Starting phenix.real_space_refine on Sun Oct 12 17:18:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x4z_38056/10_2025/8x4z_38056.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x4z_38056/10_2025/8x4z_38056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x4z_38056/10_2025/8x4z_38056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x4z_38056/10_2025/8x4z_38056.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x4z_38056/10_2025/8x4z_38056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x4z_38056/10_2025/8x4z_38056.map" } resolution = 3.49 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= 0.071 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 16473 2.51 5 N 4200 2.21 5 O 5052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25839 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1008} 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: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1008} 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: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1008} 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: 6.95, per 1000 atoms: 0.27 Number of scatterers: 25839 At special positions: 0 Unit cell: (144.56, 144.56, 170.56, 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 5052 8.00 N 4200 7.00 C 16473 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.04 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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: 2.66 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 53 sheets defined 25.0% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.534A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.112A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 617 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 760 through 783 Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.645A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.618A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 881 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.357A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.752A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.613A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.001A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1144 removed outlier: 4.444A pdb=" N LEU A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1139 through 1144' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.050A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 627 removed outlier: 3.785A pdb=" N HIS B 625 " --> pdb=" O SER B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.623A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.702A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 868 through 881 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.333A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.729A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.121A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1144 removed outlier: 4.390A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1139 through 1144' Processing helix chain 'C' and resid 212 through 216 removed outlier: 3.792A pdb=" N ASP C 215 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE C 216 " --> pdb=" O GLY C 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 216' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.844A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.894A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 617 through 627 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: 3.825A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.682A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.676A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 884 removed outlier: 3.629A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.826A 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 912 through 919 removed outlier: 4.319A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.763A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.041A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1144 removed outlier: 4.322A pdb=" N LEU C1143 " --> pdb=" O ASP C1139 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1139 through 1144' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.310A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASP A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 95 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.894A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 170 removed outlier: 4.903A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.663A 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: 7.151A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.561A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.501A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.821A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.905A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 575 through 577 removed outlier: 3.638A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.375A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 713 through 715 removed outlier: 3.519A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.174A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.240A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.313A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.651A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 167 through 169 removed outlier: 3.529A pdb=" N THR B 167 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.116A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.878A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.548A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.820A 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: 3.979A 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: 6.184A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.702A 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: 3.774A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.601A 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 722 Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.168A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.388A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 788 removed outlier: 3.538A pdb=" N ILE B 788 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.285A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR C 95 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.672A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.682A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.121A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.986A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.599A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA C 435 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.912A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.017A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 575 through 577 removed outlier: 3.611A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.195A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 713 through 715 removed outlier: 3.507A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.595A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.348A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 867 hydrogen bonds defined for protein. 2382 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: 6.69 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8139 1.35 - 1.47: 6784 1.47 - 1.59: 11374 1.59 - 1.71: 1 1.71 - 1.83: 141 Bond restraints: 26439 Sorted by residual: bond pdb=" CG PRO B 217 " pdb=" CD PRO B 217 " ideal model delta sigma weight residual 1.503 1.269 0.234 3.40e-02 8.65e+02 4.72e+01 bond pdb=" N PRO B 217 " pdb=" CD PRO B 217 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" CB PRO B 217 " pdb=" CG PRO B 217 " ideal model delta sigma weight residual 1.492 1.656 -0.164 5.00e-02 4.00e+02 1.08e+01 bond pdb=" N PRO B 217 " pdb=" CA PRO B 217 " ideal model delta sigma weight residual 1.466 1.428 0.038 1.21e-02 6.83e+03 9.89e+00 ... (remaining 26434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.52: 35672 3.52 - 7.03: 288 7.03 - 10.55: 18 10.55 - 14.07: 3 14.07 - 17.58: 4 Bond angle restraints: 35985 Sorted by residual: angle pdb=" CA PRO B 217 " pdb=" N PRO B 217 " pdb=" CD PRO B 217 " ideal model delta sigma weight residual 112.00 94.42 17.58 1.40e+00 5.10e-01 1.58e+02 angle pdb=" N PRO B 217 " pdb=" CD PRO B 217 " pdb=" CG PRO B 217 " ideal model delta sigma weight residual 103.20 90.91 12.29 1.50e+00 4.44e-01 6.71e+01 angle pdb=" C ASN A1074 " pdb=" N PHE A1075 " pdb=" CA PHE A1075 " ideal model delta sigma weight residual 121.90 114.96 6.94 1.26e+00 6.30e-01 3.04e+01 angle pdb=" C ASN C1074 " pdb=" N PHE C1075 " pdb=" CA PHE C1075 " ideal model delta sigma weight residual 121.90 115.10 6.80 1.26e+00 6.30e-01 2.91e+01 angle pdb=" N GLN B 218 " pdb=" CA GLN B 218 " pdb=" C GLN B 218 " ideal model delta sigma weight residual 114.39 107.23 7.16 1.45e+00 4.76e-01 2.44e+01 ... (remaining 35980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.98: 14713 22.98 - 45.96: 1396 45.96 - 68.94: 198 68.94 - 91.92: 143 91.92 - 114.90: 119 Dihedral angle restraints: 16569 sinusoidal: 7284 harmonic: 9285 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 13.03 79.97 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 159.12 -66.12 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 29.34 63.66 1 1.00e+01 1.00e-02 5.34e+01 ... (remaining 16566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 4225 0.175 - 0.349: 32 0.349 - 0.524: 0 0.524 - 0.698: 0 0.698 - 0.873: 3 Chirality restraints: 4260 Sorted by residual: 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 -1.53 -0.87 2.00e-01 2.50e+01 1.91e+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 -1.54 -0.86 2.00e-01 2.50e+01 1.86e+01 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 -1.57 -0.83 2.00e-01 2.50e+01 1.74e+01 ... (remaining 4257 not shown) Planarity restraints: 4608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 216 " 0.143 5.00e-02 4.00e+02 1.94e-01 5.99e+01 pdb=" N PRO B 217 " -0.333 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " 0.109 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO C 209 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 371 " -0.018 2.00e-02 2.50e+03 2.82e-02 1.39e+01 pdb=" CG PHE B 371 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE B 371 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 371 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 371 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 PHE B 371 " 0.028 2.00e-02 2.50e+03 pdb=" CZ PHE B 371 " -0.055 2.00e-02 2.50e+03 ... (remaining 4605 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 495 2.66 - 3.22: 24264 3.22 - 3.78: 38661 3.78 - 4.34: 52485 4.34 - 4.90: 87510 Nonbonded interactions: 203415 Sorted by model distance: nonbonded pdb=" O CYS A 590 " pdb=" OH TYR C 837 " model vdw 2.094 3.040 nonbonded pdb=" OH TYR B 837 " pdb=" O CYS C 590 " model vdw 2.123 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.154 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.162 3.040 nonbonded pdb=" OH TYR A 837 " pdb=" O CYS B 590 " model vdw 2.173 3.040 ... (remaining 203410 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain '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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.640 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 0.234 26544 Z= 0.225 Angle : 0.859 17.583 36261 Z= 0.426 Chirality : 0.057 0.873 4260 Planarity : 0.006 0.194 4560 Dihedral : 21.367 114.901 10488 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.65 % Favored : 92.25 % Rotamer: Outliers : 0.50 % Allowed : 26.46 % Favored : 73.04 % 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: -1.62 (0.15), residues: 3162 helix: 0.71 (0.20), residues: 726 sheet: -0.92 (0.21), residues: 588 loop : -1.96 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 214 TYR 0.037 0.002 TYR B 170 PHE 0.055 0.002 PHE B 371 TRP 0.046 0.003 TRP B 633 HIS 0.005 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00496 (26439) covalent geometry : angle 0.82443 (35985) SS BOND : bond 0.00524 ( 39) SS BOND : angle 1.65900 ( 78) hydrogen bonds : bond 0.19109 ( 863) hydrogen bonds : angle 7.88534 ( 2382) link_BETA1-4 : bond 0.00421 ( 18) link_BETA1-4 : angle 2.15881 ( 54) link_NAG-ASN : bond 0.00622 ( 48) link_NAG-ASN : angle 3.53852 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 904 TYR cc_start: 0.8310 (m-10) cc_final: 0.7640 (m-10) REVERT: B 173 GLN cc_start: 0.7369 (mm-40) cc_final: 0.7083 (tp40) REVERT: B 400 PHE cc_start: 0.8467 (p90) cc_final: 0.8200 (p90) REVERT: B 495 TYR cc_start: 0.4840 (t80) cc_final: 0.4581 (t80) REVERT: B 1130 ILE cc_start: 0.9052 (mm) cc_final: 0.8773 (mt) REVERT: C 127 PHE cc_start: 0.6561 (t80) cc_final: 0.6277 (t80) REVERT: C 495 TYR cc_start: 0.5331 (OUTLIER) cc_final: 0.4463 (t80) REVERT: C 677 GLN cc_start: 0.6318 (OUTLIER) cc_final: 0.5924 (pm20) REVERT: C 1130 ILE cc_start: 0.8981 (mm) cc_final: 0.8754 (mt) outliers start: 14 outliers final: 9 residues processed: 227 average time/residue: 0.1532 time to fit residues: 58.1525 Evaluate side-chains 203 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 856 ASN 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: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 207 HIS C 339 HIS C 360 ASN C 370 ASN C 394 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C1002 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.115329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.084696 restraints weight = 55858.261| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.39 r_work: 0.3153 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 26544 Z= 0.274 Angle : 0.842 14.581 36261 Z= 0.403 Chirality : 0.054 0.620 4260 Planarity : 0.005 0.116 4560 Dihedral : 12.701 107.826 4791 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.35 % Favored : 91.56 % Rotamer: Outliers : 5.47 % Allowed : 23.29 % Favored : 71.24 % 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: -1.61 (0.15), residues: 3162 helix: 0.91 (0.21), residues: 702 sheet: -0.74 (0.20), residues: 606 loop : -2.07 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 355 TYR 0.022 0.002 TYR A 265 PHE 0.023 0.002 PHE B 456 TRP 0.026 0.002 TRP B 353 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00638 (26439) covalent geometry : angle 0.79876 (35985) SS BOND : bond 0.00471 ( 39) SS BOND : angle 2.01466 ( 78) hydrogen bonds : bond 0.05125 ( 863) hydrogen bonds : angle 5.85991 ( 2382) link_BETA1-4 : bond 0.00329 ( 18) link_BETA1-4 : angle 3.32540 ( 54) link_NAG-ASN : bond 0.00705 ( 48) link_NAG-ASN : angle 3.59293 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 190 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5496 (OUTLIER) cc_final: 0.4556 (pttp) REVERT: A 495 TYR cc_start: 0.6123 (OUTLIER) cc_final: 0.5194 (t80) REVERT: A 636 TYR cc_start: 0.7527 (t80) cc_final: 0.7259 (t80) REVERT: A 759 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7850 (t80) REVERT: A 904 TYR cc_start: 0.8474 (m-10) cc_final: 0.7870 (m-10) REVERT: A 998 THR cc_start: 0.9555 (OUTLIER) cc_final: 0.9335 (m) REVERT: B 237 ARG cc_start: 0.8281 (mtp180) cc_final: 0.8058 (mtp85) REVERT: B 358 ILE cc_start: 0.8389 (mm) cc_final: 0.8100 (mm) REVERT: B 465 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6901 (pt0) REVERT: B 495 TYR cc_start: 0.4847 (t80) cc_final: 0.4517 (t80) REVERT: B 979 ASP cc_start: 0.8579 (t0) cc_final: 0.8335 (t0) REVERT: B 1130 ILE cc_start: 0.9291 (mm) cc_final: 0.9052 (mt) REVERT: C 127 PHE cc_start: 0.7346 (t80) cc_final: 0.6826 (t80) REVERT: C 430 THR cc_start: 0.8492 (m) cc_final: 0.8163 (p) REVERT: C 495 TYR cc_start: 0.5695 (OUTLIER) cc_final: 0.4501 (t80) REVERT: C 508 TYR cc_start: 0.7658 (m-10) cc_final: 0.7355 (m-10) REVERT: C 523 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7826 (p) REVERT: C 957 GLN cc_start: 0.8644 (tt0) cc_final: 0.8160 (tm-30) REVERT: C 979 ASP cc_start: 0.8630 (t0) cc_final: 0.8426 (t0) REVERT: C 1130 ILE cc_start: 0.9255 (mm) cc_final: 0.9033 (mt) outliers start: 152 outliers final: 75 residues processed: 329 average time/residue: 0.1486 time to fit residues: 82.6781 Evaluate side-chains 240 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 158 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 281 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 245 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 312 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 255 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 HIS ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.116634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.086085 restraints weight = 55363.094| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.41 r_work: 0.3178 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26544 Z= 0.153 Angle : 0.728 14.620 36261 Z= 0.346 Chirality : 0.050 0.605 4260 Planarity : 0.005 0.078 4560 Dihedral : 9.913 101.878 4780 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 4.61 % Allowed : 24.12 % Favored : 71.27 % 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: -1.46 (0.15), residues: 3162 helix: 1.11 (0.21), residues: 699 sheet: -0.72 (0.20), residues: 648 loop : -2.01 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.018 0.001 TYR A 396 PHE 0.015 0.001 PHE C 216 TRP 0.018 0.002 TRP C 353 HIS 0.004 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00353 (26439) covalent geometry : angle 0.68134 (35985) SS BOND : bond 0.00360 ( 39) SS BOND : angle 1.47999 ( 78) hydrogen bonds : bond 0.04531 ( 863) hydrogen bonds : angle 5.52847 ( 2382) link_BETA1-4 : bond 0.00340 ( 18) link_BETA1-4 : angle 3.15254 ( 54) link_NAG-ASN : bond 0.00549 ( 48) link_NAG-ASN : angle 3.51965 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 178 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5599 (OUTLIER) cc_final: 0.4717 (pttp) REVERT: A 218 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7999 (pm20) REVERT: A 357 ARG cc_start: 0.8209 (ptm160) cc_final: 0.7575 (ptm160) REVERT: A 495 TYR cc_start: 0.6005 (OUTLIER) cc_final: 0.5054 (t80) REVERT: A 759 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7764 (t80) REVERT: A 904 TYR cc_start: 0.8410 (m-10) cc_final: 0.7868 (m-10) REVERT: A 957 GLN cc_start: 0.8676 (tt0) cc_final: 0.8239 (tm-30) REVERT: A 998 THR cc_start: 0.9531 (OUTLIER) cc_final: 0.9300 (m) REVERT: B 237 ARG cc_start: 0.8209 (mtp180) cc_final: 0.8004 (mtp85) REVERT: B 358 ILE cc_start: 0.8440 (mm) cc_final: 0.8114 (mm) REVERT: B 465 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6887 (pt0) REVERT: B 495 TYR cc_start: 0.4762 (t80) cc_final: 0.4490 (t80) REVERT: B 759 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.8004 (t80) REVERT: B 979 ASP cc_start: 0.8567 (t0) cc_final: 0.8272 (t0) REVERT: B 1130 ILE cc_start: 0.9316 (mm) cc_final: 0.9080 (mt) REVERT: C 127 PHE cc_start: 0.7104 (t80) cc_final: 0.6417 (t80) REVERT: C 393 THR cc_start: 0.7467 (OUTLIER) cc_final: 0.7026 (t) REVERT: C 430 THR cc_start: 0.8413 (m) cc_final: 0.8151 (p) REVERT: C 495 TYR cc_start: 0.5546 (OUTLIER) cc_final: 0.4381 (t80) REVERT: C 508 TYR cc_start: 0.7774 (m-10) cc_final: 0.7437 (m-10) REVERT: C 523 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7864 (p) REVERT: C 759 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7793 (t80) REVERT: C 979 ASP cc_start: 0.8701 (t0) cc_final: 0.8454 (t0) REVERT: C 1130 ILE cc_start: 0.9236 (mm) cc_final: 0.9031 (mt) outliers start: 128 outliers final: 63 residues processed: 292 average time/residue: 0.1480 time to fit residues: 72.8744 Evaluate side-chains 231 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 157 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 84 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 314 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 294 optimal weight: 1.9990 chunk 270 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 804 GLN B1071 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 677 GLN C1054 GLN C1071 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.115590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.085111 restraints weight = 55348.540| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.39 r_work: 0.3160 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26544 Z= 0.162 Angle : 0.692 15.312 36261 Z= 0.335 Chirality : 0.049 0.592 4260 Planarity : 0.004 0.065 4560 Dihedral : 8.124 95.883 4780 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.37 % Favored : 92.50 % Rotamer: Outliers : 5.58 % Allowed : 23.87 % Favored : 70.55 % 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: -1.38 (0.15), residues: 3162 helix: 1.16 (0.21), residues: 705 sheet: -0.74 (0.20), residues: 657 loop : -1.93 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 355 TYR 0.017 0.001 TYR B 265 PHE 0.022 0.001 PHE C 456 TRP 0.013 0.002 TRP B 353 HIS 0.004 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00383 (26439) covalent geometry : angle 0.65054 (35985) SS BOND : bond 0.00397 ( 39) SS BOND : angle 1.32916 ( 78) hydrogen bonds : bond 0.04228 ( 863) hydrogen bonds : angle 5.24671 ( 2382) link_BETA1-4 : bond 0.00308 ( 18) link_BETA1-4 : angle 2.52854 ( 54) link_NAG-ASN : bond 0.00537 ( 48) link_NAG-ASN : angle 3.37541 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 182 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5467 (OUTLIER) cc_final: 0.4378 (pttp) REVERT: A 127 PHE cc_start: 0.6854 (t80) cc_final: 0.6535 (t80) REVERT: A 218 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7918 (pm20) REVERT: A 357 ARG cc_start: 0.8191 (ptm160) cc_final: 0.7581 (ptm160) REVERT: A 495 TYR cc_start: 0.6111 (OUTLIER) cc_final: 0.5075 (t80) REVERT: A 759 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7883 (t80) REVERT: A 904 TYR cc_start: 0.8382 (m-10) cc_final: 0.7891 (m-10) REVERT: A 957 GLN cc_start: 0.8718 (tt0) cc_final: 0.8285 (tm-30) REVERT: A 998 THR cc_start: 0.9531 (OUTLIER) cc_final: 0.9295 (m) REVERT: A 1029 MET cc_start: 0.9209 (tpp) cc_final: 0.8618 (ttm) REVERT: B 358 ILE cc_start: 0.8671 (mm) cc_final: 0.8364 (mm) REVERT: B 430 THR cc_start: 0.8474 (m) cc_final: 0.8244 (p) REVERT: B 759 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7806 (t80) REVERT: B 788 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8998 (mt) REVERT: B 957 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7783 (tm-30) REVERT: B 979 ASP cc_start: 0.8659 (t0) cc_final: 0.8371 (t0) REVERT: B 1130 ILE cc_start: 0.9352 (mm) cc_final: 0.9138 (mt) REVERT: C 127 PHE cc_start: 0.7213 (t80) cc_final: 0.6613 (t80) REVERT: C 216 PHE cc_start: 0.6878 (t80) cc_final: 0.6633 (t80) REVERT: C 393 THR cc_start: 0.7231 (OUTLIER) cc_final: 0.6895 (t) REVERT: C 430 THR cc_start: 0.8418 (m) cc_final: 0.8186 (p) REVERT: C 495 TYR cc_start: 0.5714 (OUTLIER) cc_final: 0.4542 (t80) REVERT: C 523 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7922 (p) REVERT: C 677 GLN cc_start: 0.6256 (pt0) cc_final: 0.5925 (pm20) REVERT: C 759 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7776 (t80) REVERT: C 869 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8556 (mtm) REVERT: C 904 TYR cc_start: 0.8529 (m-10) cc_final: 0.8307 (m-80) REVERT: C 957 GLN cc_start: 0.8779 (tt0) cc_final: 0.8240 (tm-30) REVERT: C 979 ASP cc_start: 0.8731 (t0) cc_final: 0.8509 (t0) outliers start: 155 outliers final: 86 residues processed: 319 average time/residue: 0.1480 time to fit residues: 79.7330 Evaluate side-chains 263 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 165 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 264 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 247 optimal weight: 8.9990 chunk 239 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 293 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** 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 = 0.3823 r_free = 0.3823 target = 0.116748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.086611 restraints weight = 55054.524| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.39 r_work: 0.3186 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26544 Z= 0.119 Angle : 0.658 13.611 36261 Z= 0.317 Chirality : 0.048 0.592 4260 Planarity : 0.004 0.053 4560 Dihedral : 7.842 92.459 4776 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.74 % Favored : 93.17 % Rotamer: Outliers : 3.89 % Allowed : 25.31 % Favored : 70.81 % 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: -1.27 (0.15), residues: 3162 helix: 1.23 (0.21), residues: 714 sheet: -0.66 (0.20), residues: 660 loop : -1.87 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 214 TYR 0.014 0.001 TYR B1067 PHE 0.018 0.001 PHE C 456 TRP 0.011 0.001 TRP B 633 HIS 0.002 0.000 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00273 (26439) covalent geometry : angle 0.61836 (35985) SS BOND : bond 0.00373 ( 39) SS BOND : angle 1.25234 ( 78) hydrogen bonds : bond 0.03861 ( 863) hydrogen bonds : angle 5.09233 ( 2382) link_BETA1-4 : bond 0.00429 ( 18) link_BETA1-4 : angle 2.25019 ( 54) link_NAG-ASN : bond 0.00502 ( 48) link_NAG-ASN : angle 3.27495 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 177 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5242 (OUTLIER) cc_final: 0.4150 (pttp) REVERT: A 218 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: A 357 ARG cc_start: 0.8182 (ptm160) cc_final: 0.7920 (ttp-110) REVERT: A 495 TYR cc_start: 0.6223 (OUTLIER) cc_final: 0.5197 (t80) REVERT: A 759 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7667 (t80) REVERT: A 904 TYR cc_start: 0.8347 (m-10) cc_final: 0.7882 (m-10) REVERT: A 998 THR cc_start: 0.9505 (OUTLIER) cc_final: 0.9266 (m) REVERT: A 1029 MET cc_start: 0.9198 (tpp) cc_final: 0.8709 (ttm) REVERT: B 127 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.6696 (m-80) REVERT: B 296 LEU cc_start: 0.8433 (pp) cc_final: 0.8137 (tp) REVERT: B 430 THR cc_start: 0.8387 (m) cc_final: 0.8145 (p) REVERT: B 759 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7864 (t80) REVERT: B 957 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7742 (tm-30) REVERT: B 979 ASP cc_start: 0.8584 (t0) cc_final: 0.8278 (t0) REVERT: C 127 PHE cc_start: 0.7075 (t80) cc_final: 0.6446 (t80) REVERT: C 246 ARG cc_start: 0.1824 (OUTLIER) cc_final: -0.1137 (mtt90) REVERT: C 393 THR cc_start: 0.7011 (OUTLIER) cc_final: 0.6617 (t) REVERT: C 430 THR cc_start: 0.8271 (m) cc_final: 0.7817 (p) REVERT: C 495 TYR cc_start: 0.5645 (OUTLIER) cc_final: 0.4506 (t80) REVERT: C 523 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7851 (p) REVERT: C 677 GLN cc_start: 0.6403 (pt0) cc_final: 0.6203 (pm20) REVERT: C 759 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7733 (t80) REVERT: C 869 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8518 (mtm) REVERT: C 957 GLN cc_start: 0.8697 (tt0) cc_final: 0.8189 (tm-30) REVERT: C 979 ASP cc_start: 0.8718 (t0) cc_final: 0.8505 (t0) outliers start: 108 outliers final: 57 residues processed: 270 average time/residue: 0.1473 time to fit residues: 66.2857 Evaluate side-chains 234 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 164 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 30 optimal weight: 0.9980 chunk 305 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 233 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 191 optimal weight: 0.4980 chunk 35 optimal weight: 0.4980 chunk 231 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN B 394 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.117067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.086975 restraints weight = 55148.559| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.39 r_work: 0.3194 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26544 Z= 0.114 Angle : 0.650 15.643 36261 Z= 0.311 Chirality : 0.048 0.584 4260 Planarity : 0.004 0.047 4560 Dihedral : 7.578 89.907 4776 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.74 % Favored : 93.17 % Rotamer: Outliers : 4.57 % Allowed : 25.02 % Favored : 70.41 % 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: -1.14 (0.15), residues: 3162 helix: 1.34 (0.21), residues: 714 sheet: -0.59 (0.20), residues: 660 loop : -1.79 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 237 TYR 0.015 0.001 TYR A 265 PHE 0.026 0.001 PHE A 168 TRP 0.010 0.001 TRP B 633 HIS 0.002 0.000 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00264 (26439) covalent geometry : angle 0.61162 (35985) SS BOND : bond 0.00365 ( 39) SS BOND : angle 1.17312 ( 78) hydrogen bonds : bond 0.03709 ( 863) hydrogen bonds : angle 4.97469 ( 2382) link_BETA1-4 : bond 0.00412 ( 18) link_BETA1-4 : angle 2.12962 ( 54) link_NAG-ASN : bond 0.00538 ( 48) link_NAG-ASN : angle 3.24128 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 178 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5175 (OUTLIER) cc_final: 0.4149 (pttp) REVERT: A 127 PHE cc_start: 0.6694 (t80) cc_final: 0.6281 (t80) REVERT: A 190 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8356 (mtt-85) REVERT: A 218 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: A 353 TRP cc_start: 0.8384 (OUTLIER) cc_final: 0.6522 (p-90) REVERT: A 357 ARG cc_start: 0.8225 (ptm160) cc_final: 0.7869 (ptm160) REVERT: A 389 ASP cc_start: 0.8336 (m-30) cc_final: 0.7800 (t0) REVERT: A 495 TYR cc_start: 0.6168 (OUTLIER) cc_final: 0.5134 (t80) REVERT: A 636 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.7215 (t80) REVERT: A 904 TYR cc_start: 0.8391 (m-10) cc_final: 0.7915 (m-10) REVERT: A 957 GLN cc_start: 0.8696 (tt0) cc_final: 0.8196 (tm-30) REVERT: A 998 THR cc_start: 0.9494 (OUTLIER) cc_final: 0.9246 (m) REVERT: A 1029 MET cc_start: 0.9217 (tpp) cc_final: 0.8750 (ttm) REVERT: B 296 LEU cc_start: 0.8414 (pp) cc_final: 0.8136 (tp) REVERT: B 430 THR cc_start: 0.8375 (m) cc_final: 0.8093 (p) REVERT: B 449 TYR cc_start: 0.7803 (p90) cc_final: 0.7092 (m-80) REVERT: B 957 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7710 (tm-30) REVERT: B 979 ASP cc_start: 0.8546 (t0) cc_final: 0.8233 (t0) REVERT: C 127 PHE cc_start: 0.7118 (t80) cc_final: 0.6488 (t80) REVERT: C 246 ARG cc_start: 0.1854 (OUTLIER) cc_final: -0.0951 (tpt170) REVERT: C 393 THR cc_start: 0.7052 (OUTLIER) cc_final: 0.6553 (t) REVERT: C 495 TYR cc_start: 0.5688 (OUTLIER) cc_final: 0.4486 (t80) REVERT: C 523 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7919 (p) REVERT: C 759 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7716 (t80) REVERT: C 869 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8533 (mtm) REVERT: C 957 GLN cc_start: 0.8638 (tt0) cc_final: 0.8180 (tm-30) REVERT: C 979 ASP cc_start: 0.8722 (t0) cc_final: 0.8513 (t0) outliers start: 127 outliers final: 72 residues processed: 292 average time/residue: 0.1473 time to fit residues: 71.7590 Evaluate side-chains 246 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 161 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE 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 1030 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 145 optimal weight: 0.0060 chunk 293 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 273 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 148 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 677 GLN C1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.112868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.082594 restraints weight = 55442.463| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.37 r_work: 0.3117 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 26544 Z= 0.218 Angle : 0.718 14.815 36261 Z= 0.347 Chirality : 0.049 0.571 4260 Planarity : 0.004 0.052 4560 Dihedral : 7.872 90.655 4776 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.03 % Favored : 91.84 % Rotamer: Outliers : 5.22 % Allowed : 25.02 % Favored : 69.76 % 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: -1.30 (0.15), residues: 3162 helix: 1.25 (0.21), residues: 705 sheet: -0.70 (0.20), residues: 657 loop : -1.88 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 237 TYR 0.020 0.001 TYR A 265 PHE 0.019 0.002 PHE C 456 TRP 0.047 0.002 TRP B 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00519 (26439) covalent geometry : angle 0.67880 (35985) SS BOND : bond 0.00466 ( 39) SS BOND : angle 1.67713 ( 78) hydrogen bonds : bond 0.04473 ( 863) hydrogen bonds : angle 5.14307 ( 2382) link_BETA1-4 : bond 0.00229 ( 18) link_BETA1-4 : angle 1.99694 ( 54) link_NAG-ASN : bond 0.00548 ( 48) link_NAG-ASN : angle 3.39484 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 173 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5431 (OUTLIER) cc_final: 0.4130 (pttp) REVERT: A 127 PHE cc_start: 0.6984 (t80) cc_final: 0.6532 (t80) REVERT: A 218 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7859 (pm20) REVERT: A 221 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8585 (p) REVERT: A 338 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7958 (m-80) REVERT: A 389 ASP cc_start: 0.8385 (m-30) cc_final: 0.7909 (t0) REVERT: A 495 TYR cc_start: 0.6280 (OUTLIER) cc_final: 0.5115 (t80) REVERT: A 904 TYR cc_start: 0.8427 (m-10) cc_final: 0.7956 (m-10) REVERT: A 957 GLN cc_start: 0.8754 (tt0) cc_final: 0.8295 (tm-30) REVERT: A 998 THR cc_start: 0.9522 (OUTLIER) cc_final: 0.9291 (m) REVERT: A 1029 MET cc_start: 0.9269 (tpp) cc_final: 0.8723 (ttm) REVERT: B 237 ARG cc_start: 0.8238 (mtp180) cc_final: 0.7974 (mtp85) REVERT: B 296 LEU cc_start: 0.8528 (pp) cc_final: 0.8250 (tp) REVERT: B 430 THR cc_start: 0.8563 (m) cc_final: 0.8145 (p) REVERT: B 449 TYR cc_start: 0.7883 (p90) cc_final: 0.7104 (m-80) REVERT: B 465 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6928 (pt0) REVERT: B 523 THR cc_start: 0.8397 (m) cc_final: 0.8014 (p) REVERT: B 957 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7747 (tm-30) REVERT: B 981 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8900 (mp) REVERT: C 102 ARG cc_start: 0.8315 (mmt90) cc_final: 0.7774 (mpt180) REVERT: C 127 PHE cc_start: 0.7366 (t80) cc_final: 0.6733 (t80) REVERT: C 200 TYR cc_start: 0.7200 (m-10) cc_final: 0.6817 (m-80) REVERT: C 246 ARG cc_start: 0.2426 (OUTLIER) cc_final: -0.1037 (mtt-85) REVERT: C 346 ARG cc_start: 0.8574 (ttm110) cc_final: 0.8297 (tpt170) REVERT: C 355 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8170 (ttm-80) REVERT: C 495 TYR cc_start: 0.5769 (OUTLIER) cc_final: 0.4581 (t80) REVERT: C 557 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8166 (mttp) REVERT: C 759 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7751 (t80) REVERT: C 957 GLN cc_start: 0.8731 (tt0) cc_final: 0.8111 (tm-30) REVERT: C 979 ASP cc_start: 0.8712 (t0) cc_final: 0.8492 (t0) REVERT: C 1029 MET cc_start: 0.9228 (tpp) cc_final: 0.8900 (ttm) outliers start: 145 outliers final: 88 residues processed: 304 average time/residue: 0.1467 time to fit residues: 75.2047 Evaluate side-chains 267 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 166 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 94 optimal weight: 0.5980 chunk 241 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 304 optimal weight: 0.8980 chunk 270 optimal weight: 0.9990 chunk 255 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 289 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 901 GLN B 99 ASN B 901 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.114888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.084791 restraints weight = 54977.996| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.38 r_work: 0.3159 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26544 Z= 0.126 Angle : 0.667 16.209 36261 Z= 0.321 Chirality : 0.048 0.570 4260 Planarity : 0.004 0.046 4560 Dihedral : 7.533 88.787 4776 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.48 % Favored : 93.39 % Rotamer: Outliers : 4.39 % Allowed : 25.92 % Favored : 69.69 % 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: -1.19 (0.15), residues: 3162 helix: 1.36 (0.21), residues: 705 sheet: -0.67 (0.20), residues: 657 loop : -1.80 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1107 TYR 0.015 0.001 TYR A 265 PHE 0.030 0.001 PHE A 592 TRP 0.032 0.001 TRP B 353 HIS 0.001 0.000 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00293 (26439) covalent geometry : angle 0.62971 (35985) SS BOND : bond 0.00532 ( 39) SS BOND : angle 1.26248 ( 78) hydrogen bonds : bond 0.03925 ( 863) hydrogen bonds : angle 5.04355 ( 2382) link_BETA1-4 : bond 0.00417 ( 18) link_BETA1-4 : angle 1.98435 ( 54) link_NAG-ASN : bond 0.00506 ( 48) link_NAG-ASN : angle 3.27292 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 172 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5531 (OUTLIER) cc_final: 0.4343 (pttp) REVERT: A 127 PHE cc_start: 0.6858 (t80) cc_final: 0.6380 (t80) REVERT: A 221 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8510 (p) REVERT: A 338 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7970 (m-80) REVERT: A 353 TRP cc_start: 0.8473 (OUTLIER) cc_final: 0.6680 (p-90) REVERT: A 357 ARG cc_start: 0.8424 (ptm160) cc_final: 0.8205 (ttp-110) REVERT: A 389 ASP cc_start: 0.8403 (m-30) cc_final: 0.7754 (t0) REVERT: A 495 TYR cc_start: 0.6338 (OUTLIER) cc_final: 0.5181 (t80) REVERT: A 759 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7844 (t80) REVERT: A 904 TYR cc_start: 0.8375 (m-10) cc_final: 0.8000 (m-10) REVERT: A 957 GLN cc_start: 0.8699 (tt0) cc_final: 0.8206 (tm-30) REVERT: A 998 THR cc_start: 0.9499 (OUTLIER) cc_final: 0.9265 (m) REVERT: A 1029 MET cc_start: 0.9228 (tpp) cc_final: 0.8732 (ttm) REVERT: B 188 ASN cc_start: 0.7295 (OUTLIER) cc_final: 0.5563 (p0) REVERT: B 246 ARG cc_start: 0.1501 (OUTLIER) cc_final: -0.1366 (mtt90) REVERT: B 296 LEU cc_start: 0.8434 (pp) cc_final: 0.8133 (tp) REVERT: B 449 TYR cc_start: 0.7817 (p90) cc_final: 0.7124 (m-80) REVERT: B 523 THR cc_start: 0.8349 (m) cc_final: 0.7974 (p) REVERT: B 957 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7720 (tm-30) REVERT: C 102 ARG cc_start: 0.8286 (mmt90) cc_final: 0.7898 (mpt180) REVERT: C 127 PHE cc_start: 0.7279 (t80) cc_final: 0.6763 (t80) REVERT: C 200 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.6768 (m-80) REVERT: C 246 ARG cc_start: 0.2364 (OUTLIER) cc_final: -0.1069 (mtt-85) REVERT: C 346 ARG cc_start: 0.8590 (ttm110) cc_final: 0.8241 (tpt170) REVERT: C 495 TYR cc_start: 0.5727 (OUTLIER) cc_final: 0.4542 (t80) REVERT: C 557 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8113 (mttm) REVERT: C 759 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7716 (t80) REVERT: C 850 ILE cc_start: 0.4216 (OUTLIER) cc_final: 0.3442 (mm) REVERT: C 957 GLN cc_start: 0.8660 (tt0) cc_final: 0.8168 (tm-30) REVERT: C 979 ASP cc_start: 0.8704 (t0) cc_final: 0.8503 (t0) REVERT: C 1029 MET cc_start: 0.9203 (tpp) cc_final: 0.8899 (ttm) outliers start: 122 outliers final: 85 residues processed: 281 average time/residue: 0.1548 time to fit residues: 72.5456 Evaluate side-chains 265 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 165 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 828 LEU 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 1030 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 4 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 310 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 255 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** C 207 HIS ** 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 = 0.3772 r_free = 0.3772 target = 0.113643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083510 restraints weight = 55163.502| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.37 r_work: 0.3135 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26544 Z= 0.172 Angle : 0.691 15.890 36261 Z= 0.333 Chirality : 0.048 0.562 4260 Planarity : 0.004 0.056 4560 Dihedral : 7.595 88.322 4776 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.96 % Favored : 92.92 % Rotamer: Outliers : 4.50 % Allowed : 25.95 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.15), residues: 3162 helix: 1.31 (0.20), residues: 708 sheet: -0.71 (0.20), residues: 657 loop : -1.81 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 237 TYR 0.017 0.001 TYR A 265 PHE 0.035 0.001 PHE A 592 TRP 0.039 0.002 TRP C 633 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00408 (26439) covalent geometry : angle 0.65269 (35985) SS BOND : bond 0.00468 ( 39) SS BOND : angle 1.57900 ( 78) hydrogen bonds : bond 0.04077 ( 863) hydrogen bonds : angle 5.04736 ( 2382) link_BETA1-4 : bond 0.00294 ( 18) link_BETA1-4 : angle 1.94337 ( 54) link_NAG-ASN : bond 0.00509 ( 48) link_NAG-ASN : angle 3.31321 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 163 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5572 (OUTLIER) cc_final: 0.4382 (pttp) REVERT: A 119 ILE cc_start: 0.8909 (mt) cc_final: 0.8553 (mm) REVERT: A 127 PHE cc_start: 0.7102 (t80) cc_final: 0.6656 (t80) REVERT: A 191 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8202 (mm-30) REVERT: A 218 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: A 221 SER cc_start: 0.8843 (OUTLIER) cc_final: 0.8547 (p) REVERT: A 338 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: A 353 TRP cc_start: 0.8516 (OUTLIER) cc_final: 0.7827 (p-90) REVERT: A 389 ASP cc_start: 0.8366 (m-30) cc_final: 0.7796 (t0) REVERT: A 495 TYR cc_start: 0.6506 (OUTLIER) cc_final: 0.5294 (t80) REVERT: A 759 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7740 (t80) REVERT: A 904 TYR cc_start: 0.8438 (m-10) cc_final: 0.8039 (m-10) REVERT: A 957 GLN cc_start: 0.8727 (tt0) cc_final: 0.8230 (tm-30) REVERT: A 998 THR cc_start: 0.9511 (OUTLIER) cc_final: 0.9288 (m) REVERT: A 1029 MET cc_start: 0.9251 (tpp) cc_final: 0.8770 (ttm) REVERT: B 127 PHE cc_start: 0.7259 (t80) cc_final: 0.6936 (t80) REVERT: B 246 ARG cc_start: 0.1857 (OUTLIER) cc_final: -0.1351 (mtt90) REVERT: B 296 LEU cc_start: 0.8469 (pp) cc_final: 0.8179 (tp) REVERT: B 383 SER cc_start: 0.8960 (t) cc_final: 0.8607 (p) REVERT: B 449 TYR cc_start: 0.7859 (p90) cc_final: 0.7209 (m-80) REVERT: B 523 THR cc_start: 0.8311 (m) cc_final: 0.7926 (p) REVERT: B 784 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8218 (mp10) REVERT: B 957 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7742 (tm-30) REVERT: C 102 ARG cc_start: 0.8306 (mmt90) cc_final: 0.7775 (mpt180) REVERT: C 127 PHE cc_start: 0.7418 (t80) cc_final: 0.6843 (t80) REVERT: C 200 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.6940 (m-80) REVERT: C 246 ARG cc_start: 0.2525 (OUTLIER) cc_final: -0.1029 (mtt-85) REVERT: C 346 ARG cc_start: 0.8549 (ttm110) cc_final: 0.8227 (tpt170) REVERT: C 355 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8156 (ttm-80) REVERT: C 493 GLN cc_start: 0.7318 (tm-30) cc_final: 0.6996 (mp10) REVERT: C 495 TYR cc_start: 0.5913 (OUTLIER) cc_final: 0.4739 (t80) REVERT: C 557 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8141 (mttp) REVERT: C 759 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7784 (t80) REVERT: C 850 ILE cc_start: 0.4237 (OUTLIER) cc_final: 0.3478 (mm) REVERT: C 957 GLN cc_start: 0.8677 (tt0) cc_final: 0.8134 (tm-30) REVERT: C 979 ASP cc_start: 0.8699 (t0) cc_final: 0.8493 (t0) REVERT: C 1029 MET cc_start: 0.9223 (tpp) cc_final: 0.8911 (ttm) outliers start: 125 outliers final: 93 residues processed: 274 average time/residue: 0.1543 time to fit residues: 70.1540 Evaluate side-chains 271 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 160 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 37 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 275 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 205 optimal weight: 0.7980 chunk 202 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 280 optimal weight: 4.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN A 901 GLN B 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.114697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.084718 restraints weight = 54846.278| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.37 r_work: 0.3156 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26544 Z= 0.129 Angle : 0.670 15.722 36261 Z= 0.322 Chirality : 0.048 0.561 4260 Planarity : 0.004 0.059 4560 Dihedral : 7.430 87.707 4776 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.49 % Rotamer: Outliers : 4.32 % Allowed : 25.99 % Favored : 69.69 % 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: -1.14 (0.15), residues: 3162 helix: 1.39 (0.20), residues: 708 sheet: -0.69 (0.20), residues: 657 loop : -1.75 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.015 0.001 TYR A 265 PHE 0.029 0.001 PHE A 592 TRP 0.029 0.001 TRP C 633 HIS 0.003 0.000 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00303 (26439) covalent geometry : angle 0.63312 (35985) SS BOND : bond 0.00384 ( 39) SS BOND : angle 1.33209 ( 78) hydrogen bonds : bond 0.03846 ( 863) hydrogen bonds : angle 4.99877 ( 2382) link_BETA1-4 : bond 0.00431 ( 18) link_BETA1-4 : angle 1.94520 ( 54) link_NAG-ASN : bond 0.00501 ( 48) link_NAG-ASN : angle 3.24000 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 167 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5358 (OUTLIER) cc_final: 0.3312 (tttt) REVERT: A 127 PHE cc_start: 0.7025 (t80) cc_final: 0.6575 (t80) REVERT: A 191 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8254 (mm-30) REVERT: A 221 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8454 (p) REVERT: A 338 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: A 353 TRP cc_start: 0.8486 (OUTLIER) cc_final: 0.7787 (p-90) REVERT: A 389 ASP cc_start: 0.8416 (m-30) cc_final: 0.7819 (t0) REVERT: A 495 TYR cc_start: 0.6407 (OUTLIER) cc_final: 0.5302 (t80) REVERT: A 759 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7718 (t80) REVERT: A 904 TYR cc_start: 0.8344 (m-10) cc_final: 0.7953 (m-10) REVERT: A 957 GLN cc_start: 0.8674 (tt0) cc_final: 0.8165 (tm-30) REVERT: A 998 THR cc_start: 0.9493 (OUTLIER) cc_final: 0.9262 (m) REVERT: A 1029 MET cc_start: 0.9230 (tpp) cc_final: 0.8767 (ttm) REVERT: B 113 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7342 (mptt) REVERT: B 127 PHE cc_start: 0.7179 (t80) cc_final: 0.6819 (t80) REVERT: B 246 ARG cc_start: 0.1759 (OUTLIER) cc_final: -0.1592 (mtt90) REVERT: B 296 LEU cc_start: 0.8433 (pp) cc_final: 0.8134 (tp) REVERT: B 383 SER cc_start: 0.8955 (t) cc_final: 0.8707 (p) REVERT: B 449 TYR cc_start: 0.7826 (p90) cc_final: 0.7199 (m-80) REVERT: B 523 THR cc_start: 0.8272 (m) cc_final: 0.7889 (p) REVERT: B 784 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8235 (mp10) REVERT: B 957 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7697 (tm-30) REVERT: C 102 ARG cc_start: 0.8330 (mmt90) cc_final: 0.7935 (mpt180) REVERT: C 127 PHE cc_start: 0.7329 (t80) cc_final: 0.6744 (t80) REVERT: C 246 ARG cc_start: 0.2456 (OUTLIER) cc_final: -0.0920 (tpt170) REVERT: C 346 ARG cc_start: 0.8589 (ttm110) cc_final: 0.8233 (tpt170) REVERT: C 355 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8116 (ttm-80) REVERT: C 495 TYR cc_start: 0.5859 (OUTLIER) cc_final: 0.4714 (t80) REVERT: C 557 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8083 (mttm) REVERT: C 759 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7697 (t80) REVERT: C 850 ILE cc_start: 0.4440 (OUTLIER) cc_final: 0.3673 (mm) REVERT: C 957 GLN cc_start: 0.8648 (tt0) cc_final: 0.8144 (tm-30) REVERT: C 1029 MET cc_start: 0.9236 (tpp) cc_final: 0.8933 (ttm) outliers start: 120 outliers final: 89 residues processed: 273 average time/residue: 0.1532 time to fit residues: 69.5945 Evaluate side-chains 268 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 163 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 223 optimal weight: 0.0370 chunk 107 optimal weight: 4.9990 chunk 224 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 226 optimal weight: 0.9990 chunk 278 optimal weight: 0.0670 chunk 175 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 99 ASN C 556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.114805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.084894 restraints weight = 54725.558| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.37 r_work: 0.3162 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26544 Z= 0.126 Angle : 0.674 15.677 36261 Z= 0.322 Chirality : 0.048 0.559 4260 Planarity : 0.004 0.056 4560 Dihedral : 7.352 86.860 4776 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.58 % Favored : 93.30 % Rotamer: Outliers : 3.89 % Allowed : 26.53 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.15), residues: 3162 helix: 1.65 (0.21), residues: 672 sheet: -0.66 (0.20), residues: 657 loop : -1.72 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.015 0.001 TYR A 265 PHE 0.027 0.001 PHE A 592 TRP 0.027 0.001 TRP C 633 HIS 0.002 0.000 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00294 (26439) covalent geometry : angle 0.63785 (35985) SS BOND : bond 0.00408 ( 39) SS BOND : angle 1.44542 ( 78) hydrogen bonds : bond 0.03766 ( 863) hydrogen bonds : angle 4.96222 ( 2382) link_BETA1-4 : bond 0.00380 ( 18) link_BETA1-4 : angle 1.92712 ( 54) link_NAG-ASN : bond 0.00503 ( 48) link_NAG-ASN : angle 3.21319 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5089.83 seconds wall clock time: 88 minutes 33.38 seconds (5313.38 seconds total)