Starting phenix.real_space_refine on Mon Aug 25 06:59:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8whw_37550/08_2025/8whw_37550.cif Found real_map, /net/cci-nas-00/data/ceres_data/8whw_37550/08_2025/8whw_37550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8whw_37550/08_2025/8whw_37550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8whw_37550/08_2025/8whw_37550.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8whw_37550/08_2025/8whw_37550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8whw_37550/08_2025/8whw_37550.map" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.058 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 114 5.16 5 C 16452 2.51 5 N 4197 2.21 5 O 5044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25807 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "S" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "T" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.16, per 1000 atoms: 0.20 Number of scatterers: 25807 At special positions: 0 Unit cell: (147, 135, 189, 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 114 16.00 O 5044 8.00 N 4197 7.00 C 16452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.02 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 538 " - pdb=" SG CYS A 590 " 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " 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=2.03 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " 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=2.01 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " BMA D 2 " " NAG E 1 " - " BMA E 2 " " NAG F 1 " - " BMA F 2 " " NAG G 1 " - " BMA G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " BMA L 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " BMA N 2 " " NAG O 1 " - " BMA O 2 " " NAG P 1 " - " BMA P 2 " " NAG Q 1 " - " BMA Q 2 " " NAG R 1 " - " BMA R 2 " " NAG S 1 " - " BMA S 2 " " NAG T 1 " - " BMA T 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 234 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 354 " " NAG B1311 " - " ASN B 343 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 343 " " NAG C1309 " - " ASN C 234 " " NAG C1310 " - " ASN C 331 " " NAG D 1 " - " ASN A 354 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 282 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN C 354 " " NAG P 1 " - " ASN C 282 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C1098 " Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 829.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5958 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 53 sheets defined 25.7% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.547A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.831A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.793A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 616 through 626 removed outlier: 3.581A pdb=" N VAL A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 840 through 844 removed outlier: 4.283A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.602A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.161A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.848A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.502A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.906A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.691A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.680A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.901A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.570A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 626 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.641A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.733A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 844 removed outlier: 4.203A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.666A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.073A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.581A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.802A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.395A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1144 removed outlier: 4.654A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1139 through 1144' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.729A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.874A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.550A pdb=" N GLY C 545 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 627 removed outlier: 3.568A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.573A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.612A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 868 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.310A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.694A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.540A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.726A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.146A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.797A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.681A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.939A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 removed outlier: 4.573A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 540 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.645A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.879A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.850A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.814A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.713A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.296A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 713 through 715 removed outlier: 4.059A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 722 removed outlier: 7.254A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 734 removed outlier: 3.759A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.086A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.605A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.524A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.167A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 326 removed outlier: 4.355A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.780A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.701A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.946A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.078A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.723A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.372A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.154A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AE1, first strand: chain 'B' and resid 1077 through 1078 removed outlier: 3.913A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE3, first strand: chain 'C' and resid 26 through 30 removed outlier: 6.948A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR C 95 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.624A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.014A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL C 120 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.403A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.790A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.222A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.818A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 539 through 541 removed outlier: 3.685A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.313A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 713 through 715 removed outlier: 3.732A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.184A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.084A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.506A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 909 hydrogen bonds defined for protein. 2490 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.48 Time building geometry restraints manager: 2.07 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: 4837 1.33 - 1.45: 7048 1.45 - 1.58: 14380 1.58 - 1.70: 1 1.70 - 1.83: 141 Bond restraints: 26407 Sorted by residual: bond pdb=" CA PHE C 216 " pdb=" C PHE C 216 " ideal model delta sigma weight residual 1.534 1.490 0.044 9.50e-03 1.11e+04 2.12e+01 bond pdb=" N THR A 588 " pdb=" CA THR A 588 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.86e+01 bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.74e+01 bond pdb=" CA HIS B 207 " pdb=" C HIS B 207 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.25e-02 6.40e+03 1.72e+01 bond pdb=" CA THR B 208 " pdb=" C THR B 208 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.26e-02 6.30e+03 1.27e+01 ... (remaining 26402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 34999 2.67 - 5.33: 822 5.33 - 8.00: 108 8.00 - 10.67: 9 10.67 - 13.33: 2 Bond angle restraints: 35940 Sorted by residual: angle pdb=" C GLN A 218 " pdb=" N GLY A 219 " pdb=" CA GLY A 219 " ideal model delta sigma weight residual 120.10 113.74 6.36 9.50e-01 1.11e+00 4.49e+01 angle pdb=" N GLY B 213 " pdb=" CA GLY B 213 " pdb=" C GLY B 213 " ideal model delta sigma weight residual 115.21 106.68 8.53 1.30e+00 5.92e-01 4.30e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 118.66 -7.96 1.22e+00 6.72e-01 4.25e+01 angle pdb=" N PRO B 209 " pdb=" CA PRO B 209 " pdb=" C PRO B 209 " ideal model delta sigma weight residual 112.47 99.14 13.33 2.06e+00 2.36e-01 4.19e+01 angle pdb=" N VAL C 570 " pdb=" CA VAL C 570 " pdb=" C VAL C 570 " ideal model delta sigma weight residual 106.21 112.30 -6.09 1.07e+00 8.73e-01 3.24e+01 ... (remaining 35935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.11: 14728 23.11 - 46.21: 1382 46.21 - 69.32: 171 69.32 - 92.42: 139 92.42 - 115.53: 118 Dihedral angle restraints: 16538 sinusoidal: 7262 harmonic: 9276 Sorted by residual: dihedral pdb=" CD ARG C 328 " pdb=" NE ARG C 328 " pdb=" CZ ARG C 328 " pdb=" NH1 ARG C 328 " ideal model delta sinusoidal sigma weight residual 0.00 -64.56 64.56 1 1.00e+01 1.00e-02 5.48e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 39.96 53.04 1 1.00e+01 1.00e-02 3.83e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 142.22 -49.22 1 1.00e+01 1.00e-02 3.33e+01 ... (remaining 16535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 4184 0.182 - 0.364: 58 0.364 - 0.547: 3 0.547 - 0.729: 0 0.729 - 0.911: 3 Chirality restraints: 4248 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.49 -0.91 2.00e-01 2.50e+01 2.07e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.87e+01 ... (remaining 4245 not shown) Planarity restraints: 4604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1303 " 0.251 2.00e-02 2.50e+03 2.09e-01 5.44e+02 pdb=" C7 NAG C1303 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG C1303 " 0.175 2.00e-02 2.50e+03 pdb=" N2 NAG C1303 " -0.345 2.00e-02 2.50e+03 pdb=" O7 NAG C1303 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1303 " -0.240 2.00e-02 2.50e+03 2.06e-01 5.30e+02 pdb=" C7 NAG B1303 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG B1303 " 0.023 2.00e-02 2.50e+03 pdb=" N2 NAG B1303 " 0.345 2.00e-02 2.50e+03 pdb=" O7 NAG B1303 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " -0.212 2.00e-02 2.50e+03 1.78e-01 3.96e+02 pdb=" C7 NAG C1301 " 0.055 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " 0.298 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " 0.006 2.00e-02 2.50e+03 ... (remaining 4601 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 911 2.68 - 3.24: 26089 3.24 - 3.79: 41366 3.79 - 4.35: 53807 4.35 - 4.90: 87967 Nonbonded interactions: 210140 Sorted by model distance: nonbonded pdb=" O PRO C 486 " pdb=" ND2 ASN C 487 " model vdw 2.128 3.120 nonbonded pdb=" OD1 ASP A 53 " pdb=" N LEU A 54 " model vdw 2.183 3.120 nonbonded pdb=" O ASN C 417 " pdb=" ND2 ASN C 422 " model vdw 2.195 3.120 nonbonded pdb=" CG2 ILE B 210 " pdb=" N ILE B 212 " model vdw 2.199 3.540 nonbonded pdb=" OG1 THR C 393 " pdb=" OE1 GLU C 516 " model vdw 2.202 3.040 ... (remaining 210135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 23 through 1310) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.350 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.006 0.093 26510 Z= 0.371 Angle : 0.978 14.259 36210 Z= 0.563 Chirality : 0.065 0.911 4248 Planarity : 0.012 0.444 4557 Dihedral : 21.278 115.525 10463 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.80 % Favored : 90.63 % Rotamer: Outliers : 1.91 % Allowed : 24.00 % Favored : 74.09 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.14), residues: 3159 helix: 0.49 (0.20), residues: 716 sheet: -1.28 (0.21), residues: 598 loop : -2.18 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 847 TYR 0.022 0.002 TYR B 501 PHE 0.022 0.002 PHE C 338 TRP 0.023 0.002 TRP C 633 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00614 (26407) covalent geometry : angle 0.94732 (35940) SS BOND : bond 0.00474 ( 39) SS BOND : angle 1.43425 ( 78) hydrogen bonds : bond 0.21263 ( 901) hydrogen bonds : angle 8.86076 ( 2490) link_BETA1-4 : bond 0.00532 ( 17) link_BETA1-4 : angle 2.42938 ( 51) link_NAG-ASN : bond 0.00676 ( 47) link_NAG-ASN : angle 3.72299 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 192 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6394 (mmp) cc_final: 0.5799 (mmp) REVERT: A 591 SER cc_start: 0.7715 (t) cc_final: 0.7321 (p) REVERT: A 896 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9053 (mt) REVERT: B 270 LEU cc_start: 0.9136 (mp) cc_final: 0.8626 (mp) REVERT: B 568 ASP cc_start: 0.6673 (t0) cc_final: 0.6455 (t0) REVERT: B 619 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8081 (tm-30) REVERT: B 740 MET cc_start: 0.8058 (ttm) cc_final: 0.7768 (ttm) REVERT: B 773 GLU cc_start: 0.6789 (tm-30) cc_final: 0.6536 (tm-30) REVERT: B 850 ILE cc_start: 0.7890 (mm) cc_final: 0.7458 (mm) REVERT: C 303 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8886 (pp) REVERT: C 327 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.9119 (t) REVERT: C 453 TYR cc_start: 0.7355 (p90) cc_final: 0.7127 (p90) outliers start: 53 outliers final: 17 residues processed: 236 average time/residue: 0.1502 time to fit residues: 57.6521 Evaluate side-chains 172 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 532 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 409 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 804 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.097572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.070843 restraints weight = 84320.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.072936 restraints weight = 47403.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.074320 restraints weight = 32607.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.075244 restraints weight = 25488.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.075805 restraints weight = 21768.130| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26510 Z= 0.157 Angle : 0.776 15.321 36210 Z= 0.374 Chirality : 0.051 0.614 4248 Planarity : 0.005 0.065 4557 Dihedral : 15.064 112.019 4785 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.47 % Favored : 92.31 % Rotamer: Outliers : 3.96 % Allowed : 22.05 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.14), residues: 3159 helix: 1.00 (0.20), residues: 701 sheet: -1.20 (0.20), residues: 619 loop : -1.97 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 847 TYR 0.021 0.001 TYR B 501 PHE 0.022 0.001 PHE B 216 TRP 0.027 0.002 TRP B 633 HIS 0.003 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00349 (26407) covalent geometry : angle 0.72646 (35940) SS BOND : bond 0.00456 ( 39) SS BOND : angle 1.90775 ( 78) hydrogen bonds : bond 0.04634 ( 901) hydrogen bonds : angle 6.40289 ( 2490) link_BETA1-4 : bond 0.00586 ( 17) link_BETA1-4 : angle 3.23272 ( 51) link_NAG-ASN : bond 0.00629 ( 47) link_NAG-ASN : angle 3.78358 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 191 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9343 (t) cc_final: 0.8926 (p) REVERT: A 630 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8147 (m) REVERT: B 84 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6996 (mm) REVERT: B 104 TRP cc_start: 0.6340 (m-10) cc_final: 0.6078 (m-10) REVERT: B 164 ASN cc_start: 0.3418 (OUTLIER) cc_final: 0.3048 (p0) REVERT: B 270 LEU cc_start: 0.9163 (mp) cc_final: 0.8852 (mp) REVERT: B 304 LYS cc_start: 0.9472 (OUTLIER) cc_final: 0.9119 (mtmt) REVERT: B 734 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8773 (p) REVERT: B 740 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7926 (ttm) REVERT: B 773 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7002 (tm-30) REVERT: B 850 ILE cc_start: 0.7777 (mm) cc_final: 0.7352 (mm) REVERT: B 873 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.8071 (t80) REVERT: C 1037 SER cc_start: 0.9156 (OUTLIER) cc_final: 0.8922 (t) outliers start: 110 outliers final: 37 residues processed: 289 average time/residue: 0.1318 time to fit residues: 64.9056 Evaluate side-chains 196 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 271 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 138 optimal weight: 30.0000 chunk 206 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 219 optimal weight: 0.0470 chunk 74 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 overall best weight: 2.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS A1106 GLN B 188 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.093803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.066508 restraints weight = 85693.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.068519 restraints weight = 49440.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.069829 restraints weight = 34372.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.070673 restraints weight = 27219.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.071230 restraints weight = 23436.463| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 26510 Z= 0.214 Angle : 0.770 14.930 36210 Z= 0.372 Chirality : 0.051 0.595 4248 Planarity : 0.005 0.064 4557 Dihedral : 10.457 110.325 4770 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.31 % Favored : 92.62 % Rotamer: Outliers : 4.50 % Allowed : 22.13 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.14), residues: 3159 helix: 0.99 (0.20), residues: 711 sheet: -1.23 (0.20), residues: 569 loop : -1.96 (0.13), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 815 TYR 0.022 0.002 TYR B 501 PHE 0.026 0.002 PHE B 92 TRP 0.023 0.002 TRP A 633 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00484 (26407) covalent geometry : angle 0.72138 (35940) SS BOND : bond 0.00414 ( 39) SS BOND : angle 1.72754 ( 78) hydrogen bonds : bond 0.04424 ( 901) hydrogen bonds : angle 5.92289 ( 2490) link_BETA1-4 : bond 0.00498 ( 17) link_BETA1-4 : angle 3.11927 ( 51) link_NAG-ASN : bond 0.00596 ( 47) link_NAG-ASN : angle 3.81264 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 148 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.7760 (m-80) cc_final: 0.7294 (m-80) REVERT: A 495 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6550 (m-80) REVERT: A 714 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8959 (pt) REVERT: A 816 SER cc_start: 0.8738 (OUTLIER) cc_final: 0.8369 (m) REVERT: A 1039 ARG cc_start: 0.9409 (OUTLIER) cc_final: 0.8286 (ptm160) REVERT: B 84 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7278 (mm) REVERT: B 164 ASN cc_start: 0.3528 (OUTLIER) cc_final: 0.3251 (p0) REVERT: B 270 LEU cc_start: 0.9226 (mp) cc_final: 0.8950 (mp) REVERT: B 613 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8581 (mt0) REVERT: B 698 SER cc_start: 0.8777 (OUTLIER) cc_final: 0.8430 (p) REVERT: B 740 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.8010 (ttm) REVERT: B 773 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7078 (tm-30) REVERT: B 850 ILE cc_start: 0.7963 (mm) cc_final: 0.7563 (mm) REVERT: B 873 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.7927 (t80) REVERT: B 955 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8387 (t0) REVERT: C 918 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7422 (mm-30) REVERT: C 1037 SER cc_start: 0.9229 (OUTLIER) cc_final: 0.8998 (t) outliers start: 125 outliers final: 71 residues processed: 257 average time/residue: 0.1429 time to fit residues: 61.8236 Evaluate side-chains 218 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 134 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 169 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 294 optimal weight: 0.9980 chunk 213 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 218 optimal weight: 0.1980 chunk 70 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1036 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.094453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.067216 restraints weight = 85348.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.069214 restraints weight = 49603.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.070545 restraints weight = 34702.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.071367 restraints weight = 27506.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.071949 restraints weight = 23777.165| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 26510 Z= 0.146 Angle : 0.693 14.867 36210 Z= 0.336 Chirality : 0.049 0.602 4248 Planarity : 0.004 0.072 4557 Dihedral : 8.710 104.478 4769 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.00 % Favored : 92.97 % Rotamer: Outliers : 3.86 % Allowed : 23.03 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.15), residues: 3159 helix: 1.10 (0.20), residues: 717 sheet: -1.13 (0.20), residues: 622 loop : -1.90 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 905 TYR 0.019 0.001 TYR B 265 PHE 0.020 0.001 PHE C 133 TRP 0.032 0.002 TRP B 633 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00335 (26407) covalent geometry : angle 0.64467 (35940) SS BOND : bond 0.00369 ( 39) SS BOND : angle 1.59982 ( 78) hydrogen bonds : bond 0.03970 ( 901) hydrogen bonds : angle 5.64086 ( 2490) link_BETA1-4 : bond 0.00447 ( 17) link_BETA1-4 : angle 2.91944 ( 51) link_NAG-ASN : bond 0.00560 ( 47) link_NAG-ASN : angle 3.61200 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 166 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.7731 (m-80) cc_final: 0.7275 (m-80) REVERT: A 495 TYR cc_start: 0.6961 (OUTLIER) cc_final: 0.6498 (m-80) REVERT: A 592 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7313 (t80) REVERT: A 816 SER cc_start: 0.8753 (OUTLIER) cc_final: 0.8424 (m) REVERT: B 84 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7075 (mm) REVERT: B 270 LEU cc_start: 0.9229 (mp) cc_final: 0.8982 (mp) REVERT: B 592 PHE cc_start: 0.7641 (t80) cc_final: 0.7302 (t80) REVERT: B 613 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8500 (mt0) REVERT: B 740 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7947 (ttm) REVERT: B 773 GLU cc_start: 0.7377 (tm-30) cc_final: 0.6914 (tm-30) REVERT: B 850 ILE cc_start: 0.7863 (mm) cc_final: 0.7499 (mm) REVERT: B 873 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7960 (t80) REVERT: C 918 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7361 (mm-30) REVERT: C 996 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9075 (mm) REVERT: C 1037 SER cc_start: 0.9196 (OUTLIER) cc_final: 0.8919 (t) REVERT: C 1050 MET cc_start: 0.7994 (mtm) cc_final: 0.7741 (mtm) outliers start: 107 outliers final: 63 residues processed: 258 average time/residue: 0.1309 time to fit residues: 57.1002 Evaluate side-chains 212 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 139 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 53 optimal weight: 0.0060 chunk 298 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 29 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 309 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 282 optimal weight: 3.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** 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 = 0.3768 r_free = 0.3768 target = 0.095125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.068117 restraints weight = 86043.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.070075 restraints weight = 50922.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.071379 restraints weight = 35934.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.072223 restraints weight = 28641.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.072770 restraints weight = 24776.340| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26510 Z= 0.127 Angle : 0.677 14.596 36210 Z= 0.328 Chirality : 0.049 0.604 4248 Planarity : 0.004 0.063 4557 Dihedral : 7.925 99.988 4767 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.90 % Favored : 93.07 % Rotamer: Outliers : 3.86 % Allowed : 23.53 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.15), residues: 3159 helix: 1.32 (0.20), residues: 703 sheet: -1.08 (0.20), residues: 631 loop : -1.83 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 454 TYR 0.027 0.001 TYR B 495 PHE 0.019 0.001 PHE B 92 TRP 0.046 0.002 TRP B 104 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00290 (26407) covalent geometry : angle 0.62947 (35940) SS BOND : bond 0.00398 ( 39) SS BOND : angle 1.63157 ( 78) hydrogen bonds : bond 0.03806 ( 901) hydrogen bonds : angle 5.48102 ( 2490) link_BETA1-4 : bond 0.00531 ( 17) link_BETA1-4 : angle 2.56031 ( 51) link_NAG-ASN : bond 0.00561 ( 47) link_NAG-ASN : angle 3.60572 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 166 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6072 (mmp) cc_final: 0.5186 (mmm) REVERT: A 456 PHE cc_start: 0.7644 (m-80) cc_final: 0.7226 (m-80) REVERT: A 495 TYR cc_start: 0.6977 (OUTLIER) cc_final: 0.6434 (m-80) REVERT: B 84 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7118 (mm) REVERT: B 270 LEU cc_start: 0.9135 (mp) cc_final: 0.8896 (mp) REVERT: B 773 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6852 (tm-30) REVERT: B 850 ILE cc_start: 0.7901 (mm) cc_final: 0.7530 (mm) REVERT: B 873 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.7882 (t80) REVERT: C 918 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7315 (mm-30) REVERT: C 996 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9059 (mm) REVERT: C 1037 SER cc_start: 0.9105 (OUTLIER) cc_final: 0.8873 (t) outliers start: 107 outliers final: 69 residues processed: 262 average time/residue: 0.1296 time to fit residues: 58.2987 Evaluate side-chains 213 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 138 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 152 optimal weight: 0.9980 chunk 240 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 301 optimal weight: 5.9990 chunk 292 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 268 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 274 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 GLN B 965 GLN B1010 GLN B1036 GLN B1106 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.091419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.064113 restraints weight = 86801.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.066024 restraints weight = 50849.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.067283 restraints weight = 35758.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.068118 restraints weight = 28477.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.068654 restraints weight = 24611.133| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 26510 Z= 0.242 Angle : 0.745 14.882 36210 Z= 0.366 Chirality : 0.049 0.591 4248 Planarity : 0.005 0.074 4557 Dihedral : 7.941 99.571 4767 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.85 % Favored : 92.12 % Rotamer: Outliers : 4.25 % Allowed : 23.82 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.14), residues: 3159 helix: 1.08 (0.19), residues: 715 sheet: -1.14 (0.20), residues: 640 loop : -1.91 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 847 TYR 0.021 0.002 TYR B 265 PHE 0.018 0.002 PHE B 592 TRP 0.066 0.002 TRP B 104 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00550 (26407) covalent geometry : angle 0.70180 (35940) SS BOND : bond 0.00418 ( 39) SS BOND : angle 1.97414 ( 78) hydrogen bonds : bond 0.04237 ( 901) hydrogen bonds : angle 5.55927 ( 2490) link_BETA1-4 : bond 0.00427 ( 17) link_BETA1-4 : angle 2.39174 ( 51) link_NAG-ASN : bond 0.00586 ( 47) link_NAG-ASN : angle 3.55145 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 136 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7677 (m-40) cc_final: 0.6997 (t0) REVERT: A 177 MET cc_start: 0.6451 (mmp) cc_final: 0.5621 (mmp) REVERT: A 456 PHE cc_start: 0.7610 (m-80) cc_final: 0.7211 (m-80) REVERT: A 495 TYR cc_start: 0.6874 (OUTLIER) cc_final: 0.6246 (m-80) REVERT: B 84 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7261 (mm) REVERT: B 270 LEU cc_start: 0.9275 (mp) cc_final: 0.8978 (mp) REVERT: B 613 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8610 (mt0) REVERT: B 773 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7176 (tm-30) REVERT: C 544 ASN cc_start: 0.8397 (t0) cc_final: 0.8187 (t0) REVERT: C 611 LEU cc_start: 0.9394 (tp) cc_final: 0.9184 (tt) REVERT: C 918 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7706 (mm-30) REVERT: C 955 ASN cc_start: 0.8672 (m-40) cc_final: 0.8297 (t0) REVERT: C 1037 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.9065 (t) REVERT: C 1097 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8266 (p) outliers start: 118 outliers final: 84 residues processed: 244 average time/residue: 0.1296 time to fit residues: 53.8835 Evaluate side-chains 213 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 123 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 79 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 177 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 247 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 0.0070 chunk 87 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 239 GLN A1036 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN B1036 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.093839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.066733 restraints weight = 85784.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.068696 restraints weight = 49701.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.070030 restraints weight = 34855.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.070877 restraints weight = 27578.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.071417 restraints weight = 23803.728| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26510 Z= 0.122 Angle : 0.676 14.526 36210 Z= 0.328 Chirality : 0.048 0.610 4248 Planarity : 0.004 0.055 4557 Dihedral : 7.584 99.179 4767 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.55 % Favored : 93.42 % Rotamer: Outliers : 3.75 % Allowed : 24.47 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.15), residues: 3159 helix: 1.29 (0.20), residues: 710 sheet: -1.09 (0.20), residues: 612 loop : -1.75 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.033 0.001 TYR C 369 PHE 0.015 0.001 PHE B 238 TRP 0.073 0.002 TRP B 104 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00280 (26407) covalent geometry : angle 0.63144 (35940) SS BOND : bond 0.00321 ( 39) SS BOND : angle 1.88977 ( 78) hydrogen bonds : bond 0.03785 ( 901) hydrogen bonds : angle 5.38809 ( 2490) link_BETA1-4 : bond 0.00491 ( 17) link_BETA1-4 : angle 2.20957 ( 51) link_NAG-ASN : bond 0.00535 ( 47) link_NAG-ASN : angle 3.46865 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 153 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.9466 (p) cc_final: 0.9244 (m) REVERT: A 246 ARG cc_start: 0.1440 (OUTLIER) cc_final: -0.1869 (mpt180) REVERT: A 456 PHE cc_start: 0.7627 (m-80) cc_final: 0.7244 (m-80) REVERT: A 495 TYR cc_start: 0.6967 (OUTLIER) cc_final: 0.6361 (m-80) REVERT: B 43 PHE cc_start: 0.6238 (t80) cc_final: 0.6011 (t80) REVERT: B 84 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7245 (mm) REVERT: B 242 LEU cc_start: 0.6556 (mm) cc_final: 0.6274 (mm) REVERT: B 270 LEU cc_start: 0.9204 (mp) cc_final: 0.8951 (mp) REVERT: B 613 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8433 (mt0) REVERT: B 630 THR cc_start: 0.7872 (p) cc_final: 0.7655 (t) REVERT: B 697 MET cc_start: 0.8085 (mmm) cc_final: 0.7624 (mmm) REVERT: B 773 GLU cc_start: 0.7437 (tm-30) cc_final: 0.6987 (tm-30) REVERT: B 873 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7921 (t80) REVERT: C 740 MET cc_start: 0.7366 (ttm) cc_final: 0.6715 (ttm) REVERT: C 918 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: C 996 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9087 (mm) REVERT: C 1037 SER cc_start: 0.9182 (OUTLIER) cc_final: 0.8886 (t) outliers start: 104 outliers final: 69 residues processed: 247 average time/residue: 0.1271 time to fit residues: 53.3654 Evaluate side-chains 217 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 140 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 89 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 76 optimal weight: 30.0000 chunk 242 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 250 optimal weight: 9.9990 chunk 183 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 360 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.092656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.065248 restraints weight = 86362.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.067195 restraints weight = 50701.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.068500 restraints weight = 35723.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.069341 restraints weight = 28384.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.069864 restraints weight = 24533.219| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26510 Z= 0.168 Angle : 0.693 14.617 36210 Z= 0.336 Chirality : 0.048 0.602 4248 Planarity : 0.004 0.053 4557 Dihedral : 7.539 98.788 4767 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.93 % Favored : 93.04 % Rotamer: Outliers : 3.93 % Allowed : 24.11 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.15), residues: 3159 helix: 1.27 (0.20), residues: 715 sheet: -1.12 (0.20), residues: 654 loop : -1.77 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.028 0.001 TYR C 369 PHE 0.026 0.001 PHE A 592 TRP 0.052 0.002 TRP B 104 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00388 (26407) covalent geometry : angle 0.65031 (35940) SS BOND : bond 0.00370 ( 39) SS BOND : angle 1.79730 ( 78) hydrogen bonds : bond 0.03862 ( 901) hydrogen bonds : angle 5.35596 ( 2490) link_BETA1-4 : bond 0.00434 ( 17) link_BETA1-4 : angle 2.17816 ( 51) link_NAG-ASN : bond 0.00518 ( 47) link_NAG-ASN : angle 3.45963 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 140 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.9463 (p) cc_final: 0.9253 (m) REVERT: A 246 ARG cc_start: 0.1665 (OUTLIER) cc_final: -0.1900 (mpt180) REVERT: A 406 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5742 (mp0) REVERT: A 456 PHE cc_start: 0.7531 (m-80) cc_final: 0.7156 (m-80) REVERT: B 43 PHE cc_start: 0.6447 (t80) cc_final: 0.6218 (t80) REVERT: B 242 LEU cc_start: 0.6698 (mm) cc_final: 0.6181 (tp) REVERT: B 270 LEU cc_start: 0.9234 (mp) cc_final: 0.8982 (mp) REVERT: B 630 THR cc_start: 0.7757 (p) cc_final: 0.7504 (t) REVERT: B 697 MET cc_start: 0.8223 (mmm) cc_final: 0.7918 (mmm) REVERT: B 773 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7044 (tm-30) REVERT: B 869 MET cc_start: 0.8547 (ptt) cc_final: 0.8255 (ptt) REVERT: B 873 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.7951 (t80) REVERT: C 918 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7439 (mm-30) REVERT: C 955 ASN cc_start: 0.8640 (m-40) cc_final: 0.8340 (t0) REVERT: C 996 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9100 (mm) REVERT: C 1037 SER cc_start: 0.9212 (OUTLIER) cc_final: 0.8966 (t) outliers start: 109 outliers final: 83 residues processed: 240 average time/residue: 0.1326 time to fit residues: 54.2443 Evaluate side-chains 223 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 134 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 217 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 246 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 315 optimal weight: 7.9990 chunk 76 optimal weight: 30.0000 chunk 101 optimal weight: 0.4980 chunk 42 optimal weight: 20.0000 chunk 68 optimal weight: 0.6980 chunk 237 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A1036 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 532 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.093371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.066465 restraints weight = 86226.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.068394 restraints weight = 51090.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.069692 restraints weight = 36083.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.070533 restraints weight = 28726.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.070930 restraints weight = 24798.304| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26510 Z= 0.134 Angle : 0.683 14.373 36210 Z= 0.329 Chirality : 0.048 0.606 4248 Planarity : 0.004 0.054 4557 Dihedral : 7.346 94.876 4767 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.65 % Favored : 93.32 % Rotamer: Outliers : 3.35 % Allowed : 24.79 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.15), residues: 3159 helix: 1.34 (0.20), residues: 709 sheet: -1.09 (0.20), residues: 636 loop : -1.73 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.031 0.001 TYR C 369 PHE 0.022 0.001 PHE A 592 TRP 0.047 0.002 TRP B 633 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00311 (26407) covalent geometry : angle 0.64148 (35940) SS BOND : bond 0.00331 ( 39) SS BOND : angle 1.66972 ( 78) hydrogen bonds : bond 0.03761 ( 901) hydrogen bonds : angle 5.28239 ( 2490) link_BETA1-4 : bond 0.00475 ( 17) link_BETA1-4 : angle 2.11347 ( 51) link_NAG-ASN : bond 0.00508 ( 47) link_NAG-ASN : angle 3.42384 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 154 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.9467 (p) cc_final: 0.9257 (m) REVERT: A 246 ARG cc_start: 0.1729 (OUTLIER) cc_final: -0.1960 (mpt180) REVERT: A 406 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.5670 (mp0) REVERT: A 456 PHE cc_start: 0.7641 (m-80) cc_final: 0.7239 (m-80) REVERT: A 737 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7690 (p0) REVERT: B 43 PHE cc_start: 0.6438 (t80) cc_final: 0.5939 (t80) REVERT: B 270 LEU cc_start: 0.9212 (mp) cc_final: 0.8954 (mp) REVERT: B 630 THR cc_start: 0.7716 (p) cc_final: 0.7449 (t) REVERT: B 697 MET cc_start: 0.8156 (mmm) cc_final: 0.7876 (mmm) REVERT: B 773 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7159 (tm-30) REVERT: B 774 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8320 (mm-40) REVERT: B 869 MET cc_start: 0.8424 (ptt) cc_final: 0.8081 (ptt) REVERT: B 873 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.8000 (t80) REVERT: C 918 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7511 (mm-30) REVERT: C 996 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9102 (mm) REVERT: C 1037 SER cc_start: 0.9160 (OUTLIER) cc_final: 0.8877 (t) outliers start: 93 outliers final: 80 residues processed: 239 average time/residue: 0.1299 time to fit residues: 52.8741 Evaluate side-chains 230 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 143 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 248 optimal weight: 3.9990 chunk 268 optimal weight: 0.6980 chunk 274 optimal weight: 0.3980 chunk 74 optimal weight: 6.9990 chunk 307 optimal weight: 1.9990 chunk 286 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 284 optimal weight: 0.9990 chunk 257 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1036 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** 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 = 0.3729 r_free = 0.3729 target = 0.093009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.066124 restraints weight = 85866.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.068020 restraints weight = 50913.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.069276 restraints weight = 36108.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.070113 restraints weight = 28868.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.070581 restraints weight = 24964.689| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26510 Z= 0.143 Angle : 0.685 14.450 36210 Z= 0.331 Chirality : 0.048 0.600 4248 Planarity : 0.004 0.054 4557 Dihedral : 7.290 94.360 4767 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.77 % Favored : 93.19 % Rotamer: Outliers : 3.42 % Allowed : 24.83 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.15), residues: 3159 helix: 1.31 (0.20), residues: 712 sheet: -1.06 (0.20), residues: 631 loop : -1.69 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 634 TYR 0.031 0.001 TYR C 369 PHE 0.025 0.001 PHE A 592 TRP 0.052 0.002 TRP B 633 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00332 (26407) covalent geometry : angle 0.64437 (35940) SS BOND : bond 0.00317 ( 39) SS BOND : angle 1.65067 ( 78) hydrogen bonds : bond 0.03757 ( 901) hydrogen bonds : angle 5.26180 ( 2490) link_BETA1-4 : bond 0.00437 ( 17) link_BETA1-4 : angle 2.07971 ( 51) link_NAG-ASN : bond 0.00500 ( 47) link_NAG-ASN : angle 3.40071 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 151 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.9464 (p) cc_final: 0.9253 (m) REVERT: A 121 ASN cc_start: 0.7634 (m-40) cc_final: 0.6880 (t0) REVERT: A 246 ARG cc_start: 0.1858 (OUTLIER) cc_final: -0.1893 (mpt180) REVERT: A 406 GLU cc_start: 0.6084 (OUTLIER) cc_final: 0.5684 (mp0) REVERT: A 456 PHE cc_start: 0.7567 (m-80) cc_final: 0.7174 (m-80) REVERT: A 737 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7704 (p0) REVERT: B 208 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7744 (m) REVERT: B 270 LEU cc_start: 0.9213 (mp) cc_final: 0.8961 (mp) REVERT: B 630 THR cc_start: 0.7886 (p) cc_final: 0.7622 (t) REVERT: B 697 MET cc_start: 0.8184 (mmm) cc_final: 0.7947 (mmm) REVERT: B 773 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7164 (tm-30) REVERT: B 774 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8337 (mm-40) REVERT: B 869 MET cc_start: 0.8421 (ptt) cc_final: 0.8100 (ptt) REVERT: B 873 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7994 (t80) REVERT: C 611 LEU cc_start: 0.9301 (tp) cc_final: 0.9084 (tt) REVERT: C 918 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: C 996 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9091 (mm) REVERT: C 1037 SER cc_start: 0.9145 (OUTLIER) cc_final: 0.8917 (t) outliers start: 95 outliers final: 81 residues processed: 238 average time/residue: 0.1329 time to fit residues: 53.4320 Evaluate side-chains 229 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 140 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 217 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 78 optimal weight: 0.2980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1036 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN C 532 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.093553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.066469 restraints weight = 85732.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.068442 restraints weight = 50003.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.069772 restraints weight = 35092.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070602 restraints weight = 27785.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.071175 restraints weight = 23993.763| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26510 Z= 0.129 Angle : 0.675 14.246 36210 Z= 0.325 Chirality : 0.048 0.599 4248 Planarity : 0.004 0.057 4557 Dihedral : 7.137 94.032 4763 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.68 % Favored : 93.29 % Rotamer: Outliers : 3.46 % Allowed : 25.05 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.15), residues: 3159 helix: 1.39 (0.20), residues: 712 sheet: -1.04 (0.20), residues: 627 loop : -1.69 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 646 TYR 0.032 0.001 TYR C 369 PHE 0.028 0.001 PHE B 92 TRP 0.047 0.002 TRP B 633 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00298 (26407) covalent geometry : angle 0.63529 (35940) SS BOND : bond 0.00298 ( 39) SS BOND : angle 1.51768 ( 78) hydrogen bonds : bond 0.03692 ( 901) hydrogen bonds : angle 5.20845 ( 2490) link_BETA1-4 : bond 0.00484 ( 17) link_BETA1-4 : angle 2.06759 ( 51) link_NAG-ASN : bond 0.00496 ( 47) link_NAG-ASN : angle 3.37413 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3869.98 seconds wall clock time: 68 minutes 5.50 seconds (4085.50 seconds total)