (26007) covalent geometry : angle 0.53705 (35397) SS BOND : bond 0.00252 ( 36) SS BOND : angle 0.95043 ( 72) hydrogen bonds : bond 0.03773 ( 755) hydrogen bonds : angle 4.66720 ( 2013) link_BETA1-4 : bond 0.00473 ( 21) link_BETA1-4 : angle 1.19991 ( 63) link_NAG-ASN : bond 0.00241 ( 48) link_NAG-ASN : angle 1.81952 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 902 MET cc_start: 0.8424 (tpt) cc_final: 0.7980 (tpt) REVERT: A 1002 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7392 (mp10) REVERT: B 780 GLU cc_start: 0.8197 (tt0) cc_final: 0.7996 (tt0) REVERT: B 1029 MET cc_start: 0.9130 (tpp) cc_final: 0.8766 (ttm) REVERT: C 878 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8711 (tt) outliers start: 52 outliers final: 31 residues processed: 185 average time/residue: 0.1354 time to fit residues: 44.1086 Evaluate side-chains 171 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 54 optimal weight: 4.9990 chunk 260 optimal weight: 0.9990 chunk 301 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.110944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.082615 restraints weight = 53772.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.084945 restraints weight = 38864.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.085276 restraints weight = 26016.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.085634 restraints weight = 25207.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.085982 restraints weight = 24075.033| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26112 Z= 0.141 Angle : 0.566 12.948 35676 Z= 0.283 Chirality : 0.044 0.234 4209 Planarity : 0.004 0.037 4482 Dihedral : 5.165 43.236 4787 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.41 % Allowed : 12.43 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.15), residues: 3084 helix: 0.90 (0.22), residues: 651 sheet: -0.40 (0.20), residues: 660 loop : -1.68 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 765 TYR 0.026 0.001 TYR B 170 PHE 0.019 0.001 PHE C 375 TRP 0.008 0.001 TRP C 633 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00348 (26007) covalent geometry : angle 0.55083 (35397) SS BOND : bond 0.00324 ( 36) SS BOND : angle 1.14457 ( 72) hydrogen bonds : bond 0.03997 ( 755) hydrogen bonds : angle 4.73100 ( 2013) link_BETA1-4 : bond 0.00474 ( 21) link_BETA1-4 : angle 1.16806 ( 63) link_NAG-ASN : bond 0.00240 ( 48) link_NAG-ASN : angle 1.87880 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 152 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8438 (m-80) cc_final: 0.7956 (m-80) REVERT: A 902 MET cc_start: 0.8567 (tpt) cc_final: 0.8059 (tpt) REVERT: A 985 ASP cc_start: 0.7019 (p0) cc_final: 0.6734 (p0) REVERT: A 1002 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7637 (mp10) REVERT: B 780 GLU cc_start: 0.8353 (tt0) cc_final: 0.8099 (tt0) REVERT: B 1029 MET cc_start: 0.9209 (tpp) cc_final: 0.8851 (ttm) REVERT: C 303 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7817 (pp) REVERT: C 421 TYR cc_start: 0.8131 (m-80) cc_final: 0.7863 (m-80) REVERT: C 878 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8607 (tt) REVERT: C 1029 MET cc_start: 0.9274 (tpp) cc_final: 0.8866 (ttm) outliers start: 66 outliers final: 51 residues processed: 202 average time/residue: 0.1487 time to fit residues: 52.2686 Evaluate side-chains 189 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 135 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 86 optimal weight: 2.9990 chunk 300 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 263 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** C 422 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 = 0.3592 r_free = 0.3592 target = 0.110910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.082618 restraints weight = 53342.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.085078 restraints weight = 36941.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.085590 restraints weight = 24261.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.085843 restraints weight = 22028.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.086004 restraints weight = 21026.765| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 26112 Z= 0.131 Angle : 0.566 13.105 35676 Z= 0.282 Chirality : 0.043 0.211 4209 Planarity : 0.004 0.036 4482 Dihedral : 5.122 42.442 4787 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.56 % Allowed : 13.01 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.15), residues: 3084 helix: 0.89 (0.22), residues: 651 sheet: -0.36 (0.20), residues: 645 loop : -1.68 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 765 TYR 0.028 0.001 TYR C 170 PHE 0.028 0.001 PHE C 375 TRP 0.010 0.001 TRP C 633 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00319 (26007) covalent geometry : angle 0.55096 (35397) SS BOND : bond 0.00349 ( 36) SS BOND : angle 1.02764 ( 72) hydrogen bonds : bond 0.03918 ( 755) hydrogen bonds : angle 4.67886 ( 2013) link_BETA1-4 : bond 0.00482 ( 21) link_BETA1-4 : angle 1.15506 ( 63) link_NAG-ASN : bond 0.00235 ( 48) link_NAG-ASN : angle 1.87212 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 141 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8452 (m-80) cc_final: 0.7911 (m-80) REVERT: A 902 MET cc_start: 0.8665 (tpt) cc_final: 0.8163 (tpt) REVERT: A 1002 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7625 (mp10) REVERT: B 303 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7837 (pp) REVERT: B 780 GLU cc_start: 0.8464 (tt0) cc_final: 0.8205 (tt0) REVERT: B 1029 MET cc_start: 0.9133 (tpp) cc_final: 0.8867 (ttm) REVERT: C 303 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7564 (pp) REVERT: C 421 TYR cc_start: 0.8170 (m-80) cc_final: 0.7799 (m-80) REVERT: C 855 PHE cc_start: 0.7578 (m-80) cc_final: 0.7262 (m-80) REVERT: C 878 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8496 (tt) REVERT: C 1029 MET cc_start: 0.9243 (tpp) cc_final: 0.8899 (ttm) outliers start: 70 outliers final: 54 residues processed: 197 average time/residue: 0.1391 time to fit residues: 48.7493 Evaluate side-chains 195 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 137 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 36 optimal weight: 1.9990 chunk 257 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 123 optimal weight: 5.9990 chunk 50 optimal weight: 0.1980 chunk 72 optimal weight: 3.9990 chunk 252 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN B 901 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.111215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.083045 restraints weight = 53508.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.085326 restraints weight = 38574.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.085655 restraints weight = 25887.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.086066 restraints weight = 25079.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.086188 restraints weight = 23658.101| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26112 Z= 0.117 Angle : 0.563 21.540 35676 Z= 0.277 Chirality : 0.043 0.203 4209 Planarity : 0.004 0.041 4482 Dihedral : 5.003 41.540 4787 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.41 % Allowed : 13.41 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.15), residues: 3084 helix: 0.92 (0.22), residues: 651 sheet: -0.33 (0.20), residues: 645 loop : -1.67 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 765 TYR 0.018 0.001 TYR C 170 PHE 0.028 0.001 PHE C 375 TRP 0.011 0.001 TRP B 633 HIS 0.002 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00283 (26007) covalent geometry : angle 0.54948 (35397) SS BOND : bond 0.00261 ( 36) SS BOND : angle 0.93221 ( 72) hydrogen bonds : bond 0.03733 ( 755) hydrogen bonds : angle 4.59702 ( 2013) link_BETA1-4 : bond 0.00495 ( 21) link_BETA1-4 : angle 1.14731 ( 63) link_NAG-ASN : bond 0.00229 ( 48) link_NAG-ASN : angle 1.83260 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 147 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 375 PHE cc_start: 0.8575 (t80) cc_final: 0.8125 (t80) REVERT: A 421 TYR cc_start: 0.8374 (m-80) cc_final: 0.7867 (m-80) REVERT: A 1002 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7652 (mp10) REVERT: B 303 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8111 (pp) REVERT: B 780 GLU cc_start: 0.8356 (tt0) cc_final: 0.8111 (tt0) REVERT: B 1029 MET cc_start: 0.9181 (tpp) cc_final: 0.8842 (ttm) REVERT: C 303 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7789 (pp) REVERT: C 421 TYR cc_start: 0.8094 (m-80) cc_final: 0.7731 (m-80) REVERT: C 855 PHE cc_start: 0.7507 (m-80) cc_final: 0.7216 (m-80) REVERT: C 878 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8604 (tt) REVERT: C 1029 MET cc_start: 0.9256 (tpp) cc_final: 0.8882 (ttm) outliers start: 66 outliers final: 55 residues processed: 200 average time/residue: 0.1455 time to fit residues: 51.1461 Evaluate side-chains 200 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 141 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 266 optimal weight: 0.9980 chunk 276 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 120 optimal weight: 0.0370 chunk 200 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 422 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 = 0.3599 r_free = 0.3599 target = 0.111354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.083468 restraints weight = 53512.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.084941 restraints weight = 45254.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.085626 restraints weight = 30274.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.086150 restraints weight = 26998.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.086331 restraints weight = 24942.793| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26112 Z= 0.113 Angle : 0.554 17.442 35676 Z= 0.274 Chirality : 0.043 0.187 4209 Planarity : 0.004 0.038 4482 Dihedral : 4.923 41.056 4787 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.34 % Allowed : 13.56 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.15), residues: 3084 helix: 0.93 (0.22), residues: 651 sheet: -0.31 (0.20), residues: 645 loop : -1.66 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 905 TYR 0.025 0.001 TYR B 170 PHE 0.022 0.001 PHE C 375 TRP 0.008 0.001 TRP B 633 HIS 0.002 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00270 (26007) covalent geometry : angle 0.54059 (35397) SS BOND : bond 0.00241 ( 36) SS BOND : angle 0.89360 ( 72) hydrogen bonds : bond 0.03671 ( 755) hydrogen bonds : angle 4.55730 ( 2013) link_BETA1-4 : bond 0.00505 ( 21) link_BETA1-4 : angle 1.14163 ( 63) link_NAG-ASN : bond 0.00224 ( 48) link_NAG-ASN : angle 1.80792 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 145 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 PHE cc_start: 0.8620 (t80) cc_final: 0.8147 (t80) REVERT: A 421 TYR cc_start: 0.8367 (m-80) cc_final: 0.7873 (m-80) REVERT: A 1002 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7603 (mp10) REVERT: B 303 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8108 (pp) REVERT: B 780 GLU cc_start: 0.8346 (tt0) cc_final: 0.8099 (tt0) REVERT: B 1029 MET cc_start: 0.9156 (tpp) cc_final: 0.8850 (ttm) REVERT: C 303 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7839 (pp) REVERT: C 421 TYR cc_start: 0.8017 (m-80) cc_final: 0.7625 (m-80) REVERT: C 855 PHE cc_start: 0.7547 (m-80) cc_final: 0.7248 (m-80) REVERT: C 878 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8611 (tt) REVERT: C 1029 MET cc_start: 0.9258 (tpp) cc_final: 0.8866 (ttm) outliers start: 64 outliers final: 55 residues processed: 197 average time/residue: 0.1439 time to fit residues: 49.8867 Evaluate side-chains 199 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 140 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 253 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 302 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 103 optimal weight: 0.0570 chunk 160 optimal weight: 9.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN B 414 GLN B 901 GLN C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.109133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.080810 restraints weight = 53588.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.082962 restraints weight = 39234.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.083315 restraints weight = 26550.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.083658 restraints weight = 25583.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.083794 restraints weight = 24231.428| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 26112 Z= 0.197 Angle : 0.628 20.901 35676 Z= 0.312 Chirality : 0.045 0.189 4209 Planarity : 0.004 0.037 4482 Dihedral : 5.491 43.518 4787 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.38 % Allowed : 13.60 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.15), residues: 3084 helix: 0.85 (0.22), residues: 642 sheet: -0.64 (0.19), residues: 696 loop : -1.75 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.024 0.001 TYR B 265 PHE 0.023 0.002 PHE C 375 TRP 0.006 0.001 TRP B 633 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00488 (26007) covalent geometry : angle 0.61164 (35397) SS BOND : bond 0.00371 ( 36) SS BOND : angle 1.23808 ( 72) hydrogen bonds : bond 0.04660 ( 755) hydrogen bonds : angle 4.80137 ( 2013) link_BETA1-4 : bond 0.00471 ( 21) link_BETA1-4 : angle 1.14616 ( 63) link_NAG-ASN : bond 0.00297 ( 48) link_NAG-ASN : angle 2.06749 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 145 time to evaluate : 1.063 Fit side-chains REVERT: A 421 TYR cc_start: 0.8423 (m-80) cc_final: 0.7857 (m-80) REVERT: A 1002 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: B 303 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8085 (pp) REVERT: B 780 GLU cc_start: 0.8383 (tt0) cc_final: 0.8143 (tt0) REVERT: B 1029 MET cc_start: 0.9190 (tpp) cc_final: 0.8910 (ttm) REVERT: C 303 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7791 (pp) REVERT: C 421 TYR cc_start: 0.8104 (m-80) cc_final: 0.7719 (m-80) REVERT: C 855 PHE cc_start: 0.7704 (m-80) cc_final: 0.7290 (m-80) REVERT: C 878 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8625 (tt) REVERT: C 1029 MET cc_start: 0.9234 (tpp) cc_final: 0.8937 (ttm) outliers start: 65 outliers final: 56 residues processed: 196 average time/residue: 0.1430 time to fit residues: 49.4849 Evaluate side-chains 198 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 138 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 50 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 281 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 271 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN ** C 422 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 = 0.3598 r_free = 0.3598 target = 0.111291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.082938 restraints weight = 53261.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.084939 restraints weight = 38611.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.085610 restraints weight = 26309.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.086973 restraints weight = 25081.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.087022 restraints weight = 21982.634| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26112 Z= 0.104 Angle : 0.565 21.126 35676 Z= 0.278 Chirality : 0.043 0.192 4209 Planarity : 0.004 0.038 4482 Dihedral : 5.054 40.286 4787 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.16 % Allowed : 13.82 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.15), residues: 3084 helix: 0.93 (0.22), residues: 648 sheet: -0.53 (0.20), residues: 666 loop : -1.64 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 765 TYR 0.027 0.001 TYR C 170 PHE 0.024 0.001 PHE A 375 TRP 0.008 0.001 TRP B 633 HIS 0.002 0.000 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00241 (26007) covalent geometry : angle 0.55095 (35397) SS BOND : bond 0.00232 ( 36) SS BOND : angle 0.89343 ( 72) hydrogen bonds : bond 0.03665 ( 755) hydrogen bonds : angle 4.58284 ( 2013) link_BETA1-4 : bond 0.00517 ( 21) link_BETA1-4 : angle 1.16513 ( 63) link_NAG-ASN : bond 0.00232 ( 48) link_NAG-ASN : angle 1.86468 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3416.70 seconds wall clock time: 60 minutes 26.46 seconds (3626.46 seconds total)