Starting phenix.real_space_refine on Sun Jun 22 08:03:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqw_34037/06_2025/7yqw_34037.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqw_34037/06_2025/7yqw_34037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yqw_34037/06_2025/7yqw_34037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqw_34037/06_2025/7yqw_34037.map" model { file = "/net/cci-nas-00/data/ceres_data/7yqw_34037/06_2025/7yqw_34037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqw_34037/06_2025/7yqw_34037.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25422 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8158 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 985} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 8158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8158 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 985} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 8158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8158 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 985} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 14.27, per 1000 atoms: 0.56 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: 6.80 Conformation dependent library (CDL) restraints added in 3.2 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: 4.09 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: 10.67 Time building geometry restraints manager: 7.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4469 1.33 - 1.45: 7079 1.45 - 1.57: 14321 1.57 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 26007 Sorted by residual: bond pdb=" CA SER B 591 " pdb=" CB SER B 591 " ideal model delta sigma weight residual 1.530 1.480 0.050 1.57e-02 4.06e+03 1.00e+01 bond pdb=" CA SER A 591 " pdb=" CB SER A 591 " ideal model delta sigma weight residual 1.530 1.481 0.049 1.57e-02 4.06e+03 9.94e+00 bond pdb=" CA SER C 591 " pdb=" CB SER C 591 " ideal model delta sigma weight residual 1.530 1.481 0.049 1.57e-02 4.06e+03 9.61e+00 bond pdb=" C PRO B 589 " pdb=" O PRO B 589 " ideal model delta sigma weight residual 1.235 1.202 0.033 1.30e-02 5.92e+03 6.53e+00 bond pdb=" C PRO A 589 " pdb=" O PRO A 589 " ideal model delta sigma weight residual 1.235 1.203 0.033 1.30e-02 5.92e+03 6.27e+00 ... (remaining 26002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 34297 1.68 - 3.36: 960 3.36 - 5.03: 106 5.03 - 6.71: 28 6.71 - 8.39: 6 Bond angle restraints: 35397 Sorted by residual: angle pdb=" C PRO A 589 " pdb=" CA PRO A 589 " pdb=" CB PRO A 589 " ideal model delta sigma weight residual 111.56 106.15 5.41 1.65e+00 3.67e-01 1.07e+01 angle pdb=" CA SER A 591 " pdb=" C SER A 591 " pdb=" O SER A 591 " ideal model delta sigma weight residual 120.96 117.78 3.18 1.09e+00 8.42e-01 8.53e+00 angle pdb=" CA SER C 591 " pdb=" C SER C 591 " pdb=" O SER C 591 " ideal model delta sigma weight residual 120.96 117.80 3.16 1.09e+00 8.42e-01 8.42e+00 angle pdb=" CA SER B 591 " pdb=" C SER B 591 " pdb=" O SER B 591 " ideal model delta sigma weight residual 120.96 117.85 3.11 1.09e+00 8.42e-01 8.16e+00 angle pdb=" C PRO B 589 " pdb=" CA PRO B 589 " pdb=" CB PRO B 589 " ideal model delta sigma weight residual 111.56 107.00 4.56 1.65e+00 3.67e-01 7.65e+00 ... (remaining 35392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 15138 21.80 - 43.59: 1032 43.59 - 65.39: 117 65.39 - 87.19: 57 87.19 - 108.99: 27 Dihedral angle restraints: 16371 sinusoidal: 7263 harmonic: 9108 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -22.89 -63.11 1 1.00e+01 1.00e-02 5.26e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -22.89 -63.11 1 1.00e+01 1.00e-02 5.26e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -22.91 -63.09 1 1.00e+01 1.00e-02 5.26e+01 ... (remaining 16368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3375 0.055 - 0.111: 729 0.111 - 0.166: 82 0.166 - 0.221: 14 0.221 - 0.276: 9 Chirality restraints: 4209 Sorted by residual: chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 4206 not shown) Planarity restraints: 4530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 586 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.59e+00 pdb=" C ASP C 586 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP C 586 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE C 587 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 586 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C ASP B 586 " 0.038 2.00e-02 2.50e+03 pdb=" O ASP B 586 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE B 587 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO C 986 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.019 5.00e-02 4.00e+02 ... (remaining 4527 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 77 2.44 - 3.05: 16330 3.05 - 3.67: 33892 3.67 - 4.28: 48906 4.28 - 4.90: 85027 Nonbonded interactions: 184232 Sorted by model distance: nonbonded pdb=" CG1 VAL B1094 " pdb=" OH TYR C 904 " model vdw 1.820 3.460 nonbonded pdb=" OH TYR A 904 " pdb=" CG1 VAL C1094 " model vdw 1.830 3.460 nonbonded pdb=" CG1 VAL A1094 " pdb=" OH TYR B 904 " model vdw 1.837 3.460 nonbonded pdb=" OE1 GLN A 957 " pdb=" NH2 ARG B 765 " model vdw 1.953 3.120 nonbonded pdb=" OE1 GLN B 957 " pdb=" NH2 ARG C 765 " model vdw 1.953 3.120 ... (remaining 184227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.16 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: 2.460 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: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 58.940 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.150 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 26112 Z= 0.207 Angle : 0.655 8.390 35676 Z= 0.326 Chirality : 0.048 0.276 4209 Planarity : 0.004 0.035 4482 Dihedral : 15.071 108.986 10401 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.75 % Favored : 92.22 % Rotamer: Outliers : 0.18 % Allowed : 0.33 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (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 TRP 0.017 0.001 TRP B 633 HIS 0.008 0.001 HIS B 339 PHE 0.017 0.001 PHE A 906 TYR 0.016 0.001 TYR B 265 ARG 0.003 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 48) link_NAG-ASN : angle 1.97422 ( 144) link_BETA1-4 : bond 0.00581 ( 21) link_BETA1-4 : angle 1.34757 ( 63) hydrogen bonds : bond 0.16122 ( 755) hydrogen bonds : angle 6.52208 ( 2013) SS BOND : bond 0.00293 ( 36) SS BOND : angle 1.12981 ( 72) covalent geometry : bond 0.00436 (26007) covalent geometry : angle 0.64134 (35397) *********************** 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 : 3.078 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: 0.3054 time to fit residues: 102.1511 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 : 2.716 ------------------------------------------------------------------------------- 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 263 optimal weight: 0.5980 chunk 236 optimal weight: 10.0000 chunk 131 optimal weight: 0.0770 chunk 80 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 0.7980 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN A 965 GLN B 913 GLN B 965 GLN C 913 GLN C 965 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.111336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.082988 restraints weight = 53172.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.085059 restraints weight = 39140.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.085729 restraints weight = 25503.600| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26112 Z= 0.129 Angle : 0.601 11.102 35676 Z= 0.300 Chirality : 0.044 0.173 4209 Planarity : 0.004 0.043 4482 Dihedral : 9.187 68.306 4790 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.84 % Allowed : 6.83 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.15), residues: 3084 helix: 0.82 (0.22), residues: 627 sheet: -0.50 (0.20), residues: 657 loop : -1.76 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 436 HIS 0.002 0.000 HIS A 519 PHE 0.020 0.001 PHE A 375 TYR 0.016 0.001 TYR B 265 ARG 0.003 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 48) link_NAG-ASN : angle 2.01383 ( 144) link_BETA1-4 : bond 0.00614 ( 21) link_BETA1-4 : angle 1.75826 ( 63) hydrogen bonds : bond 0.04420 ( 755) hydrogen bonds : angle 5.26941 ( 2013) SS BOND : bond 0.00304 ( 36) SS BOND : angle 1.11359 ( 72) covalent geometry : bond 0.00305 (26007) covalent geometry : angle 0.58221 (35397) *********************** 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 175 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 2.613 Fit side-chains REVERT: A 633 TRP cc_start: 0.6826 (p90) cc_final: 0.6528 (p90) REVERT: A 965 GLN cc_start: 0.9332 (OUTLIER) cc_final: 0.9065 (tp-100) REVERT: A 990 GLU cc_start: 0.7728 (pm20) cc_final: 0.7429 (pm20) REVERT: B 168 PHE cc_start: 0.7989 (t80) cc_final: 0.7683 (t80) REVERT: B 421 TYR cc_start: 0.8705 (m-80) cc_final: 0.8188 (m-80) REVERT: B 633 TRP cc_start: 0.7133 (p90) cc_final: 0.6803 (p90) REVERT: B 780 GLU cc_start: 0.8450 (tt0) cc_final: 0.8175 (tt0) REVERT: C 168 PHE cc_start: 0.7834 (t80) cc_final: 0.7470 (t80) REVERT: C 633 TRP cc_start: 0.6793 (p90) cc_final: 0.6498 (p90) REVERT: C 869 MET cc_start: 0.8305 (ptp) cc_final: 0.8093 (ptm) outliers start: 23 outliers final: 15 residues processed: 162 average time/residue: 0.3162 time to fit residues: 88.8864 Evaluate side-chains 156 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 2.628 ------------------------------------------------------------------------------- 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 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 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 24 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 254 optimal weight: 0.0870 chunk 236 optimal weight: 9.9990 chunk 278 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 chunk 229 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.108764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.080384 restraints weight = 53633.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.082093 restraints weight = 36372.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.082635 restraints weight = 24827.302| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 26112 Z= 0.210 Angle : 0.640 8.489 35676 Z= 0.321 Chirality : 0.046 0.172 4209 Planarity : 0.004 0.043 4482 Dihedral : 7.341 50.853 4789 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.64 % Allowed : 11.00 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.15), residues: 3084 helix: 0.61 (0.21), residues: 657 sheet: -0.79 (0.19), residues: 654 loop : -1.89 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 633 HIS 0.004 0.001 HIS B1088 PHE 0.022 0.002 PHE B 855 TYR 0.027 0.002 TYR B 265 ARG 0.003 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 48) link_NAG-ASN : angle 2.20044 ( 144) link_BETA1-4 : bond 0.00543 ( 21) link_BETA1-4 : angle 1.51023 ( 63) hydrogen bonds : bond 0.05124 ( 755) hydrogen bonds : angle 5.16710 ( 2013) SS BOND : bond 0.00385 ( 36) SS BOND : angle 1.30268 ( 72) covalent geometry : bond 0.00524 (26007) covalent geometry : angle 0.62075 (35397) *********************** 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 192 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 147 time to evaluate : 2.844 Fit side-chains REVERT: A 633 TRP cc_start: 0.6853 (p90) cc_final: 0.6630 (p90) REVERT: A 904 TYR cc_start: 0.7983 (m-10) cc_final: 0.7395 (m-10) REVERT: B 421 TYR cc_start: 0.8714 (m-80) cc_final: 0.7567 (m-80) REVERT: B 633 TRP cc_start: 0.7063 (p90) cc_final: 0.6828 (p90) REVERT: B 780 GLU cc_start: 0.8483 (tt0) cc_final: 0.8213 (tt0) REVERT: B 904 TYR cc_start: 0.7884 (m-10) cc_final: 0.7664 (m-10) REVERT: B 965 GLN cc_start: 0.9366 (OUTLIER) cc_final: 0.9013 (tp-100) REVERT: C 633 TRP cc_start: 0.6844 (p90) cc_final: 0.6567 (p90) REVERT: C 1092 GLU cc_start: 0.7592 (tp30) cc_final: 0.7390 (tp30) outliers start: 45 outliers final: 24 residues processed: 176 average time/residue: 0.3161 time to fit residues: 95.6662 Evaluate side-chains 158 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 3.029 ------------------------------------------------------------------------------- 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 385 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 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 133 PHE Chi-restraints excluded: chain C residue 135 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 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 91 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 221 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 156 optimal weight: 0.7980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 913 GLN C 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.108546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.080110 restraints weight = 54027.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.081880 restraints weight = 35188.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.082454 restraints weight = 24417.296| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 26112 Z= 0.198 Angle : 0.620 8.444 35676 Z= 0.313 Chirality : 0.045 0.223 4209 Planarity : 0.004 0.042 4482 Dihedral : 6.333 52.116 4789 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.27 % Allowed : 12.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.15), residues: 3084 helix: 0.59 (0.21), residues: 657 sheet: -0.98 (0.19), residues: 678 loop : -1.92 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 633 HIS 0.003 0.001 HIS A 519 PHE 0.028 0.002 PHE B 168 TYR 0.026 0.001 TYR B 265 ARG 0.002 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 48) link_NAG-ASN : angle 2.25119 ( 144) link_BETA1-4 : bond 0.00487 ( 21) link_BETA1-4 : angle 1.33643 ( 63) hydrogen bonds : bond 0.04864 ( 755) hydrogen bonds : angle 5.07067 ( 2013) SS BOND : bond 0.00374 ( 36) SS BOND : angle 1.25020 ( 72) covalent geometry : bond 0.00492 (26007) covalent geometry : angle 0.60025 (35397) *********************** 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 208 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 146 time to evaluate : 2.717 Fit side-chains REVERT: A 1002 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8000 (mp10) REVERT: B 421 TYR cc_start: 0.8432 (m-80) cc_final: 0.7779 (m-80) REVERT: B 780 GLU cc_start: 0.8414 (tt0) cc_final: 0.8121 (tt0) REVERT: B 904 TYR cc_start: 0.7979 (m-10) cc_final: 0.7772 (m-10) REVERT: B 965 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.9063 (tp-100) REVERT: C 855 PHE cc_start: 0.7697 (m-80) cc_final: 0.7352 (m-80) REVERT: C 878 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8635 (tt) REVERT: C 1092 GLU cc_start: 0.7510 (tp30) cc_final: 0.7303 (tp30) outliers start: 62 outliers final: 35 residues processed: 193 average time/residue: 0.2889 time to fit residues: 97.5020 Evaluate side-chains 173 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 2.676 ------------------------------------------------------------------------------- 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 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 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 430 THR 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 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 B residue 1096 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 186 PHE Chi-restraints excluded: chain C residue 231 ILE 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 511 VAL 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 1094 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 16 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 310 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 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 = 0.3539 r_free = 0.3539 target = 0.107469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.079131 restraints weight = 54400.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.080976 restraints weight = 42020.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081399 restraints weight = 28718.138| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 26112 Z= 0.235 Angle : 0.659 11.623 35676 Z= 0.333 Chirality : 0.046 0.183 4209 Planarity : 0.004 0.042 4482 Dihedral : 6.402 57.613 4788 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.74 % Allowed : 13.08 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.15), residues: 3084 helix: 0.42 (0.21), residues: 666 sheet: -0.94 (0.18), residues: 714 loop : -2.09 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 633 HIS 0.004 0.001 HIS B1048 PHE 0.025 0.002 PHE B 375 TYR 0.031 0.002 TYR B 265 ARG 0.002 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 48) link_NAG-ASN : angle 2.38677 ( 144) link_BETA1-4 : bond 0.00453 ( 21) link_BETA1-4 : angle 1.19305 ( 63) hydrogen bonds : bond 0.05269 ( 755) hydrogen bonds : angle 5.15702 ( 2013) SS BOND : bond 0.00535 ( 36) SS BOND : angle 1.34963 ( 72) covalent geometry : bond 0.00587 (26007) covalent geometry : angle 0.63851 (35397) *********************** 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 223 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 148 time to evaluate : 3.015 Fit side-chains REVERT: A 1002 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: B 303 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8304 (pp) REVERT: B 421 TYR cc_start: 0.8388 (m-80) cc_final: 0.7808 (m-80) REVERT: B 780 GLU cc_start: 0.8286 (tt0) cc_final: 0.8022 (tt0) REVERT: C 303 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7981 (pp) REVERT: C 421 TYR cc_start: 0.8475 (m-80) cc_final: 0.7955 (m-80) REVERT: C 855 PHE cc_start: 0.7687 (m-80) cc_final: 0.7328 (m-80) REVERT: C 878 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8696 (tt) outliers start: 75 outliers final: 49 residues processed: 211 average time/residue: 0.3093 time to fit residues: 113.5917 Evaluate side-chains 185 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 132 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 179 LEU 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 385 THR Chi-restraints excluded: chain B residue 420 ASP 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 590 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain 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 135 PHE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 778 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 1094 VAL 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 105 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 248 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.110124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.082180 restraints weight = 53593.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.083740 restraints weight = 43627.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.084387 restraints weight = 29414.812| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26112 Z= 0.113 Angle : 0.571 12.241 35676 Z= 0.287 Chirality : 0.044 0.174 4209 Planarity : 0.004 0.043 4482 Dihedral : 5.741 59.184 4788 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.34 % Allowed : 14.55 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.15), residues: 3084 helix: 0.81 (0.22), residues: 642 sheet: -0.87 (0.18), residues: 726 loop : -1.94 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 633 HIS 0.002 0.000 HIS A 519 PHE 0.020 0.001 PHE B 168 TYR 0.021 0.001 TYR C 170 ARG 0.002 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 48) link_NAG-ASN : angle 2.09832 ( 144) link_BETA1-4 : bond 0.00528 ( 21) link_BETA1-4 : angle 1.22027 ( 63) hydrogen bonds : bond 0.04046 ( 755) hydrogen bonds : angle 4.88758 ( 2013) SS BOND : bond 0.00281 ( 36) SS BOND : angle 1.22219 ( 72) covalent geometry : bond 0.00267 (26007) covalent geometry : angle 0.55222 (35397) *********************** 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 219 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 155 time to evaluate : 2.770 Fit side-chains REVERT: A 421 TYR cc_start: 0.8403 (m-80) cc_final: 0.7902 (m-80) REVERT: B 303 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8198 (pp) REVERT: B 421 TYR cc_start: 0.8329 (m-80) cc_final: 0.7792 (m-80) REVERT: B 780 GLU cc_start: 0.8320 (tt0) cc_final: 0.8044 (tt0) REVERT: C 303 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7901 (pp) REVERT: C 421 TYR cc_start: 0.8443 (m-80) cc_final: 0.7875 (m-80) REVERT: C 855 PHE cc_start: 0.7680 (m-80) cc_final: 0.7351 (m-80) REVERT: C 878 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8678 (tt) outliers start: 64 outliers final: 44 residues processed: 211 average time/residue: 0.2936 time to fit residues: 108.1135 Evaluate side-chains 185 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 138 time to evaluate : 2.699 ------------------------------------------------------------------------------- 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 179 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 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 590 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 66 HIS 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 231 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 175 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 0.2980 chunk 132 optimal weight: 10.0000 chunk 189 optimal weight: 7.9990 chunk 260 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 302 optimal weight: 0.9980 chunk 290 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.108343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.080278 restraints weight = 54291.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.081945 restraints weight = 45117.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.082533 restraints weight = 29928.385| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 26112 Z= 0.187 Angle : 0.627 14.708 35676 Z= 0.312 Chirality : 0.045 0.243 4209 Planarity : 0.004 0.044 4482 Dihedral : 5.903 53.779 4788 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.85 % Allowed : 14.36 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.15), residues: 3084 helix: 0.79 (0.22), residues: 639 sheet: -0.96 (0.18), residues: 726 loop : -1.93 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 633 HIS 0.003 0.001 HIS B1064 PHE 0.032 0.002 PHE A 168 TYR 0.028 0.001 TYR A 170 ARG 0.002 0.000 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 48) link_NAG-ASN : angle 2.20295 ( 144) link_BETA1-4 : bond 0.00463 ( 21) link_BETA1-4 : angle 1.15882 ( 63) hydrogen bonds : bond 0.04716 ( 755) hydrogen bonds : angle 4.95324 ( 2013) SS BOND : bond 0.00380 ( 36) SS BOND : angle 1.33145 ( 72) covalent geometry : bond 0.00465 (26007) covalent geometry : angle 0.60877 (35397) *********************** 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 219 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 141 time to evaluate : 3.051 Fit side-chains REVERT: A 421 TYR cc_start: 0.8432 (m-80) cc_final: 0.7882 (m-80) REVERT: B 303 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8245 (pp) REVERT: B 421 TYR cc_start: 0.8380 (m-80) cc_final: 0.7774 (m-80) REVERT: B 780 GLU cc_start: 0.8348 (tt0) cc_final: 0.8068 (tt0) REVERT: C 303 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7909 (pp) REVERT: C 421 TYR cc_start: 0.8447 (m-80) cc_final: 0.7881 (m-80) REVERT: C 855 PHE cc_start: 0.7761 (m-80) cc_final: 0.7381 (m-80) REVERT: C 878 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8668 (tt) outliers start: 78 outliers final: 60 residues processed: 208 average time/residue: 0.3046 time to fit residues: 110.2387 Evaluate side-chains 194 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 131 time to evaluate : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 128 ILE 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 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain 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 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 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 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 309 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 277 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.109969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.084098 restraints weight = 53122.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.084594 restraints weight = 41610.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.084854 restraints weight = 39021.292| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26112 Z= 0.122 Angle : 0.584 13.935 35676 Z= 0.291 Chirality : 0.044 0.244 4209 Planarity : 0.004 0.044 4482 Dihedral : 5.557 43.656 4788 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.74 % Allowed : 14.91 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.15), residues: 3084 helix: 0.83 (0.22), residues: 645 sheet: -0.86 (0.19), residues: 726 loop : -1.90 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 633 HIS 0.002 0.000 HIS A 519 PHE 0.026 0.001 PHE B 375 TYR 0.026 0.001 TYR C 170 ARG 0.002 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 48) link_NAG-ASN : angle 2.07209 ( 144) link_BETA1-4 : bond 0.00513 ( 21) link_BETA1-4 : angle 1.18583 ( 63) hydrogen bonds : bond 0.04034 ( 755) hydrogen bonds : angle 4.78700 ( 2013) SS BOND : bond 0.00277 ( 36) SS BOND : angle 1.05827 ( 72) covalent geometry : bond 0.00292 (26007) covalent geometry : angle 0.56727 (35397) *********************** 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 220 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 145 time to evaluate : 2.709 Fit side-chains REVERT: A 421 TYR cc_start: 0.8324 (m-80) cc_final: 0.7940 (m-80) REVERT: B 303 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8372 (pp) REVERT: B 421 TYR cc_start: 0.8336 (m-80) cc_final: 0.7829 (m-80) REVERT: B 780 GLU cc_start: 0.8190 (tt0) cc_final: 0.7923 (tt0) REVERT: C 303 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8114 (pp) REVERT: C 421 TYR cc_start: 0.8335 (m-80) cc_final: 0.7875 (m-80) REVERT: C 855 PHE cc_start: 0.7617 (m-80) cc_final: 0.7298 (m-80) REVERT: C 878 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8745 (tt) outliers start: 75 outliers final: 62 residues processed: 209 average time/residue: 0.2882 time to fit residues: 105.5335 Evaluate side-chains 206 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 141 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 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 231 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL 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 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 590 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 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 1077 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 272 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 203 optimal weight: 0.7980 chunk 252 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 213 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.109681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.081790 restraints weight = 53696.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.083365 restraints weight = 44578.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.083938 restraints weight = 30084.897| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 26112 Z= 0.128 Angle : 0.582 15.477 35676 Z= 0.290 Chirality : 0.044 0.227 4209 Planarity : 0.004 0.045 4482 Dihedral : 5.410 41.898 4788 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.74 % Allowed : 15.06 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.15), residues: 3084 helix: 0.86 (0.22), residues: 645 sheet: -0.86 (0.19), residues: 726 loop : -1.87 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 633 HIS 0.002 0.000 HIS A 519 PHE 0.025 0.001 PHE C 375 TYR 0.026 0.001 TYR B 170 ARG 0.002 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 48) link_NAG-ASN : angle 2.02533 ( 144) link_BETA1-4 : bond 0.00496 ( 21) link_BETA1-4 : angle 1.16537 ( 63) hydrogen bonds : bond 0.04021 ( 755) hydrogen bonds : angle 4.73044 ( 2013) SS BOND : bond 0.00282 ( 36) SS BOND : angle 1.03002 ( 72) covalent geometry : bond 0.00312 (26007) covalent geometry : angle 0.56632 (35397) *********************** 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 220 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 145 time to evaluate : 2.748 Fit side-chains REVERT: A 375 PHE cc_start: 0.8556 (t80) cc_final: 0.8167 (t80) REVERT: A 421 TYR cc_start: 0.8429 (m-80) cc_final: 0.7908 (m-80) REVERT: B 303 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8189 (pp) REVERT: B 421 TYR cc_start: 0.8405 (m-80) cc_final: 0.7793 (m-80) REVERT: B 780 GLU cc_start: 0.8298 (tt0) cc_final: 0.8010 (tt0) REVERT: C 303 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7930 (pp) REVERT: C 421 TYR cc_start: 0.8396 (m-80) cc_final: 0.7831 (m-80) REVERT: C 855 PHE cc_start: 0.7755 (m-80) cc_final: 0.7388 (m-80) REVERT: C 878 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8703 (tt) outliers start: 75 outliers final: 67 residues processed: 209 average time/residue: 0.2917 time to fit residues: 106.7046 Evaluate side-chains 212 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 142 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 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 231 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 154 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 308 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 chunk 118 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 310 optimal weight: 0.1980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.110646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.081734 restraints weight = 53335.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.085314 restraints weight = 30095.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.086267 restraints weight = 20252.419| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26112 Z= 0.107 Angle : 0.560 15.026 35676 Z= 0.279 Chirality : 0.044 0.232 4209 Planarity : 0.004 0.043 4482 Dihedral : 5.106 40.741 4787 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.56 % Allowed : 15.28 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.15), residues: 3084 helix: 0.91 (0.22), residues: 648 sheet: -0.70 (0.19), residues: 690 loop : -1.77 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 633 HIS 0.002 0.000 HIS A 519 PHE 0.025 0.001 PHE C 375 TYR 0.030 0.001 TYR A 170 ARG 0.001 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 48) link_NAG-ASN : angle 1.91253 ( 144) link_BETA1-4 : bond 0.00516 ( 21) link_BETA1-4 : angle 1.16385 ( 63) hydrogen bonds : bond 0.03614 ( 755) hydrogen bonds : angle 4.60341 ( 2013) SS BOND : bond 0.00235 ( 36) SS BOND : angle 0.91877 ( 72) covalent geometry : bond 0.00251 (26007) covalent geometry : angle 0.54506 (35397) ********************** 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 217 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 147 time to evaluate : 2.911 Fit side-chains revert: symmetry clash REVERT: A 375 PHE cc_start: 0.8509 (t80) cc_final: 0.8135 (t80) REVERT: B 303 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8035 (pp) REVERT: B 421 TYR cc_start: 0.8392 (m-80) cc_final: 0.7693 (m-80) REVERT: B 780 GLU cc_start: 0.8389 (tt0) cc_final: 0.8090 (tt0) REVERT: C 303 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7754 (pp) REVERT: C 421 TYR cc_start: 0.8365 (m-80) cc_final: 0.7680 (m-80) REVERT: C 471 GLU cc_start: 0.6160 (tt0) cc_final: 0.5920 (pp20) REVERT: C 855 PHE cc_start: 0.7734 (m-80) cc_final: 0.7370 (m-80) REVERT: C 878 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8640 (tt) REVERT: C 1029 MET cc_start: 0.9275 (tpp) cc_final: 0.8848 (ttm) outliers start: 70 outliers final: 60 residues processed: 208 average time/residue: 0.2972 time to fit residues: 108.1605 Evaluate side-chains 204 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 141 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 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 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL 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 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 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 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 430 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 chunk 275 optimal weight: 0.3980 chunk 28 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.110828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.085103 restraints weight = 53080.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.085752 restraints weight = 40871.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.086043 restraints weight = 36759.662| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26112 Z= 0.107 Angle : 0.552 11.608 35676 Z= 0.276 Chirality : 0.043 0.224 4209 Planarity : 0.004 0.039 4482 Dihedral : 4.990 40.979 4787 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.45 % Allowed : 15.35 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 3084 helix: 0.88 (0.22), residues: 654 sheet: -0.59 (0.19), residues: 696 loop : -1.73 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 633 HIS 0.002 0.000 HIS A 519 PHE 0.025 0.001 PHE C 375 TYR 0.022 0.001 TYR A 170 ARG 0.001 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 48) link_NAG-ASN : angle 1.87303 ( 144) link_BETA1-4 : bond 0.00509 ( 21) link_BETA1-4 : angle 1.15166 ( 63) hydrogen bonds : bond 0.03590 ( 755) hydrogen bonds : angle 4.56496 ( 2013) SS BOND : bond 0.00233 ( 36) SS BOND : angle 0.87564 ( 72) covalent geometry : bond 0.00253 (26007) covalent geometry : angle 0.53800 (35397) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6493.70 seconds wall clock time: 114 minutes 45.28 seconds (6885.28 seconds total)