Starting phenix.real_space_refine on Mon Aug 25 06:47:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8whv_37549/08_2025/8whv_37549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8whv_37549/08_2025/8whv_37549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8whv_37549/08_2025/8whv_37549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8whv_37549/08_2025/8whv_37549.map" model { file = "/net/cci-nas-00/data/ceres_data/8whv_37549/08_2025/8whv_37549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8whv_37549/08_2025/8whv_37549.cif" } resolution = 3.32 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= 0.079 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 16458 2.51 5 N 4197 2.21 5 O 5049 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.01s 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: 25818 Number of models: 1 Model: "" Number of chains: 24 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: "U" 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: 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: "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: 4.64, per 1000 atoms: 0.18 Number of scatterers: 25818 At special positions: 0 Unit cell: (144, 144, 170, 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 5049 8.00 N 4197 7.00 C 16458 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=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 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=2.02 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 U 1 " - " BMA U 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG D 1 " - " ASN A 354 " " NAG E 1 " - " ASN A 282 " " 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 354 " " NAG K 1 " - " ASN B 282 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN C 354 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C1134 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C1098 " Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 892.9 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: 68 helices and 52 sheets defined 24.5% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 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: 3.543A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.759A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.883A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.603A 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 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 758 through 783 removed outlier: 4.044A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.704A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.575A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 884 removed outlier: 3.581A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.746A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 Processing helix chain 'A' and resid 965 through 968 removed outlier: 3.674A pdb=" N SER A 968 " --> pdb=" O GLN A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.670A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.038A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.578A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.931A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.519A 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 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.973A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.791A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 869 through 882 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.707A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 937 " --> pdb=" O LYS B 933 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.773A pdb=" N SER B 968 " --> pdb=" O GLN B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.597A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.149A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.814A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.695A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.850A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.581A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.871A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.783A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 868 through 884 removed outlier: 3.615A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.758A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER C 937 " --> pdb=" O LYS C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 Processing helix chain 'C' and resid 965 through 967 No H-bonds generated for 'chain 'C' and resid 965 through 967' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.544A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.026A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.056A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR A 95 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (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: 3.710A 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: 3.903A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.058A 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: 6.979A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.720A 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 565 through 566 removed outlier: 7.019A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.114A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 713 through 715 removed outlier: 3.780A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.206A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.249A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.053A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.594A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.912A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.506A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B 167 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.102A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.934A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.716A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.820A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.038A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.794A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.270A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.248A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 26 through 30 removed outlier: 3.523A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR C 95 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.635A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.072A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 116 through 118 removed outlier: 3.583A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.094A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 326 removed outlier: 6.941A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.578A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA C 435 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.706A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.722A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.099A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 713 through 715 removed outlier: 3.723A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.266A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.196A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 848 hydrogen bonds defined for protein. 2280 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4166 1.32 - 1.44: 7487 1.44 - 1.57: 14624 1.57 - 1.69: 0 1.69 - 1.82: 141 Bond restraints: 26418 Sorted by residual: bond pdb=" CA THR C 208 " pdb=" C THR C 208 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.00e-02 1.00e+04 2.96e+01 bond pdb=" CA THR B 208 " pdb=" C THR B 208 " ideal model delta sigma weight residual 1.520 1.463 0.057 1.18e-02 7.18e+03 2.33e+01 bond pdb=" CA SER B 305 " pdb=" CB SER B 305 " ideal model delta sigma weight residual 1.533 1.459 0.074 1.66e-02 3.63e+03 2.00e+01 bond pdb=" N GLN C 506 " pdb=" CA GLN C 506 " ideal model delta sigma weight residual 1.453 1.490 -0.037 8.30e-03 1.45e+04 1.95e+01 bond pdb=" CA SER C 305 " pdb=" CB SER C 305 " ideal model delta sigma weight residual 1.533 1.461 0.072 1.65e-02 3.67e+03 1.89e+01 ... (remaining 26413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 35149 2.72 - 5.44: 709 5.44 - 8.17: 86 8.17 - 10.89: 7 10.89 - 13.61: 4 Bond angle restraints: 35955 Sorted by residual: angle pdb=" N THR C 302 " pdb=" CA THR C 302 " pdb=" C THR C 302 " ideal model delta sigma weight residual 113.55 102.10 11.45 1.26e+00 6.30e-01 8.25e+01 angle pdb=" N THR B 302 " pdb=" CA THR B 302 " pdb=" C THR B 302 " ideal model delta sigma weight residual 114.04 102.96 11.08 1.24e+00 6.50e-01 7.99e+01 angle pdb=" N THR A 302 " pdb=" CA THR A 302 " pdb=" C THR A 302 " ideal model delta sigma weight residual 114.04 103.44 10.60 1.24e+00 6.50e-01 7.31e+01 angle pdb=" N GLY C 213 " pdb=" CA GLY C 213 " pdb=" C GLY C 213 " ideal model delta sigma weight residual 115.32 105.78 9.54 1.31e+00 5.83e-01 5.30e+01 angle pdb=" N LEU B 303 " pdb=" CA LEU B 303 " pdb=" C LEU B 303 " ideal model delta sigma weight residual 112.93 104.80 8.13 1.12e+00 7.97e-01 5.27e+01 ... (remaining 35950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.54: 15049 24.54 - 49.09: 1146 49.09 - 73.63: 132 73.63 - 98.18: 120 98.18 - 122.72: 110 Dihedral angle restraints: 16557 sinusoidal: 7281 harmonic: 9276 Sorted by residual: dihedral pdb=" CA ILE C 210 " pdb=" C ILE C 210 " pdb=" N ILE C 212 " pdb=" CA ILE C 212 " ideal model delta harmonic sigma weight residual 180.00 57.28 122.72 0 5.00e+00 4.00e-02 6.02e+02 dihedral pdb=" CA ILE B 210 " pdb=" C ILE B 210 " pdb=" N ILE B 212 " pdb=" CA ILE B 212 " ideal model delta harmonic sigma weight residual 180.00 75.51 104.49 0 5.00e+00 4.00e-02 4.37e+02 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 41.22 51.78 1 1.00e+01 1.00e-02 3.66e+01 ... (remaining 16554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.195: 4214 0.195 - 0.390: 37 0.390 - 0.586: 0 0.586 - 0.781: 0 0.781 - 0.976: 3 Chirality restraints: 4254 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-01 2.50e+01 2.38e+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 -1.43 -0.97 2.00e-01 2.50e+01 2.37e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.27e+01 ... (remaining 4251 not shown) Planarity restraints: 4605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 34 " -0.534 9.50e-02 1.11e+02 2.39e-01 3.50e+01 pdb=" NE ARG B 34 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG B 34 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 34 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 34 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 34 " 0.500 9.50e-02 1.11e+02 2.24e-01 3.07e+01 pdb=" NE ARG A 34 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 34 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 34 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 34 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 509 " -0.418 9.50e-02 1.11e+02 1.87e-01 2.14e+01 pdb=" NE ARG B 509 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 509 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 509 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 509 " -0.014 2.00e-02 2.50e+03 ... (remaining 4602 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 308 2.56 - 3.15: 21048 3.15 - 3.73: 39185 3.73 - 4.32: 55959 4.32 - 4.90: 93131 Nonbonded interactions: 209631 Sorted by model distance: nonbonded pdb=" CD1 ILE B 210 " pdb=" CA GLY B 213 " model vdw 1.979 3.860 nonbonded pdb=" OH TYR B 837 " pdb=" O CYS C 590 " model vdw 2.086 3.040 nonbonded pdb=" CD1 ILE B 210 " pdb=" O ILE B 212 " model vdw 2.097 3.460 nonbonded pdb=" O CYS A 590 " pdb=" OH TYR C 837 " model vdw 2.105 3.040 nonbonded pdb=" OH TYR A 837 " pdb=" O CYS B 590 " model vdw 2.121 3.040 ... (remaining 209626 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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' selection = chain 'U' } 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 individual isotropic 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 20.990 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.005 0.076 26523 Z= 0.290 Angle : 0.960 15.001 36231 Z= 0.540 Chirality : 0.060 0.976 4254 Planarity : 0.008 0.239 4557 Dihedral : 20.849 122.721 10482 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.14 % Favored : 91.71 % Rotamer: Outliers : 1.19 % Allowed : 21.08 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.10 (0.15), residues: 3159 helix: 0.04 (0.21), residues: 672 sheet: -1.19 (0.20), residues: 645 loop : -2.10 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 509 TYR 0.029 0.002 TYR C 501 PHE 0.024 0.002 PHE A 759 TRP 0.061 0.003 TRP B 633 HIS 0.007 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00508 (26418) covalent geometry : angle 0.92492 (35955) SS BOND : bond 0.00511 ( 39) SS BOND : angle 1.93810 ( 78) hydrogen bonds : bond 0.19655 ( 848) hydrogen bonds : angle 8.31691 ( 2280) link_BETA1-4 : bond 0.00511 ( 18) link_BETA1-4 : angle 2.26525 ( 54) link_NAG-ASN : bond 0.00657 ( 48) link_NAG-ASN : angle 3.75817 ( 144) *********************** 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 271 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.730 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: A 53 ASP cc_start: 0.7926 (t0) cc_final: 0.7585 (t0) REVERT: A 505 HIS cc_start: -0.2529 (OUTLIER) cc_final: -0.4119 (m-70) REVERT: B 32 PHE cc_start: 0.8522 (m-10) cc_final: 0.8247 (m-10) REVERT: B 43 PHE cc_start: 0.8892 (t80) cc_final: 0.8534 (t80) REVERT: B 389 ASP cc_start: 0.7473 (m-30) cc_final: 0.7207 (m-30) REVERT: B 505 HIS cc_start: -0.2396 (OUTLIER) cc_final: -0.3895 (m90) REVERT: B 641 ASN cc_start: 0.8081 (m-40) cc_final: 0.7831 (p0) REVERT: B 856 ASN cc_start: 0.7889 (m-40) cc_final: 0.7534 (p0) REVERT: B 994 ASP cc_start: 0.8652 (t70) cc_final: 0.8239 (t0) REVERT: C 214 ARG cc_start: 0.2202 (OUTLIER) cc_final: 0.1213 (ppt90) REVERT: C 505 HIS cc_start: -0.2607 (OUTLIER) cc_final: -0.3993 (m-70) REVERT: C 508 TYR cc_start: 0.8430 (m-80) cc_final: 0.8051 (m-80) outliers start: 33 outliers final: 15 residues processed: 267 average time/residue: 0.1252 time to fit residues: 55.9731 Evaluate side-chains 212 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.0000 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS B 81 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 505 HIS C 675 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.132281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.101742 restraints weight = 46044.790| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.31 r_work: 0.3343 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 26523 Z= 0.170 Angle : 0.759 15.369 36231 Z= 0.368 Chirality : 0.052 0.664 4254 Planarity : 0.005 0.046 4557 Dihedral : 14.887 109.040 4802 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.25 % Favored : 92.66 % Rotamer: Outliers : 3.46 % Allowed : 19.06 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.84 (0.15), residues: 3159 helix: 0.33 (0.21), residues: 681 sheet: -0.83 (0.21), residues: 642 loop : -2.07 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 214 TYR 0.023 0.001 TYR C 501 PHE 0.014 0.002 PHE B 377 TRP 0.024 0.002 TRP A 633 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00392 (26418) covalent geometry : angle 0.71206 (35955) SS BOND : bond 0.00498 ( 39) SS BOND : angle 1.59151 ( 78) hydrogen bonds : bond 0.04272 ( 848) hydrogen bonds : angle 6.05289 ( 2280) link_BETA1-4 : bond 0.00611 ( 18) link_BETA1-4 : angle 3.26200 ( 54) link_NAG-ASN : bond 0.00654 ( 48) link_NAG-ASN : angle 3.62805 ( 144) *********************** 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 322 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 226 time to evaluate : 0.748 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: symmetry clash REVERT: A 53 ASP cc_start: 0.8046 (t0) cc_final: 0.7841 (t0) REVERT: A 505 HIS cc_start: -0.1955 (OUTLIER) cc_final: -0.3669 (m90) REVERT: A 988 GLU cc_start: 0.8449 (tp30) cc_final: 0.8198 (tp30) REVERT: B 43 PHE cc_start: 0.8845 (t80) cc_final: 0.8443 (t80) REVERT: B 334 ASN cc_start: 0.6708 (OUTLIER) cc_final: 0.6390 (p0) REVERT: B 360 ASN cc_start: 0.8253 (t0) cc_final: 0.8019 (t0) REVERT: B 369 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7351 (t80) REVERT: B 389 ASP cc_start: 0.7602 (m-30) cc_final: 0.7332 (m-30) REVERT: B 421 TYR cc_start: 0.9010 (m-10) cc_final: 0.8762 (m-10) REVERT: B 495 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.6371 (t80) REVERT: B 581 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8119 (p) REVERT: B 988 GLU cc_start: 0.8838 (tp30) cc_final: 0.8605 (tp30) REVERT: B 994 ASP cc_start: 0.8579 (t70) cc_final: 0.8219 (t0) REVERT: C 53 ASP cc_start: 0.7995 (t0) cc_final: 0.7731 (t0) REVERT: C 134 GLN cc_start: 0.6673 (OUTLIER) cc_final: 0.6227 (tm-30) REVERT: C 214 ARG cc_start: 0.3582 (OUTLIER) cc_final: 0.3277 (ptt90) REVERT: C 334 ASN cc_start: 0.6807 (OUTLIER) cc_final: 0.6449 (p0) REVERT: C 421 TYR cc_start: 0.8657 (m-10) cc_final: 0.8391 (m-10) REVERT: C 424 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7378 (tptm) REVERT: C 505 HIS cc_start: -0.1267 (OUTLIER) cc_final: -0.2670 (m90) REVERT: C 780 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8421 (tt0) REVERT: C 994 ASP cc_start: 0.8221 (t70) cc_final: 0.7890 (t0) outliers start: 96 outliers final: 43 residues processed: 306 average time/residue: 0.1225 time to fit residues: 63.1688 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 : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 9 optimal weight: 1.9990 chunk 256 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 12 optimal weight: 0.0060 chunk 127 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 218 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 267 optimal weight: 5.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.129708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099007 restraints weight = 46376.485| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.30 r_work: 0.3291 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 26523 Z= 0.200 Angle : 0.747 15.170 36231 Z= 0.367 Chirality : 0.053 0.667 4254 Planarity : 0.005 0.044 4557 Dihedral : 11.091 102.615 4792 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.19 % Favored : 92.72 % Rotamer: Outliers : 4.22 % Allowed : 20.29 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.82 (0.15), residues: 3159 helix: 0.43 (0.20), residues: 690 sheet: -1.03 (0.21), residues: 645 loop : -2.01 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1000 TYR 0.021 0.001 TYR B 501 PHE 0.013 0.002 PHE B 939 TRP 0.029 0.003 TRP A 633 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00460 (26418) covalent geometry : angle 0.69705 (35955) SS BOND : bond 0.00514 ( 39) SS BOND : angle 2.47471 ( 78) hydrogen bonds : bond 0.04472 ( 848) hydrogen bonds : angle 5.93391 ( 2280) link_BETA1-4 : bond 0.00573 ( 18) link_BETA1-4 : angle 2.94411 ( 54) link_NAG-ASN : bond 0.00824 ( 48) link_NAG-ASN : angle 3.53902 ( 144) *********************** 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 348 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 231 time to evaluate : 0.655 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: symmetry clash REVERT: A 129 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6682 (ptpt) REVERT: A 200 TYR cc_start: 0.7691 (OUTLIER) cc_final: 0.7056 (m-80) REVERT: A 369 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7011 (t80) REVERT: A 402 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8354 (pp) REVERT: A 505 HIS cc_start: -0.2019 (OUTLIER) cc_final: -0.3980 (m90) REVERT: A 988 GLU cc_start: 0.8482 (tp30) cc_final: 0.8210 (tp30) REVERT: A 994 ASP cc_start: 0.8491 (t70) cc_final: 0.8240 (t0) REVERT: B 43 PHE cc_start: 0.8985 (t80) cc_final: 0.8742 (t80) REVERT: B 200 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.7366 (t80) REVERT: B 360 ASN cc_start: 0.8316 (t0) cc_final: 0.8111 (t0) REVERT: B 369 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7391 (t80) REVERT: B 402 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.7764 (pp) REVERT: B 495 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.6176 (t80) REVERT: B 581 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8068 (p) REVERT: B 988 GLU cc_start: 0.8797 (tp30) cc_final: 0.8556 (tp30) REVERT: C 53 ASP cc_start: 0.8053 (t0) cc_final: 0.7820 (t0) REVERT: C 66 HIS cc_start: 0.8287 (OUTLIER) cc_final: 0.7075 (m-70) REVERT: C 134 GLN cc_start: 0.6622 (OUTLIER) cc_final: 0.6222 (tm-30) REVERT: C 200 TYR cc_start: 0.7454 (OUTLIER) cc_final: 0.7207 (t80) REVERT: C 334 ASN cc_start: 0.6762 (OUTLIER) cc_final: 0.6433 (p0) REVERT: C 402 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8250 (pp) REVERT: C 421 TYR cc_start: 0.8672 (m-10) cc_final: 0.8364 (m-10) REVERT: C 424 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7473 (tptm) REVERT: C 495 TYR cc_start: 0.7333 (OUTLIER) cc_final: 0.6225 (t80) REVERT: C 505 HIS cc_start: -0.1904 (OUTLIER) cc_final: -0.3225 (m90) REVERT: C 552 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8365 (mt) REVERT: C 578 ASP cc_start: 0.8188 (t70) cc_final: 0.7755 (t70) REVERT: C 780 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8437 (tt0) REVERT: C 994 ASP cc_start: 0.8344 (t70) cc_final: 0.8101 (t0) outliers start: 117 outliers final: 56 residues processed: 329 average time/residue: 0.1181 time to fit residues: 64.9476 Evaluate side-chains 267 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 192 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 280 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 147 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 241 optimal weight: 7.9990 chunk 263 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 295 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 804 GLN B 965 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.128124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.097282 restraints weight = 45824.938| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.28 r_work: 0.3262 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.005 0.082 26523 Z= 0.203 Angle : 0.725 15.115 36231 Z= 0.357 Chirality : 0.051 0.659 4254 Planarity : 0.005 0.043 4557 Dihedral : 9.090 94.407 4788 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.50 % Favored : 92.40 % Rotamer: Outliers : 4.58 % Allowed : 20.36 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.79 (0.15), residues: 3159 helix: 0.56 (0.21), residues: 690 sheet: -1.11 (0.20), residues: 633 loop : -1.99 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 214 TYR 0.028 0.001 TYR C 501 PHE 0.020 0.002 PHE A 133 TRP 0.025 0.002 TRP C 452 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00476 (26418) covalent geometry : angle 0.67514 (35955) SS BOND : bond 0.00671 ( 39) SS BOND : angle 2.46462 ( 78) hydrogen bonds : bond 0.04188 ( 848) hydrogen bonds : angle 5.79693 ( 2280) link_BETA1-4 : bond 0.00439 ( 18) link_BETA1-4 : angle 2.79970 ( 54) link_NAG-ASN : bond 0.00642 ( 48) link_NAG-ASN : angle 3.50242 ( 144) *********************** 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 360 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 233 time to evaluate : 0.962 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: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8025 (t0) cc_final: 0.7770 (t0) REVERT: A 129 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6769 (ptpt) REVERT: A 160 TYR cc_start: 0.5915 (p90) cc_final: 0.5509 (p90) REVERT: A 200 TYR cc_start: 0.7718 (OUTLIER) cc_final: 0.7117 (m-80) REVERT: A 369 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.7035 (t80) REVERT: A 402 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8245 (pp) REVERT: A 505 HIS cc_start: -0.2244 (OUTLIER) cc_final: -0.4289 (m90) REVERT: A 988 GLU cc_start: 0.8602 (tp30) cc_final: 0.8229 (tp30) REVERT: B 43 PHE cc_start: 0.9019 (t80) cc_final: 0.8815 (t80) REVERT: B 134 GLN cc_start: 0.6654 (OUTLIER) cc_final: 0.6253 (tm-30) REVERT: B 200 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.7415 (t80) REVERT: B 360 ASN cc_start: 0.8384 (t0) cc_final: 0.8176 (t0) REVERT: B 369 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7461 (t80) REVERT: B 402 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7810 (pp) REVERT: B 495 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6089 (t80) REVERT: B 552 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8471 (mt) REVERT: B 823 PHE cc_start: 0.7956 (m-80) cc_final: 0.7537 (m-10) REVERT: B 867 ASP cc_start: 0.8585 (t0) cc_final: 0.8253 (t0) REVERT: B 988 GLU cc_start: 0.8817 (tp30) cc_final: 0.8538 (tp30) REVERT: C 66 HIS cc_start: 0.8414 (OUTLIER) cc_final: 0.6965 (m-70) REVERT: C 127 PHE cc_start: 0.6560 (t80) cc_final: 0.6298 (t80) REVERT: C 200 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.6746 (m-80) REVERT: C 229 LEU cc_start: 0.7167 (pt) cc_final: 0.6777 (mp) REVERT: C 334 ASN cc_start: 0.6677 (OUTLIER) cc_final: 0.6436 (p0) REVERT: C 402 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8158 (pp) REVERT: C 421 TYR cc_start: 0.8720 (m-10) cc_final: 0.8385 (m-10) REVERT: C 424 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7438 (tptm) REVERT: C 495 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.6194 (t80) REVERT: C 505 HIS cc_start: -0.2145 (OUTLIER) cc_final: -0.3492 (m90) REVERT: C 578 ASP cc_start: 0.8169 (t70) cc_final: 0.7405 (t70) REVERT: C 780 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8454 (tt0) REVERT: C 994 ASP cc_start: 0.8396 (t70) cc_final: 0.8169 (t0) outliers start: 127 outliers final: 76 residues processed: 333 average time/residue: 0.1329 time to fit residues: 73.5438 Evaluate side-chains 296 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 202 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 280 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 chunk 204 optimal weight: 3.9990 chunk 110 optimal weight: 0.0970 chunk 281 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN A 907 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 628 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.129224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.098422 restraints weight = 45740.636| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.28 r_work: 0.3278 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 26523 Z= 0.155 Angle : 0.685 14.819 36231 Z= 0.336 Chirality : 0.050 0.645 4254 Planarity : 0.004 0.039 4557 Dihedral : 8.435 92.239 4787 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.84 % Favored : 93.07 % Rotamer: Outliers : 4.72 % Allowed : 20.72 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 (0.15), residues: 3159 helix: 0.70 (0.21), residues: 690 sheet: -0.93 (0.20), residues: 615 loop : -1.93 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 319 TYR 0.017 0.001 TYR B 265 PHE 0.020 0.001 PHE A 133 TRP 0.021 0.001 TRP C 452 HIS 0.003 0.000 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00363 (26418) covalent geometry : angle 0.63635 (35955) SS BOND : bond 0.00672 ( 39) SS BOND : angle 2.16358 ( 78) hydrogen bonds : bond 0.03937 ( 848) hydrogen bonds : angle 5.71891 ( 2280) link_BETA1-4 : bond 0.00465 ( 18) link_BETA1-4 : angle 2.57203 ( 54) link_NAG-ASN : bond 0.00602 ( 48) link_NAG-ASN : angle 3.44117 ( 144) *********************** 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 356 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 225 time to evaluate : 1.086 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8023 (t0) cc_final: 0.7790 (t0) REVERT: A 129 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6800 (ptpt) REVERT: A 160 TYR cc_start: 0.5967 (p90) cc_final: 0.5564 (p90) REVERT: A 200 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.7003 (m-80) REVERT: A 269 TYR cc_start: 0.8584 (m-80) cc_final: 0.8371 (m-10) REVERT: A 366 SER cc_start: 0.8457 (m) cc_final: 0.8144 (p) REVERT: A 369 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.7046 (t80) REVERT: A 402 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8000 (pp) REVERT: A 495 TYR cc_start: 0.7262 (OUTLIER) cc_final: 0.6060 (t80) REVERT: A 501 TYR cc_start: 0.5571 (m-80) cc_final: 0.5339 (m-80) REVERT: A 505 HIS cc_start: -0.2711 (OUTLIER) cc_final: -0.4714 (m90) REVERT: A 816 SER cc_start: 0.9323 (OUTLIER) cc_final: 0.8917 (m) REVERT: A 858 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7275 (mt) REVERT: A 988 GLU cc_start: 0.8563 (tp30) cc_final: 0.8240 (tp30) REVERT: B 200 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.7415 (t80) REVERT: B 360 ASN cc_start: 0.8449 (t0) cc_final: 0.8231 (t0) REVERT: B 369 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.7449 (t80) REVERT: B 402 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7663 (pp) REVERT: B 421 TYR cc_start: 0.8867 (m-10) cc_final: 0.8398 (m-10) REVERT: B 495 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.5858 (t80) REVERT: B 552 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8412 (mt) REVERT: B 823 PHE cc_start: 0.7878 (m-80) cc_final: 0.7395 (m-10) REVERT: B 867 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8263 (t0) REVERT: B 988 GLU cc_start: 0.8843 (tp30) cc_final: 0.8589 (tp30) REVERT: C 66 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.6844 (m-70) REVERT: C 200 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6753 (m-80) REVERT: C 346 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7570 (tpt170) REVERT: C 402 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8186 (pp) REVERT: C 421 TYR cc_start: 0.8705 (m-10) cc_final: 0.8316 (m-10) REVERT: C 424 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7407 (tptm) REVERT: C 495 TYR cc_start: 0.7391 (OUTLIER) cc_final: 0.6173 (t80) REVERT: C 505 HIS cc_start: -0.1961 (OUTLIER) cc_final: -0.3506 (m90) REVERT: C 552 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8392 (mt) REVERT: C 578 ASP cc_start: 0.8212 (t70) cc_final: 0.7759 (t70) REVERT: C 780 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8346 (tt0) REVERT: C 994 ASP cc_start: 0.8320 (t70) cc_final: 0.7955 (t0) REVERT: C 998 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8977 (m) REVERT: C 1039 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8910 (ptm160) outliers start: 131 outliers final: 77 residues processed: 331 average time/residue: 0.1321 time to fit residues: 73.4788 Evaluate side-chains 302 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 201 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 547 THR 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 632 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 106 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.125463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.093871 restraints weight = 46568.799| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.31 r_work: 0.3216 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 26523 Z= 0.240 Angle : 0.742 14.783 36231 Z= 0.366 Chirality : 0.051 0.667 4254 Planarity : 0.005 0.042 4557 Dihedral : 8.206 90.958 4786 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.72 % Favored : 92.18 % Rotamer: Outliers : 5.26 % Allowed : 20.97 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.72 (0.15), residues: 3159 helix: 0.63 (0.21), residues: 690 sheet: -1.20 (0.20), residues: 651 loop : -1.90 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 319 TYR 0.024 0.002 TYR B 265 PHE 0.021 0.002 PHE C 823 TRP 0.023 0.002 TRP B 452 HIS 0.006 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00566 (26418) covalent geometry : angle 0.69689 (35955) SS BOND : bond 0.00479 ( 39) SS BOND : angle 2.41013 ( 78) hydrogen bonds : bond 0.04259 ( 848) hydrogen bonds : angle 5.70192 ( 2280) link_BETA1-4 : bond 0.00399 ( 18) link_BETA1-4 : angle 2.35636 ( 54) link_NAG-ASN : bond 0.00616 ( 48) link_NAG-ASN : angle 3.49121 ( 144) *********************** 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 366 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 220 time to evaluate : 0.891 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 129 LYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6533 (ptmm) REVERT: A 131 CYS cc_start: 0.4492 (t) cc_final: 0.4047 (t) REVERT: A 200 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7113 (m-80) REVERT: A 324 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7456 (tm-30) REVERT: A 366 SER cc_start: 0.8438 (m) cc_final: 0.8142 (p) REVERT: A 369 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.7036 (t80) REVERT: A 402 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8051 (pp) REVERT: A 495 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6148 (t80) REVERT: A 501 TYR cc_start: 0.5357 (m-80) cc_final: 0.5118 (m-80) REVERT: A 505 HIS cc_start: -0.2064 (OUTLIER) cc_final: -0.4033 (m90) REVERT: A 816 SER cc_start: 0.9306 (OUTLIER) cc_final: 0.8918 (m) REVERT: A 858 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7739 (mt) REVERT: A 988 GLU cc_start: 0.8753 (tp30) cc_final: 0.8355 (tp30) REVERT: B 131 CYS cc_start: 0.3182 (t) cc_final: 0.2717 (t) REVERT: B 200 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7475 (t80) REVERT: B 369 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.7546 (t80) REVERT: B 402 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.7860 (pp) REVERT: B 421 TYR cc_start: 0.8874 (m-10) cc_final: 0.8340 (m-10) REVERT: B 495 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.5796 (t80) REVERT: B 552 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8657 (mt) REVERT: B 823 PHE cc_start: 0.7979 (m-80) cc_final: 0.7474 (m-80) REVERT: B 867 ASP cc_start: 0.8643 (t0) cc_final: 0.8291 (t0) REVERT: B 988 GLU cc_start: 0.8812 (tp30) cc_final: 0.8574 (tp30) REVERT: B 994 ASP cc_start: 0.8654 (t70) cc_final: 0.8365 (t0) REVERT: C 66 HIS cc_start: 0.8541 (OUTLIER) cc_final: 0.6815 (m-70) REVERT: C 129 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.6796 (ptmm) REVERT: C 131 CYS cc_start: 0.2932 (t) cc_final: 0.2433 (t) REVERT: C 200 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.6911 (m-80) REVERT: C 346 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7582 (tpt170) REVERT: C 402 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8195 (pp) REVERT: C 421 TYR cc_start: 0.8829 (m-10) cc_final: 0.8472 (m-10) REVERT: C 424 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7480 (tptm) REVERT: C 495 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.6243 (t80) REVERT: C 505 HIS cc_start: -0.2744 (OUTLIER) cc_final: -0.4285 (m90) REVERT: C 552 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8487 (mt) REVERT: C 568 ASP cc_start: 0.7546 (t0) cc_final: 0.7223 (t0) REVERT: C 578 ASP cc_start: 0.8186 (t70) cc_final: 0.7464 (t70) REVERT: C 780 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8485 (tt0) REVERT: C 998 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.9063 (m) outliers start: 146 outliers final: 85 residues processed: 338 average time/residue: 0.1396 time to fit residues: 78.4016 Evaluate side-chains 314 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 205 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 547 THR 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 632 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 68 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 313 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 200 optimal weight: 0.6980 chunk 247 optimal weight: 2.9990 chunk 274 optimal weight: 8.9990 chunk 146 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 203 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 955 ASN ** C1002 GLN ** 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 = 0.3853 r_free = 0.3853 target = 0.128334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.097196 restraints weight = 46051.231| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.31 r_work: 0.3276 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26523 Z= 0.137 Angle : 0.681 14.554 36231 Z= 0.334 Chirality : 0.049 0.646 4254 Planarity : 0.004 0.038 4557 Dihedral : 7.914 88.746 4786 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.84 % Favored : 93.07 % Rotamer: Outliers : 4.54 % Allowed : 21.80 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.59 (0.15), residues: 3159 helix: 0.74 (0.21), residues: 690 sheet: -0.94 (0.21), residues: 612 loop : -1.87 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.022 0.001 TYR B 170 PHE 0.018 0.001 PHE C 823 TRP 0.019 0.001 TRP B 452 HIS 0.003 0.000 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00320 (26418) covalent geometry : angle 0.63650 (35955) SS BOND : bond 0.00373 ( 39) SS BOND : angle 2.01012 ( 78) hydrogen bonds : bond 0.03807 ( 848) hydrogen bonds : angle 5.59839 ( 2280) link_BETA1-4 : bond 0.00487 ( 18) link_BETA1-4 : angle 2.20272 ( 54) link_NAG-ASN : bond 0.00568 ( 48) link_NAG-ASN : angle 3.40677 ( 144) *********************** 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 361 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 235 time to evaluate : 0.773 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: A 160 TYR cc_start: 0.6066 (p90) cc_final: 0.5798 (p90) REVERT: A 200 TYR cc_start: 0.7642 (OUTLIER) cc_final: 0.6988 (m-80) REVERT: A 324 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: A 369 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.6989 (t80) REVERT: A 402 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.7951 (pp) REVERT: A 495 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.6096 (t80) REVERT: A 505 HIS cc_start: -0.1886 (OUTLIER) cc_final: -0.3934 (m90) REVERT: A 816 SER cc_start: 0.9301 (OUTLIER) cc_final: 0.8937 (m) REVERT: A 988 GLU cc_start: 0.8649 (tp30) cc_final: 0.8351 (tp30) REVERT: B 40 ASP cc_start: 0.8373 (m-30) cc_final: 0.8140 (m-30) REVERT: B 200 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.7400 (t80) REVERT: B 369 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7432 (t80) REVERT: B 383 SER cc_start: 0.8817 (t) cc_final: 0.8233 (p) REVERT: B 402 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7724 (pp) REVERT: B 421 TYR cc_start: 0.8868 (m-10) cc_final: 0.8277 (m-10) REVERT: B 495 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.5775 (t80) REVERT: B 552 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8607 (mt) REVERT: B 823 PHE cc_start: 0.7864 (m-80) cc_final: 0.7380 (m-10) REVERT: B 867 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8314 (t0) REVERT: B 988 GLU cc_start: 0.8838 (tp30) cc_final: 0.8609 (tp30) REVERT: B 994 ASP cc_start: 0.8594 (t70) cc_final: 0.8319 (t0) REVERT: B 1019 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7764 (tpp-160) REVERT: C 66 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.6718 (m-70) REVERT: C 200 TYR cc_start: 0.7445 (OUTLIER) cc_final: 0.6743 (m-80) REVERT: C 402 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8122 (pp) REVERT: C 421 TYR cc_start: 0.8784 (m-10) cc_final: 0.8283 (m-10) REVERT: C 424 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7429 (tptm) REVERT: C 495 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.6276 (t80) REVERT: C 505 HIS cc_start: -0.2064 (OUTLIER) cc_final: -0.3827 (m90) REVERT: C 552 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8521 (mt) REVERT: C 568 ASP cc_start: 0.7357 (t70) cc_final: 0.7053 (t0) REVERT: C 578 ASP cc_start: 0.8172 (t70) cc_final: 0.7468 (t70) REVERT: C 780 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8435 (tt0) REVERT: C 867 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8319 (t0) REVERT: C 994 ASP cc_start: 0.8319 (t70) cc_final: 0.7968 (t0) REVERT: C 998 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.9033 (m) outliers start: 126 outliers final: 68 residues processed: 338 average time/residue: 0.1410 time to fit residues: 79.5529 Evaluate side-chains 298 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 208 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 97 optimal weight: 0.7980 chunk 148 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 222 optimal weight: 0.4980 chunk 139 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 233 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 316 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.132619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.102666 restraints weight = 45089.342| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.23 r_work: 0.3361 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26523 Z= 0.130 Angle : 0.680 14.307 36231 Z= 0.331 Chirality : 0.049 0.637 4254 Planarity : 0.004 0.042 4557 Dihedral : 7.727 86.986 4786 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.43 % Favored : 93.48 % Rotamer: Outliers : 3.89 % Allowed : 22.27 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.49 (0.15), residues: 3159 helix: 0.83 (0.21), residues: 690 sheet: -1.06 (0.20), residues: 654 loop : -1.75 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 214 TYR 0.020 0.001 TYR B 170 PHE 0.017 0.001 PHE C 823 TRP 0.048 0.002 TRP C 633 HIS 0.003 0.000 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00303 (26418) covalent geometry : angle 0.63644 (35955) SS BOND : bond 0.00377 ( 39) SS BOND : angle 1.94647 ( 78) hydrogen bonds : bond 0.03704 ( 848) hydrogen bonds : angle 5.50392 ( 2280) link_BETA1-4 : bond 0.00491 ( 18) link_BETA1-4 : angle 2.11304 ( 54) link_NAG-ASN : bond 0.00569 ( 48) link_NAG-ASN : angle 3.39177 ( 144) *********************** 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 334 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 226 time to evaluate : 0.826 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: A 134 GLN cc_start: 0.6654 (tm-30) cc_final: 0.6212 (pp30) REVERT: A 160 TYR cc_start: 0.6027 (p90) cc_final: 0.5806 (p90) REVERT: A 200 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: A 324 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: A 369 TYR cc_start: 0.7556 (OUTLIER) cc_final: 0.6993 (t80) REVERT: A 402 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.7986 (pp) REVERT: A 495 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6161 (t80) REVERT: A 505 HIS cc_start: -0.1756 (OUTLIER) cc_final: -0.3587 (m90) REVERT: A 988 GLU cc_start: 0.8577 (tp30) cc_final: 0.8365 (tp30) REVERT: B 40 ASP cc_start: 0.8276 (m-30) cc_final: 0.8038 (m-30) REVERT: B 96 GLU cc_start: 0.5841 (mt-10) cc_final: 0.5571 (mp0) REVERT: B 131 CYS cc_start: 0.3294 (t) cc_final: 0.2882 (t) REVERT: B 200 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.7375 (t80) REVERT: B 369 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.7472 (t80) REVERT: B 402 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7749 (pp) REVERT: B 421 TYR cc_start: 0.8873 (m-10) cc_final: 0.8238 (m-10) REVERT: B 495 TYR cc_start: 0.7420 (OUTLIER) cc_final: 0.5717 (t80) REVERT: B 552 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8599 (mt) REVERT: B 823 PHE cc_start: 0.7809 (m-80) cc_final: 0.7357 (m-10) REVERT: B 867 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8311 (t0) REVERT: B 994 ASP cc_start: 0.8613 (t70) cc_final: 0.8268 (t0) REVERT: C 53 ASP cc_start: 0.7817 (t70) cc_final: 0.7570 (t0) REVERT: C 66 HIS cc_start: 0.8286 (OUTLIER) cc_final: 0.6547 (m-70) REVERT: C 127 PHE cc_start: 0.5959 (t80) cc_final: 0.5720 (t80) REVERT: C 129 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.6807 (ptmt) REVERT: C 131 CYS cc_start: 0.3154 (t) cc_final: 0.2648 (t) REVERT: C 134 GLN cc_start: 0.6857 (tm-30) cc_final: 0.6627 (tm-30) REVERT: C 200 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.6834 (m-80) REVERT: C 229 LEU cc_start: 0.7227 (pt) cc_final: 0.6979 (pt) REVERT: C 402 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8170 (pp) REVERT: C 421 TYR cc_start: 0.8827 (m-10) cc_final: 0.8270 (m-10) REVERT: C 424 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7445 (tptm) REVERT: C 495 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.6307 (t80) REVERT: C 505 HIS cc_start: -0.2538 (OUTLIER) cc_final: -0.4231 (m90) REVERT: C 552 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8590 (mt) REVERT: C 568 ASP cc_start: 0.7413 (t70) cc_final: 0.7095 (t0) REVERT: C 578 ASP cc_start: 0.8052 (t70) cc_final: 0.7418 (t70) REVERT: C 780 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8481 (tt0) REVERT: C 867 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8342 (t0) REVERT: C 998 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.9028 (m) outliers start: 108 outliers final: 72 residues processed: 317 average time/residue: 0.1539 time to fit residues: 81.1805 Evaluate side-chains 297 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 203 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 547 THR 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 642 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 203 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 247 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 249 optimal weight: 0.0970 chunk 271 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 241 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 542 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.133016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.103268 restraints weight = 45417.878| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.17 r_work: 0.3375 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26523 Z= 0.129 Angle : 0.676 14.199 36231 Z= 0.329 Chirality : 0.049 0.629 4254 Planarity : 0.004 0.038 4557 Dihedral : 7.583 85.195 4786 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.46 % Favored : 93.48 % Rotamer: Outliers : 3.86 % Allowed : 22.49 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.44 (0.15), residues: 3159 helix: 0.86 (0.21), residues: 690 sheet: -0.71 (0.21), residues: 606 loop : -1.82 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1019 TYR 0.019 0.001 TYR B 170 PHE 0.017 0.001 PHE A 133 TRP 0.043 0.001 TRP C 633 HIS 0.003 0.000 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00301 (26418) covalent geometry : angle 0.63260 (35955) SS BOND : bond 0.00376 ( 39) SS BOND : angle 2.00834 ( 78) hydrogen bonds : bond 0.03643 ( 848) hydrogen bonds : angle 5.42549 ( 2280) link_BETA1-4 : bond 0.00497 ( 18) link_BETA1-4 : angle 2.06468 ( 54) link_NAG-ASN : bond 0.00555 ( 48) link_NAG-ASN : angle 3.37607 ( 144) *********************** 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 332 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 225 time to evaluate : 1.022 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: A 134 GLN cc_start: 0.6483 (tm-30) cc_final: 0.6247 (tm-30) REVERT: A 160 TYR cc_start: 0.5998 (p90) cc_final: 0.5739 (p90) REVERT: A 200 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.6863 (m-80) REVERT: A 324 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: A 369 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.6936 (t80) REVERT: A 402 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7961 (pp) REVERT: A 495 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.6214 (t80) REVERT: A 505 HIS cc_start: -0.1695 (OUTLIER) cc_final: -0.3330 (m90) REVERT: B 40 ASP cc_start: 0.8208 (m-30) cc_final: 0.7972 (m-30) REVERT: B 134 GLN cc_start: 0.6537 (tm-30) cc_final: 0.5248 (tm-30) REVERT: B 135 PHE cc_start: 0.3700 (OUTLIER) cc_final: 0.3419 (p90) REVERT: B 200 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.7299 (t80) REVERT: B 367 VAL cc_start: 0.9070 (m) cc_final: 0.8807 (p) REVERT: B 369 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.7414 (t80) REVERT: B 383 SER cc_start: 0.8897 (t) cc_final: 0.8382 (p) REVERT: B 402 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7775 (pp) REVERT: B 421 TYR cc_start: 0.8894 (m-10) cc_final: 0.8191 (m-10) REVERT: B 495 TYR cc_start: 0.7391 (OUTLIER) cc_final: 0.5899 (t80) REVERT: B 552 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8283 (mt) REVERT: B 634 ARG cc_start: 0.8362 (tpp-160) cc_final: 0.8159 (tpp80) REVERT: B 823 PHE cc_start: 0.7791 (m-80) cc_final: 0.7381 (m-10) REVERT: B 867 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8299 (t0) REVERT: B 994 ASP cc_start: 0.8610 (t70) cc_final: 0.8177 (t0) REVERT: B 998 THR cc_start: 0.9481 (OUTLIER) cc_final: 0.9211 (m) REVERT: C 53 ASP cc_start: 0.7767 (t70) cc_final: 0.7535 (t0) REVERT: C 66 HIS cc_start: 0.8283 (OUTLIER) cc_final: 0.6554 (m-70) REVERT: C 127 PHE cc_start: 0.6051 (t80) cc_final: 0.5819 (t80) REVERT: C 129 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.6812 (ptmt) REVERT: C 200 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.6679 (m-80) REVERT: C 402 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8179 (pp) REVERT: C 421 TYR cc_start: 0.8744 (m-10) cc_final: 0.8128 (m-10) REVERT: C 424 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7479 (tptm) REVERT: C 495 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.6163 (t80) REVERT: C 505 HIS cc_start: -0.2843 (OUTLIER) cc_final: -0.4425 (m90) REVERT: C 552 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8579 (mt) REVERT: C 568 ASP cc_start: 0.7319 (t70) cc_final: 0.7043 (t0) REVERT: C 578 ASP cc_start: 0.8109 (t70) cc_final: 0.7476 (t70) REVERT: C 994 ASP cc_start: 0.8290 (t70) cc_final: 0.7904 (t0) REVERT: C 998 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.9020 (m) outliers start: 107 outliers final: 70 residues processed: 315 average time/residue: 0.1582 time to fit residues: 83.5248 Evaluate side-chains 299 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 206 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 63 optimal weight: 0.9980 chunk 250 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 219 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 251 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 chunk 278 optimal weight: 1.9990 chunk 249 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.132825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.103099 restraints weight = 45148.763| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.16 r_work: 0.3372 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 26523 Z= 0.136 Angle : 0.698 14.108 36231 Z= 0.339 Chirality : 0.049 0.627 4254 Planarity : 0.004 0.052 4557 Dihedral : 7.550 84.399 4786 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.52 % Favored : 93.42 % Rotamer: Outliers : 3.68 % Allowed : 22.81 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.48 (0.15), residues: 3159 helix: 0.89 (0.21), residues: 690 sheet: -0.92 (0.21), residues: 633 loop : -1.82 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 214 TYR 0.019 0.001 TYR B 265 PHE 0.053 0.001 PHE A 127 TRP 0.040 0.002 TRP C 633 HIS 0.003 0.000 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00322 (26418) covalent geometry : angle 0.65252 (35955) SS BOND : bond 0.00421 ( 39) SS BOND : angle 2.37205 ( 78) hydrogen bonds : bond 0.03636 ( 848) hydrogen bonds : angle 5.38690 ( 2280) link_BETA1-4 : bond 0.00494 ( 18) link_BETA1-4 : angle 2.03718 ( 54) link_NAG-ASN : bond 0.00537 ( 48) link_NAG-ASN : angle 3.40382 ( 144) ********************** 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 323 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 221 time to evaluate : 0.818 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 134 GLN cc_start: 0.6589 (tm-30) cc_final: 0.6355 (tm-30) REVERT: A 200 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.6865 (m-80) REVERT: A 324 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: A 369 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.6926 (t80) REVERT: A 402 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7932 (pp) REVERT: A 495 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.6254 (t80) REVERT: A 505 HIS cc_start: -0.1522 (OUTLIER) cc_final: -0.3089 (m90) REVERT: B 40 ASP cc_start: 0.8223 (m-30) cc_final: 0.7989 (m-30) REVERT: B 135 PHE cc_start: 0.3752 (OUTLIER) cc_final: 0.3543 (p90) REVERT: B 200 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.7313 (t80) REVERT: B 367 VAL cc_start: 0.9019 (m) cc_final: 0.8759 (p) REVERT: B 369 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.7465 (t80) REVERT: B 383 SER cc_start: 0.8886 (t) cc_final: 0.8363 (p) REVERT: B 402 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.7837 (pp) REVERT: B 421 TYR cc_start: 0.8919 (m-10) cc_final: 0.8208 (m-10) REVERT: B 495 TYR cc_start: 0.7374 (OUTLIER) cc_final: 0.5831 (t80) REVERT: B 552 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8412 (mt) REVERT: B 867 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8271 (t0) REVERT: B 994 ASP cc_start: 0.8581 (t70) cc_final: 0.8196 (t0) REVERT: B 998 THR cc_start: 0.9443 (OUTLIER) cc_final: 0.9161 (m) REVERT: C 66 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.6681 (m-70) REVERT: C 127 PHE cc_start: 0.6102 (t80) cc_final: 0.5895 (t80) REVERT: C 129 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.6866 (ptmt) REVERT: C 200 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.6662 (m-80) REVERT: C 402 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8132 (pp) REVERT: C 421 TYR cc_start: 0.8759 (m-80) cc_final: 0.8137 (m-10) REVERT: C 424 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7492 (tptm) REVERT: C 495 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.6308 (t80) REVERT: C 505 HIS cc_start: -0.2883 (OUTLIER) cc_final: -0.4423 (m90) REVERT: C 552 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8596 (mt) REVERT: C 568 ASP cc_start: 0.7471 (t70) cc_final: 0.7196 (t0) REVERT: C 578 ASP cc_start: 0.7992 (t70) cc_final: 0.7402 (t70) REVERT: C 628 GLN cc_start: 0.8125 (pt0) cc_final: 0.7827 (pt0) REVERT: C 994 ASP cc_start: 0.8161 (t70) cc_final: 0.7777 (t0) REVERT: C 998 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8985 (m) outliers start: 102 outliers final: 74 residues processed: 307 average time/residue: 0.1533 time to fit residues: 78.9063 Evaluate side-chains 306 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 209 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 547 THR 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 699 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 306 optimal weight: 5.9990 chunk 198 optimal weight: 0.6980 chunk 276 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 297 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 234 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.133573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.103511 restraints weight = 45043.184| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 3.22 r_work: 0.3377 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26523 Z= 0.134 Angle : 0.706 14.262 36231 Z= 0.344 Chirality : 0.049 0.622 4254 Planarity : 0.004 0.044 4557 Dihedral : 7.424 83.324 4786 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.20 % Favored : 93.73 % Rotamer: Outliers : 3.78 % Allowed : 22.38 % Favored : 73.84 % 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: -1.44 (0.15), residues: 3159 helix: 0.92 (0.21), residues: 690 sheet: -0.97 (0.20), residues: 645 loop : -1.77 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 214 TYR 0.028 0.001 TYR C 501 PHE 0.047 0.001 PHE A 127 TRP 0.035 0.001 TRP C 633 HIS 0.004 0.000 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00314 (26418) covalent geometry : angle 0.65769 (35955) SS BOND : bond 0.00412 ( 39) SS BOND : angle 2.60605 ( 78) hydrogen bonds : bond 0.03597 ( 848) hydrogen bonds : angle 5.37323 ( 2280) link_BETA1-4 : bond 0.00487 ( 18) link_BETA1-4 : angle 2.01420 ( 54) link_NAG-ASN : bond 0.00558 ( 48) link_NAG-ASN : angle 3.46945 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4543.26 seconds wall clock time: 79 minutes 20.41 seconds (4760.41 seconds total)