Starting phenix.real_space_refine on Sun Jul 5 04:54:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yqw_34037/07_2026/7yqw_34037.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqw_34037/07_2026/7yqw_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 { model { file = "/net/cci-nas-00/data/ceres_data/7yqw_34037/07_2026/7yqw_34037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqw_34037/07_2026/7yqw_34037.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yqw_34037/07_2026/7yqw_34037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqw_34037/07_2026/7yqw_34037.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yqw_34037/07_2026/7yqw_34037.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yqw_34037/07_2026/7yqw_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-dev-6108/lib/python3.11/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 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 chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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 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 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 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 chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 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 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 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 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 chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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 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 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 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 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 chiralities: 11 Time building chain proxies: 5.58, per 1000 atoms: 0.22 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: 2.22 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.04 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: 5.32 Time building geometry restraints manager: 2.91 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 - 17.46: 13484 17.46 - 34.92: 1180 34.92 - 52.38: 213 52.38 - 69.83: 39 69.83 - 87.29: 18 Dihedral angle restraints: 14934 sinusoidal: 5826 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 14931 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: 0.07 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: 2.760 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.200 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 13.578 87.293 8964 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 are 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/Z covalent geometry : bond 0.00436 / 0.21 (26007) covalent geometry : angle 0.64134 / 0.32 (35397) SS BOND : bond 0.00293 / 0.19 ( 36) SS BOND : angle 1.12981 / 0.72 ( 72) hydrogen bonds : bond 0.16122 / 10.62 ( 755) hydrogen bonds : angle 6.52208 / 4.51 ( 2013) link_BETA1-4 : bond 0.00581 / 0.39 ( 21) link_BETA1-4 : angle 1.34757 / 0.87 ( 63) link_NAG-ASN : bond 0.00249 / 0.15 ( 48) link_NAG-ASN : angle 1.97422 / 1.31 ( 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 : 0.899 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: 0.1315 time to fit residues: 44.1235 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 : 1.069 ------------------------------------------------------------------------------- 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... 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 = 0.111456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.083182 restraints weight = 53474.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.085008 restraints weight = 38734.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.085557 restraints weight = 26049.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.085973 restraints weight = 23920.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.086168 restraints weight = 22198.672| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.0792 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= 0.126 Angle : 0.587 10.980 35676 Z= 0.296 Chirality : 0.044 0.174 4209 Planarity : 0.004 0.044 4482 Dihedral : 4.481 49.277 3353 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.88 % Allowed : 6.69 % Favored : 92.43 % 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 are not related in a simple way. whole: -1.34 (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 0.003 0.000 ARG C 357 TYR 0.015 0.001 TYR B 265 PHE 0.020 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/Z covalent geometry : bond 0.00296 / 0.13 (26007) covalent geometry : angle 0.57110 / 0.29 (35397) SS BOND : bond 0.00300 / 0.20 ( 36) SS BOND : angle 1.09589 / 0.71 ( 72) hydrogen bonds : bond 0.04422 / 2.94 ( 755) hydrogen bonds : angle 5.25600 / 3.64 ( 2013) link_BETA1-4 : bond 0.00535 / 0.34 ( 21) link_BETA1-4 : angle 1.29651 / 0.83 ( 63) link_NAG-ASN : bond 0.00289 / 0.17 ( 48) link_NAG-ASN : angle 1.93631 / 1.28 ( 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 180 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.966 Fit side-chains REVERT: A 633 TRP cc_start: 0.6836 (p90) cc_final: 0.6553 (p90) REVERT: A 990 GLU cc_start: 0.7725 (pm20) cc_final: 0.7433 (pm20) REVERT: B 168 PHE cc_start: 0.7977 (t80) cc_final: 0.7700 (t80) REVERT: B 421 TYR cc_start: 0.8699 (m-80) cc_final: 0.8192 (m-80) REVERT: B 633 TRP cc_start: 0.7157 (p90) cc_final: 0.6845 (p90) REVERT: B 780 GLU cc_start: 0.8431 (tt0) cc_final: 0.8176 (tt0) REVERT: C 168 PHE cc_start: 0.7841 (t80) cc_final: 0.7496 (t80) REVERT: C 633 TRP cc_start: 0.6801 (p90) cc_final: 0.6527 (p90) REVERT: C 869 MET cc_start: 0.8247 (ptp) cc_final: 0.7997 (ptm) outliers start: 24 outliers final: 15 residues processed: 167 average time/residue: 0.1293 time to fit residues: 37.4729 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 : 0.905 ------------------------------------------------------------------------------- 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: 0.9990 chunk 184 optimal weight: 0.7980 chunk 158 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 233 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3611 r_free = 0.3611 target = 0.112289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.083966 restraints weight = 53448.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.086234 restraints weight = 38370.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.086855 restraints weight = 25054.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.087093 restraints weight = 22455.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.087278 restraints weight = 21202.250| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.002 0.044 26112 Z= 0.102 Angle : 0.538 8.767 35676 Z= 0.271 Chirality : 0.043 0.164 4209 Planarity : 0.004 0.039 4482 Dihedral : 4.246 44.014 3352 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.24 % Allowed : 9.43 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.15), residues: 3084 helix: 0.83 (0.22), residues: 651 sheet: -0.44 (0.20), residues: 657 loop : -1.70 (0.14), residues: 1776 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/Z covalent geometry : bond 0.00234 / 0.10 (26007) covalent geometry : angle 0.52450 / 0.27 (35397) SS BOND : bond 0.00214 / 0.14 ( 36) SS BOND : angle 0.86922 / 0.56 ( 72) hydrogen bonds : bond 0.03793 / 2.53 ( 755) hydrogen bonds : angle 4.91837 / 3.43 ( 2013) link_BETA1-4 : bond 0.00487 / 0.32 ( 21) link_BETA1-4 : angle 1.22177 / 0.78 ( 63) link_NAG-ASN : bond 0.00278 / 0.17 ( 48) link_NAG-ASN : angle 1.75347 / 1.15 ( 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 189 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8811 (m-80) cc_final: 0.7965 (m-80) REVERT: A 904 TYR cc_start: 0.7962 (m-10) cc_final: 0.7336 (m-10) REVERT: A 965 GLN cc_start: 0.9327 (OUTLIER) cc_final: 0.9121 (tp-100) REVERT: A 1002 GLN cc_start: 0.8346 (mp10) cc_final: 0.7951 (mp10) REVERT: B 168 PHE cc_start: 0.7978 (t80) cc_final: 0.7689 (t80) REVERT: B 421 TYR cc_start: 0.8659 (m-80) cc_final: 0.7606 (m-80) REVERT: B 780 GLU cc_start: 0.8434 (tt0) cc_final: 0.8177 (tt0) REVERT: B 904 TYR cc_start: 0.7799 (m-10) cc_final: 0.7583 (m-10) REVERT: B 965 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.9044 (tp40) outliers start: 34 outliers final: 16 residues processed: 178 average time/residue: 0.1358 time to fit residues: 41.9202 Evaluate side-chains 159 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL 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 965 GLN 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 231 ILE Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 588 THR 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: 5.9990 chunk 192 optimal weight: 6.9990 chunk 269 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 124 optimal weight: 5.9990 chunk 232 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 180 optimal weight: 0.1980 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 204 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 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 = 0.3600 r_free = 0.3600 target = 0.111503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.085648 restraints weight = 53498.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.086214 restraints weight = 40050.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.086444 restraints weight = 40939.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.087398 restraints weight = 31731.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.087497 restraints weight = 27757.803| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1134 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= 0.121 Angle : 0.544 7.870 35676 Z= 0.274 Chirality : 0.043 0.219 4209 Planarity : 0.004 0.035 4482 Dihedral : 4.197 43.218 3351 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.64 % Allowed : 11.37 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.15), residues: 3084 helix: 0.85 (0.22), residues: 651 sheet: -0.41 (0.20), residues: 657 loop : -1.68 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.016 0.001 TYR A 170 PHE 0.015 0.001 PHE A 375 TRP 0.007 0.001 TRP C 633 HIS 0.002 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (26007) covalent geometry : angle 0.53061 / 0.27 (35397) SS BOND : bond 0.00243 / 0.16 ( 36) SS BOND : angle 0.87961 / 0.57 ( 72) hydrogen bonds : bond 0.03885 / 2.60 ( 755) hydrogen bonds : angle 4.80175 / 3.34 ( 2013) link_BETA1-4 : bond 0.00480 / 0.31 ( 21) link_BETA1-4 : angle 1.15686 / 0.74 ( 63) link_NAG-ASN : bond 0.00245 / 0.15 ( 48) link_NAG-ASN : angle 1.75400 / 1.16 ( 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 198 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8667 (m-80) cc_final: 0.7825 (m-80) REVERT: A 904 TYR cc_start: 0.7946 (m-10) cc_final: 0.7626 (m-10) REVERT: A 1002 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7997 (mp10) REVERT: B 421 TYR cc_start: 0.8343 (m-80) cc_final: 0.7961 (m-80) REVERT: B 780 GLU cc_start: 0.8201 (tt0) cc_final: 0.7980 (tt0) REVERT: B 904 TYR cc_start: 0.7846 (m-10) cc_final: 0.7596 (m-10) REVERT: B 965 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8955 (tp40) REVERT: C 421 TYR cc_start: 0.8322 (m-80) cc_final: 0.8008 (m-80) REVERT: C 740 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7871 (ttp) REVERT: C 1029 MET cc_start: 0.9246 (tpp) cc_final: 0.8825 (ttm) outliers start: 45 outliers final: 25 residues processed: 183 average time/residue: 0.1325 time to fit residues: 42.1370 Evaluate side-chains 169 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 231 ILE 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 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 420 ASP 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 965 GLN 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 133 PHE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 197 ILE 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 994 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 252 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 219 optimal weight: 0.0470 chunk 126 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 965 GLN ** B 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 = 0.3608 r_free = 0.3608 target = 0.112012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.086069 restraints weight = 53250.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.086975 restraints weight = 39986.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.087229 restraints weight = 38647.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.087846 restraints weight = 30980.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.088084 restraints weight = 27874.538| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26112 Z= 0.104 Angle : 0.534 12.376 35676 Z= 0.268 Chirality : 0.043 0.183 4209 Planarity : 0.004 0.037 4482 Dihedral : 4.102 42.277 3351 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.16 % Allowed : 11.62 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.15), residues: 3084 helix: 0.91 (0.22), residues: 651 sheet: -0.34 (0.20), residues: 657 loop : -1.66 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 357 TYR 0.029 0.001 TYR B 170 PHE 0.020 0.001 PHE B 168 TRP 0.012 0.001 TRP B 633 HIS 0.002 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 (26007) covalent geometry : angle 0.52221 / 0.27 (35397) SS BOND : bond 0.00220 / 0.14 ( 36) SS BOND : angle 0.80882 / 0.52 ( 72) hydrogen bonds : bond 0.03570 / 2.38 ( 755) hydrogen bonds : angle 4.68452 / 3.26 ( 2013) link_BETA1-4 : bond 0.00461 / 0.30 ( 21) link_BETA1-4 : angle 1.11467 / 0.71 ( 63) link_NAG-ASN : bond 0.00248 / 0.14 ( 48) link_NAG-ASN : angle 1.67841 / 1.11 ( 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 217 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 158 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 902 MET cc_start: 0.8424 (tpt) cc_final: 0.7868 (tpt) REVERT: B 421 TYR cc_start: 0.8300 (m-80) cc_final: 0.8009 (m-80) REVERT: B 780 GLU cc_start: 0.8198 (tt0) cc_final: 0.7997 (tt0) REVERT: C 421 TYR cc_start: 0.8375 (m-80) cc_final: 0.8131 (m-80) REVERT: C 878 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8661 (tt) REVERT: C 1029 MET cc_start: 0.9235 (tpp) cc_final: 0.8800 (ttm) outliers start: 59 outliers final: 31 residues processed: 204 average time/residue: 0.1317 time to fit residues: 47.6051 Evaluate side-chains 175 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 965 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 385 THR 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 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 420 ASP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 588 THR 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: 3.9990 chunk 301 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 138 optimal weight: 0.0980 chunk 99 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 141 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 965 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.110529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.082023 restraints weight = 53806.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.084015 restraints weight = 39645.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.084429 restraints weight = 26949.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.084884 restraints weight = 25884.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.085012 restraints weight = 24226.285| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 26112 Z= 0.157 Angle : 0.583 16.939 35676 Z= 0.291 Chirality : 0.044 0.234 4209 Planarity : 0.004 0.039 4482 Dihedral : 4.215 43.523 3350 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.38 % Allowed : 12.28 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.15), residues: 3084 helix: 0.86 (0.22), residues: 651 sheet: -0.44 (0.20), residues: 660 loop : -1.69 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.019 0.001 TYR B 265 PHE 0.028 0.001 PHE A 168 TRP 0.007 0.001 TRP B 633 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (26007) covalent geometry : angle 0.56998 / 0.29 (35397) SS BOND : bond 0.00361 / 0.24 ( 36) SS BOND : angle 1.16283 / 0.77 ( 72) hydrogen bonds : bond 0.04137 / 2.77 ( 755) hydrogen bonds : angle 4.77383 / 3.32 ( 2013) link_BETA1-4 : bond 0.00426 / 0.27 ( 21) link_BETA1-4 : angle 1.06552 / 0.68 ( 63) link_NAG-ASN : bond 0.00251 / 0.15 ( 48) link_NAG-ASN : angle 1.79407 / 1.18 ( 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 217 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 152 time to evaluate : 0.952 Fit side-chains REVERT: A 421 TYR cc_start: 0.8400 (m-80) cc_final: 0.7907 (m-80) REVERT: A 902 MET cc_start: 0.8616 (tpt) cc_final: 0.8123 (tpt) REVERT: B 421 TYR cc_start: 0.8348 (m-80) cc_final: 0.7835 (m-80) REVERT: B 780 GLU cc_start: 0.8366 (tt0) cc_final: 0.8084 (tt0) REVERT: C 303 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7825 (pp) REVERT: C 421 TYR cc_start: 0.8447 (m-80) cc_final: 0.8002 (m-80) REVERT: C 878 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8608 (tt) REVERT: C 1029 MET cc_start: 0.9249 (tpp) cc_final: 0.8899 (ttm) outliers start: 65 outliers final: 50 residues processed: 202 average time/residue: 0.1341 time to fit residues: 47.2446 Evaluate side-chains 190 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 869 MET 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 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 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 420 ASP 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 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 1094 VAL 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: 0.9990 chunk 300 optimal weight: 5.9990 chunk 40 optimal weight: 0.4980 chunk 164 optimal weight: 0.3980 chunk 151 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 263 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 245 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 965 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.112058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.083783 restraints weight = 53129.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.086442 restraints weight = 36319.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.086979 restraints weight = 23659.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.087222 restraints weight = 21732.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.087342 restraints weight = 20472.912| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26112 Z= 0.098 Angle : 0.547 15.270 35676 Z= 0.272 Chirality : 0.043 0.227 4209 Planarity : 0.004 0.039 4482 Dihedral : 4.070 41.310 3350 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.08 % Allowed : 13.41 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.15), residues: 3084 helix: 0.96 (0.22), residues: 651 sheet: -0.32 (0.20), residues: 645 loop : -1.64 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.027 0.001 TYR B 170 PHE 0.023 0.001 PHE C 375 TRP 0.011 0.001 TRP C 633 HIS 0.002 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (26007) covalent geometry : angle 0.53512 / 0.27 (35397) SS BOND : bond 0.00260 / 0.18 ( 36) SS BOND : angle 1.06879 / 0.82 ( 72) hydrogen bonds : bond 0.03507 / 2.35 ( 755) hydrogen bonds : angle 4.62532 / 3.22 ( 2013) link_BETA1-4 : bond 0.00451 / 0.29 ( 21) link_BETA1-4 : angle 1.10002 / 0.70 ( 63) link_NAG-ASN : bond 0.00242 / 0.14 ( 48) link_NAG-ASN : angle 1.66173 / 1.10 ( 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: 57 poor density : 154 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8396 (m-80) cc_final: 0.7879 (m-80) REVERT: A 1002 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7581 (mp10) REVERT: B 303 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7830 (pp) REVERT: B 421 TYR cc_start: 0.8284 (m-80) cc_final: 0.7829 (m-80) REVERT: B 780 GLU cc_start: 0.8470 (tt0) cc_final: 0.8165 (tt0) REVERT: C 168 PHE cc_start: 0.7943 (t80) cc_final: 0.7691 (t80) REVERT: C 303 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7537 (pp) REVERT: C 421 TYR cc_start: 0.8406 (m-80) cc_final: 0.7918 (m-80) REVERT: C 855 PHE cc_start: 0.7519 (m-80) cc_final: 0.7213 (m-80) REVERT: C 878 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8519 (tt) REVERT: C 1029 MET cc_start: 0.9219 (tpp) cc_final: 0.8842 (ttm) outliers start: 57 outliers final: 44 residues processed: 198 average time/residue: 0.1261 time to fit residues: 43.8916 Evaluate side-chains 193 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 965 GLN Chi-restraints excluded: chain A residue 1002 GLN 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 333 THR Chi-restraints excluded: chain B residue 339 HIS 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 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP 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 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 420 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 36 optimal weight: 0.1980 chunk 257 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 50 optimal weight: 0.0050 chunk 72 optimal weight: 2.9990 chunk 252 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 965 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.112763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.084588 restraints weight = 53324.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.086546 restraints weight = 36494.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.086969 restraints weight = 24574.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.087552 restraints weight = 23158.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.087694 restraints weight = 21482.781| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1497 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= 0.092 Angle : 0.552 21.397 35676 Z= 0.270 Chirality : 0.043 0.206 4209 Planarity : 0.004 0.041 4482 Dihedral : 3.990 40.722 3350 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.27 % Allowed : 13.49 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.15), residues: 3084 helix: 1.04 (0.22), residues: 654 sheet: -0.32 (0.21), residues: 618 loop : -1.57 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 765 TYR 0.019 0.001 TYR C 170 PHE 0.022 0.001 PHE A 375 TRP 0.010 0.001 TRP C 633 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (26007) covalent geometry : angle 0.54126 / 0.27 (35397) SS BOND : bond 0.00206 / 0.14 ( 36) SS BOND : angle 0.99077 / 0.70 ( 72) hydrogen bonds : bond 0.03283 / 2.20 ( 755) hydrogen bonds : angle 4.52986 / 3.15 ( 2013) link_BETA1-4 : bond 0.00467 / 0.31 ( 21) link_BETA1-4 : angle 1.10130 / 0.70 ( 63) link_NAG-ASN : bond 0.00231 / 0.14 ( 48) link_NAG-ASN : angle 1.60205 / 1.06 ( 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 215 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 153 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8383 (m-80) cc_final: 0.7905 (m-80) REVERT: A 1002 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: B 303 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7867 (pp) REVERT: B 421 TYR cc_start: 0.8315 (m-80) cc_final: 0.7867 (m-80) REVERT: B 780 GLU cc_start: 0.8447 (tt0) cc_final: 0.8173 (tt0) REVERT: C 303 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7596 (pp) REVERT: C 421 TYR cc_start: 0.8403 (m-80) cc_final: 0.7958 (m-80) REVERT: C 855 PHE cc_start: 0.7551 (m-80) cc_final: 0.7251 (m-80) REVERT: C 878 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8515 (tt) REVERT: C 1029 MET cc_start: 0.9230 (tpp) cc_final: 0.8971 (ttm) outliers start: 62 outliers final: 48 residues processed: 203 average time/residue: 0.1361 time to fit residues: 48.6652 Evaluate side-chains 198 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 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 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 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 512 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 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 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 420 ASP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 266 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 101 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 162 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.112755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.084557 restraints weight = 53348.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.086558 restraints weight = 35493.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.087054 restraints weight = 23776.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.087575 restraints weight = 22485.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.087697 restraints weight = 21008.318| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26112 Z= 0.096 Angle : 0.547 16.735 35676 Z= 0.269 Chirality : 0.043 0.206 4209 Planarity : 0.004 0.043 4482 Dihedral : 3.945 40.531 3350 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.16 % Allowed : 13.74 % 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 are not related in a simple way. whole: -1.03 (0.15), residues: 3084 helix: 1.08 (0.22), residues: 654 sheet: -0.31 (0.21), residues: 618 loop : -1.55 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 765 TYR 0.016 0.001 TYR C1067 PHE 0.024 0.001 PHE C 375 TRP 0.010 0.001 TRP B 633 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (26007) covalent geometry : angle 0.53685 / 0.27 (35397) SS BOND : bond 0.00216 / 0.15 ( 36) SS BOND : angle 0.92491 / 0.65 ( 72) hydrogen bonds : bond 0.03272 / 2.19 ( 755) hydrogen bonds : angle 4.47395 / 3.12 ( 2013) link_BETA1-4 : bond 0.00446 / 0.29 ( 21) link_BETA1-4 : angle 1.07758 / 0.69 ( 63) link_NAG-ASN : bond 0.00221 / 0.13 ( 48) link_NAG-ASN : angle 1.56846 / 1.04 ( 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 205 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 146 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 PHE cc_start: 0.8622 (t80) cc_final: 0.8201 (t80) REVERT: A 421 TYR cc_start: 0.8371 (m-80) cc_final: 0.7836 (m-80) REVERT: A 1002 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: B 303 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7816 (pp) REVERT: B 421 TYR cc_start: 0.8356 (m-80) cc_final: 0.7913 (m-80) REVERT: B 780 GLU cc_start: 0.8481 (tt0) cc_final: 0.8212 (tt0) REVERT: C 303 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7534 (pp) REVERT: C 421 TYR cc_start: 0.8384 (m-80) cc_final: 0.7951 (m-80) REVERT: C 855 PHE cc_start: 0.7574 (m-80) cc_final: 0.7265 (m-80) REVERT: C 878 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8476 (tt) REVERT: C 1029 MET cc_start: 0.9215 (tpp) cc_final: 0.8929 (ttm) outliers start: 59 outliers final: 47 residues processed: 194 average time/residue: 0.1325 time to fit residues: 45.2542 Evaluate side-chains 191 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 140 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 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 A residue 1104 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 512 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 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 197 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 420 ASP 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 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: 8.9990 chunk 66 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 302 optimal weight: 2.9990 chunk 150 optimal weight: 0.0970 chunk 103 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.109704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.081183 restraints weight = 53476.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.083031 restraints weight = 35129.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.083479 restraints weight = 24169.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.084045 restraints weight = 22951.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.084156 restraints weight = 21249.139| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 26112 Z= 0.181 Angle : 0.625 20.817 35676 Z= 0.308 Chirality : 0.045 0.227 4209 Planarity : 0.004 0.040 4482 Dihedral : 4.346 43.697 3350 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.16 % Allowed : 13.89 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.15), residues: 3084 helix: 0.97 (0.22), residues: 645 sheet: -0.48 (0.20), residues: 675 loop : -1.71 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.022 0.001 TYR B 265 PHE 0.022 0.001 PHE C 375 TRP 0.006 0.001 TRP B 633 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.18 (26007) covalent geometry : angle 0.61090 / 0.30 (35397) SS BOND : bond 0.00350 / 0.23 ( 36) SS BOND : angle 1.40403 / 0.97 ( 72) hydrogen bonds : bond 0.04485 / 3.00 ( 755) hydrogen bonds : angle 4.76644 / 3.31 ( 2013) link_BETA1-4 : bond 0.00429 / 0.27 ( 21) link_BETA1-4 : angle 1.04694 / 0.68 ( 63) link_NAG-ASN : bond 0.00275 / 0.17 ( 48) link_NAG-ASN : angle 1.87323 / 1.24 ( 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 204 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 145 time to evaluate : 0.976 Fit side-chains REVERT: A 375 PHE cc_start: 0.8512 (t80) cc_final: 0.8070 (t80) REVERT: A 421 TYR cc_start: 0.8399 (m-80) cc_final: 0.7767 (m-80) REVERT: A 1002 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7685 (mp10) REVERT: B 303 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7905 (pp) REVERT: B 421 TYR cc_start: 0.8430 (m-80) cc_final: 0.7770 (m-80) REVERT: B 780 GLU cc_start: 0.8485 (tt0) cc_final: 0.8211 (tt0) REVERT: C 303 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7529 (pp) REVERT: C 421 TYR cc_start: 0.8434 (m-80) cc_final: 0.7818 (m-80) REVERT: C 855 PHE cc_start: 0.7713 (m-80) cc_final: 0.7332 (m-80) REVERT: C 869 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.8034 (mtm) REVERT: C 878 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8526 (tt) REVERT: C 1029 MET cc_start: 0.9226 (tpp) cc_final: 0.8939 (ttm) outliers start: 59 outliers final: 49 residues processed: 191 average time/residue: 0.1386 time to fit residues: 46.5999 Evaluate side-chains 193 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 139 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 A residue 1104 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 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 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 420 ASP 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 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 50 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 138 optimal weight: 0.3980 chunk 251 optimal weight: 0.0170 chunk 152 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 0.0570 chunk 298 optimal weight: 1.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.111609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.083350 restraints weight = 53197.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.085271 restraints weight = 35468.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.085782 restraints weight = 23991.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.086331 restraints weight = 22644.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.086467 restraints weight = 20964.409| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1533 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= 0.103 Angle : 0.572 21.044 35676 Z= 0.279 Chirality : 0.043 0.203 4209 Planarity : 0.004 0.039 4482 Dihedral : 4.113 40.359 3350 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.16 % Allowed : 13.89 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.15), residues: 3084 helix: 0.97 (0.22), residues: 657 sheet: -0.42 (0.21), residues: 621 loop : -1.60 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 765 TYR 0.027 0.001 TYR B 170 PHE 0.024 0.001 PHE C 375 TRP 0.007 0.001 TRP B 633 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (26007) covalent geometry : angle 0.56062 / 0.28 (35397) SS BOND : bond 0.00226 / 0.15 ( 36) SS BOND : angle 1.02564 / 0.70 ( 72) hydrogen bonds : bond 0.03598 / 2.41 ( 755) hydrogen bonds : angle 4.56468 / 3.18 ( 2013) link_BETA1-4 : bond 0.00440 / 0.29 ( 21) link_BETA1-4 : angle 1.06799 / 0.69 ( 63) link_NAG-ASN : bond 0.00223 / 0.13 ( 48) link_NAG-ASN : angle 1.70466 / 1.12 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3328.38 seconds wall clock time: 59 minutes 4.35 seconds (3544.35 seconds total)