Starting phenix.real_space_refine on Mon Aug 25 21:57:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z3w_39756/08_2025/8z3w_39756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z3w_39756/08_2025/8z3w_39756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z3w_39756/08_2025/8z3w_39756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z3w_39756/08_2025/8z3w_39756.map" model { file = "/net/cci-nas-00/data/ceres_data/8z3w_39756/08_2025/8z3w_39756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z3w_39756/08_2025/8z3w_39756.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 144 5.16 5 C 19698 2.51 5 N 5059 2.21 5 O 6048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30949 Number of models: 1 Model: "" Number of chains: 28 Chain: "C" Number of atoms: 8352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8352 Classifications: {'peptide': 1068} Link IDs: {'PTRANS': 52, 'TRANS': 1015} Chain breaks: 5 Chain: "B" Number of atoms: 8439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8439 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 5 Chain: "A" Number of atoms: 8307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8307 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 51, 'TRANS': 1009} Chain breaks: 7 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: "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 Time building chain proxies: 8.39, per 1000 atoms: 0.27 Number of scatterers: 30949 At special positions: 0 Unit cell: (157.08, 177.31, 235.62, 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 144 16.00 O 6048 8.00 N 5059 7.00 C 19698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 149 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 282 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 616 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 234 " " NAG B1308 " - " ASN B 164 " " NAG B1309 " - " ASN B 122 " " NAG B1310 " - " ASN B 61 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 149 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C 234 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 331 " " NAG C1309 " - " ASN C 122 " " NAG E 1 " - " ASN C 717 " " NAG F 1 " - " ASN C 801 " " NAG G 1 " - " ASN C1098 " " NAG H 1 " - " ASN C1134 " " NAG I 1 " - " ASN C 17 " " NAG J 1 " - " ASN C 343 " " NAG K 1 " - " ASN C 616 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 343 " " NAG Q 1 " - " ASN B 149 " " NAG R 1 " - " ASN B 17 " " NAG S 1 " - " ASN A 17 " " NAG T 1 " - " ASN A1134 " " NAG U 1 " - " ASN A1098 " " NAG V 1 " - " ASN A 801 " " NAG W 1 " - " ASN A 717 " " NAG X 1 " - " ASN A 343 " " NAG Y 1 " - " ASN A 331 " Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7138 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 52 sheets defined 30.4% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.610A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.891A pdb=" N ALA C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.892A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.516A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.181A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1148 removed outlier: 3.982A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.818A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.695A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.821A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 634 through 638 removed outlier: 4.125A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.589A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.795A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.323A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.631A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.527A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.158A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 3.970A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.859A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.516A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.601A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.515A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.948A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 941 removed outlier: 7.141A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.523A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) 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 982 removed outlier: 3.539A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1033 removed outlier: 4.439A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 4.163A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.976A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.835A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.525A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.759A pdb=" N GLY D 130 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 158 through 194 removed outlier: 3.587A pdb=" N LEU D 162 " --> pdb=" O TYR D 158 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.868A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 252 removed outlier: 4.078A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.506A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.553A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 340 removed outlier: 4.153A pdb=" N VAL D 339 " --> pdb=" O PRO D 336 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN D 340 " --> pdb=" O GLY D 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 336 through 340' Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.988A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 4.094A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.555A pdb=" N LEU D 418 " --> pdb=" O THR D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 4.027A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.583A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 503 removed outlier: 4.362A pdb=" N LEU D 503 " --> pdb=" O PRO D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 509 removed outlier: 3.903A pdb=" N ASP D 509 " --> pdb=" O VAL D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.210A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.724A pdb=" N GLN D 552 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.842A pdb=" N GLU D 564 " --> pdb=" O GLY D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 571 removed outlier: 4.225A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 599 Proline residue: D 590 - end of helix removed outlier: 3.678A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.838A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.847A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.663A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.537A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 151 through 157 removed outlier: 3.843A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS C 146 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.718A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.802A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.720A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.751A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AB4, first strand: chain 'C' and resid 542 through 543 removed outlier: 3.669A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 553 through 554 removed outlier: 3.636A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.990A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AB8, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.854A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.503A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AC2, first strand: chain 'C' and resid 787 through 790 removed outlier: 5.932A pdb=" N ILE C 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.581A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.886A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 212 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASN B 188 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE B 210 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG B 190 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR B 208 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N PHE B 192 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LYS B 206 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE B 194 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N TYR B 204 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ASN B 196 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LYS B 202 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.166A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.620A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 152 through 156 removed outlier: 6.407A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC9, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.960A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 538 through 539 removed outlier: 4.832A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N PHE B 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 542 through 543 removed outlier: 3.761A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.233A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.944A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.573A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.396A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.849A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.849A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.566A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.829A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 143 through 145 Processing sheet with id=AE6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.154A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.582A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.582A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.042A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.527A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.092A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AF6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'D' and resid 347 through 350 removed outlier: 3.816A pdb=" N ARG D 357 " --> pdb=" O TRP D 349 " (cutoff:3.500A) 1180 hydrogen bonds defined for protein. 3312 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: 8.58 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9824 1.34 - 1.46: 7767 1.46 - 1.58: 13878 1.58 - 1.70: 0 1.70 - 1.82: 195 Bond restraints: 31664 Sorted by residual: bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.94e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.79e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.55e+00 ... (remaining 31659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 42526 1.93 - 3.86: 522 3.86 - 5.79: 15 5.79 - 7.71: 4 7.71 - 9.64: 2 Bond angle restraints: 43069 Sorted by residual: angle pdb=" N THR B 523 " pdb=" CA THR B 523 " pdb=" C THR B 523 " ideal model delta sigma weight residual 114.56 110.42 4.14 1.27e+00 6.20e-01 1.06e+01 angle pdb=" CA LEU A 518 " pdb=" CB LEU A 518 " pdb=" CG LEU A 518 " ideal model delta sigma weight residual 116.30 125.94 -9.64 3.50e+00 8.16e-02 7.59e+00 angle pdb=" CA LEU A 517 " pdb=" CB LEU A 517 " pdb=" CG LEU A 517 " ideal model delta sigma weight residual 116.30 124.33 -8.03 3.50e+00 8.16e-02 5.26e+00 angle pdb=" CA THR B 523 " pdb=" C THR B 523 " pdb=" N VAL B 524 " ideal model delta sigma weight residual 119.26 116.79 2.47 1.14e+00 7.69e-01 4.71e+00 angle pdb=" C THR A 323 " pdb=" N GLU A 324 " pdb=" CA GLU A 324 " ideal model delta sigma weight residual 121.54 125.51 -3.97 1.91e+00 2.74e-01 4.32e+00 ... (remaining 43064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.06: 19404 23.06 - 46.12: 290 46.12 - 69.18: 39 69.18 - 92.24: 2 92.24 - 115.30: 17 Dihedral angle restraints: 19752 sinusoidal: 8664 harmonic: 11088 Sorted by residual: dihedral pdb=" C2 NAG Y 1 " pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " pdb=" C5 NAG Y 1 " ideal model delta sinusoidal sigma weight residual -62.96 52.34 -115.30 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C1 NAG Y 1 " pdb=" C5 NAG Y 1 " pdb=" O5 NAG Y 1 " pdb=" C4 NAG Y 1 " ideal model delta sinusoidal sigma weight residual -64.11 47.50 -111.61 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" C3 NAG Y 1 " pdb=" C1 NAG Y 1 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sinusoidal sigma weight residual -55.55 55.00 -110.55 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 19749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4465 0.066 - 0.133: 553 0.133 - 0.199: 5 0.199 - 0.265: 0 0.265 - 0.331: 3 Chirality restraints: 5026 Sorted by residual: chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 5023 not shown) Planarity restraints: 5527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 582 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO D 583 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 583 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 583 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 234 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO D 235 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 235 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 235 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.22e+00 pdb=" N PRO A 330 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " 0.015 5.00e-02 4.00e+02 ... (remaining 5524 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6734 2.78 - 3.31: 28036 3.31 - 3.84: 50343 3.84 - 4.37: 56922 4.37 - 4.90: 100272 Nonbonded interactions: 242307 Sorted by model distance: nonbonded pdb=" OG SER B 884 " pdb=" OG1 THR B 887 " model vdw 2.254 3.040 nonbonded pdb=" O ILE D 151 " pdb=" OG SER D 155 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR C 645 " pdb=" O GLY C 648 " model vdw 2.259 3.040 nonbonded pdb=" O SER A 359 " pdb=" OG1 THR A 523 " model vdw 2.264 3.040 nonbonded pdb=" OD2 ASP C 571 " pdb=" OG SER B 975 " model vdw 2.265 3.040 ... (remaining 242302 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 177 or resid 185 through 827 or resid 854 throu \ gh 1309)) selection = (chain 'B' and (resid 14 through 177 or resid 185 through 260 or resid 264 throu \ gh 621 or resid 640 through 1309)) selection = (chain 'C' and (resid 14 through 69 or resid 77 through 244 or resid 254 through \ 260 or resid 264 through 621 or resid 640 through 1309)) } ncs_group { reference = 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' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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: 6.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.200 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 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 : 0.003 0.053 31780 Z= 0.138 Angle : 0.456 9.643 43372 Z= 0.218 Chirality : 0.042 0.331 5026 Planarity : 0.003 0.034 5477 Dihedral : 8.671 115.304 12479 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.56 % Allowed : 4.05 % Favored : 94.39 % 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: -1.98 (0.12), residues: 3761 helix: 0.40 (0.16), residues: 1015 sheet: -1.11 (0.18), residues: 647 loop : -2.37 (0.11), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 765 TYR 0.006 0.001 TYR A1067 PHE 0.005 0.001 PHE B1095 TRP 0.005 0.000 TRP B 152 HIS 0.001 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00270 (31664) covalent geometry : angle 0.44627 (43069) SS BOND : bond 0.00104 ( 45) SS BOND : angle 0.47313 ( 90) hydrogen bonds : bond 0.19831 ( 1172) hydrogen bonds : angle 7.60595 ( 3312) link_BETA1-4 : bond 0.00345 ( 21) link_BETA1-4 : angle 0.80980 ( 63) link_NAG-ASN : bond 0.00337 ( 50) link_NAG-ASN : angle 1.61322 ( 150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 861 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 THR cc_start: 0.8568 (p) cc_final: 0.8266 (t) REVERT: C 40 ASP cc_start: 0.7549 (p0) cc_final: 0.7293 (p0) REVERT: C 117 LEU cc_start: 0.7384 (tp) cc_final: 0.7179 (tt) REVERT: C 128 ILE cc_start: 0.8106 (mt) cc_final: 0.7876 (mp) REVERT: C 129 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7583 (tppt) REVERT: C 202 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.7088 (mtpp) REVERT: C 228 ASP cc_start: 0.6817 (t0) cc_final: 0.5999 (t70) REVERT: C 240 THR cc_start: 0.8170 (m) cc_final: 0.7920 (t) REVERT: C 267 VAL cc_start: 0.8116 (t) cc_final: 0.7863 (p) REVERT: C 276 LEU cc_start: 0.8646 (tp) cc_final: 0.8367 (tt) REVERT: C 278 LYS cc_start: 0.8216 (ttmt) cc_final: 0.7882 (ttpp) REVERT: C 284 THR cc_start: 0.8286 (m) cc_final: 0.7998 (t) REVERT: C 289 VAL cc_start: 0.7868 (p) cc_final: 0.6875 (t) REVERT: C 305 SER cc_start: 0.8883 (t) cc_final: 0.8439 (p) REVERT: C 307 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.7150 (p) REVERT: C 312 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7884 (pt) REVERT: C 353 TRP cc_start: 0.7501 (p-90) cc_final: 0.6732 (p-90) REVERT: C 355 ARG cc_start: 0.7428 (ttm170) cc_final: 0.7173 (mtp85) REVERT: C 424 LYS cc_start: 0.7262 (tttt) cc_final: 0.6487 (ttpp) REVERT: C 584 ILE cc_start: 0.7515 (mm) cc_final: 0.7207 (mm) REVERT: C 663 ASP cc_start: 0.6433 (t0) cc_final: 0.6195 (t0) REVERT: C 774 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7319 (mp10) REVERT: C 803 SER cc_start: 0.8333 (t) cc_final: 0.8073 (p) REVERT: C 870 ILE cc_start: 0.8096 (pt) cc_final: 0.7829 (mt) REVERT: C 878 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8095 (mt) REVERT: C 900 MET cc_start: 0.7759 (mtm) cc_final: 0.7345 (mtp) REVERT: C 949 GLN cc_start: 0.7660 (tp40) cc_final: 0.7354 (tp40) REVERT: C 994 ASP cc_start: 0.7259 (t70) cc_final: 0.7000 (t0) REVERT: C 1029 MET cc_start: 0.8228 (tpp) cc_final: 0.7771 (tpp) REVERT: C 1073 LYS cc_start: 0.7782 (mtpt) cc_final: 0.7504 (mtpt) REVERT: C 1091 ARG cc_start: 0.6955 (mtt-85) cc_final: 0.6138 (mtp85) REVERT: C 1103 PHE cc_start: 0.8092 (m-80) cc_final: 0.7838 (m-80) REVERT: C 1139 ASP cc_start: 0.7905 (t0) cc_final: 0.7227 (t0) REVERT: B 90 VAL cc_start: 0.8293 (t) cc_final: 0.8016 (p) REVERT: B 117 LEU cc_start: 0.8399 (tp) cc_final: 0.8190 (tt) REVERT: B 132 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6944 (mt-10) REVERT: B 195 LYS cc_start: 0.7365 (mtmt) cc_final: 0.6993 (ttmt) REVERT: B 204 TYR cc_start: 0.7028 (m-80) cc_final: 0.6573 (m-80) REVERT: B 206 LYS cc_start: 0.8090 (tptm) cc_final: 0.7576 (tptp) REVERT: B 226 LEU cc_start: 0.7542 (tp) cc_final: 0.7327 (mt) REVERT: B 275 PHE cc_start: 0.8089 (m-80) cc_final: 0.7793 (m-80) REVERT: B 296 LEU cc_start: 0.7970 (tp) cc_final: 0.7680 (tp) REVERT: B 385 THR cc_start: 0.8360 (p) cc_final: 0.8117 (p) REVERT: B 386 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7612 (mmmm) REVERT: B 576 VAL cc_start: 0.8870 (p) cc_final: 0.8453 (t) REVERT: B 587 ILE cc_start: 0.7708 (mt) cc_final: 0.7348 (mt) REVERT: B 643 PHE cc_start: 0.8303 (t80) cc_final: 0.8051 (t80) REVERT: B 644 GLN cc_start: 0.7994 (tp40) cc_final: 0.6900 (tp-100) REVERT: B 664 ILE cc_start: 0.8567 (mt) cc_final: 0.8337 (mt) REVERT: B 752 LEU cc_start: 0.7764 (mt) cc_final: 0.7561 (tp) REVERT: B 773 GLU cc_start: 0.6711 (pt0) cc_final: 0.6395 (pt0) REVERT: B 781 VAL cc_start: 0.8562 (t) cc_final: 0.8321 (p) REVERT: B 790 LYS cc_start: 0.8123 (ptmt) cc_final: 0.7869 (ptmt) REVERT: B 870 ILE cc_start: 0.8196 (mm) cc_final: 0.7931 (mt) REVERT: B 929 SER cc_start: 0.7905 (t) cc_final: 0.7584 (p) REVERT: B 968 SER cc_start: 0.8465 (m) cc_final: 0.8089 (t) REVERT: B 1086 LYS cc_start: 0.8349 (mppt) cc_final: 0.7399 (mtmm) REVERT: B 1101 HIS cc_start: 0.8029 (m90) cc_final: 0.7674 (m170) REVERT: B 1117 THR cc_start: 0.8183 (m) cc_final: 0.7851 (t) REVERT: B 1122 VAL cc_start: 0.7994 (t) cc_final: 0.7734 (p) REVERT: B 1136 THR cc_start: 0.8368 (t) cc_final: 0.8081 (p) REVERT: B 1138 TYR cc_start: 0.7436 (t80) cc_final: 0.7067 (t80) REVERT: B 1141 LEU cc_start: 0.8371 (tt) cc_final: 0.8146 (tt) REVERT: A 120 VAL cc_start: 0.7969 (t) cc_final: 0.7631 (m) REVERT: A 203 ILE cc_start: 0.7985 (mt) cc_final: 0.7704 (mm) REVERT: A 206 LYS cc_start: 0.7883 (tptm) cc_final: 0.7659 (tptm) REVERT: A 303 LEU cc_start: 0.8394 (mt) cc_final: 0.8079 (mt) REVERT: A 309 GLU cc_start: 0.6251 (mt-10) cc_final: 0.6041 (mt-10) REVERT: A 405 ASP cc_start: 0.5847 (p0) cc_final: 0.5227 (p0) REVERT: A 535 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8247 (mttp) REVERT: A 544 ASN cc_start: 0.7264 (t0) cc_final: 0.7015 (t0) REVERT: A 549 THR cc_start: 0.7766 (m) cc_final: 0.7508 (p) REVERT: A 558 LYS cc_start: 0.8064 (mmtm) cc_final: 0.7743 (mmtm) REVERT: A 560 LEU cc_start: 0.8350 (mt) cc_final: 0.7949 (mt) REVERT: A 598 ILE cc_start: 0.8108 (mp) cc_final: 0.7906 (mt) REVERT: A 721 SER cc_start: 0.7956 (t) cc_final: 0.7425 (p) REVERT: A 758 SER cc_start: 0.8553 (m) cc_final: 0.8229 (p) REVERT: A 819 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7234 (mt-10) REVERT: A 855 PHE cc_start: 0.7733 (m-10) cc_final: 0.7521 (m-80) REVERT: A 866 THR cc_start: 0.8423 (p) cc_final: 0.7857 (p) REVERT: A 868 GLU cc_start: 0.6901 (mp0) cc_final: 0.6197 (mp0) REVERT: A 933 LYS cc_start: 0.8042 (mtmm) cc_final: 0.7840 (mtmm) REVERT: A 950 ASP cc_start: 0.6723 (t0) cc_final: 0.6417 (t0) REVERT: A 986 LYS cc_start: 0.7751 (mttt) cc_final: 0.6892 (mttt) REVERT: A 1037 SER cc_start: 0.8851 (t) cc_final: 0.8503 (p) REVERT: A 1045 LYS cc_start: 0.7903 (mttt) cc_final: 0.7643 (mttt) REVERT: A 1072 GLU cc_start: 0.7791 (pm20) cc_final: 0.7265 (pm20) REVERT: A 1073 LYS cc_start: 0.8206 (mtpt) cc_final: 0.7885 (mtpp) REVERT: A 1091 ARG cc_start: 0.7208 (mtt-85) cc_final: 0.6666 (mtt-85) REVERT: A 1122 VAL cc_start: 0.8521 (t) cc_final: 0.8212 (p) REVERT: A 1141 LEU cc_start: 0.8800 (tt) cc_final: 0.8551 (tt) REVERT: D 39 LEU cc_start: 0.8431 (mt) cc_final: 0.8190 (mt) REVERT: D 41 TYR cc_start: 0.7927 (t80) cc_final: 0.7066 (t80) REVERT: D 42 GLN cc_start: 0.7905 (tp40) cc_final: 0.7128 (tp40) REVERT: D 74 LYS cc_start: 0.8615 (tppp) cc_final: 0.8077 (tppp) REVERT: D 312 GLU cc_start: 0.8738 (tt0) cc_final: 0.8479 (mm-30) REVERT: D 369 PHE cc_start: 0.8640 (t80) cc_final: 0.8367 (t80) REVERT: D 376 MET cc_start: -0.0473 (ttm) cc_final: -0.1115 (mpp) REVERT: D 391 LEU cc_start: 0.7637 (mt) cc_final: 0.6965 (pp) REVERT: D 476 LYS cc_start: 0.7739 (tppp) cc_final: 0.7478 (tptp) REVERT: D 479 GLU cc_start: 0.8015 (pt0) cc_final: 0.7519 (pp20) REVERT: D 498 CYS cc_start: 0.6356 (t) cc_final: 0.5943 (p) REVERT: D 521 TYR cc_start: 0.5107 (m-10) cc_final: 0.4488 (m-80) REVERT: D 557 MET cc_start: 0.7331 (tmm) cc_final: 0.7024 (tmm) outliers start: 52 outliers final: 14 residues processed: 901 average time/residue: 0.2206 time to fit residues: 313.8612 Evaluate side-chains 692 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 672 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 373 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.0040 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS C 125 ASN C 173 GLN C 188 ASN C 239 GLN C 388 ASN C 474 GLN C 563 GLN C 564 GLN C 703 ASN C 777 ASN C 856 ASN C 926 GLN C 955 ASN C 957 GLN C 965 GLN C1011 GLN C1071 GLN B 134 GLN B 165 ASN B 188 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 493 GLN B 501 ASN B 563 GLN B 613 GLN B 764 ASN B 787 GLN B 804 GLN B 901 GLN B1002 GLN B1071 GLN B1119 ASN A 115 GLN A 134 GLN A 354 ASN A 394 ASN A 414 GLN A 460 ASN A 493 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 690 GLN A 755 GLN A 762 GLN A 926 GLN A 957 GLN A 960 ASN A1005 GLN A1011 GLN A1071 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 89 GLN D 101 GLN D 239 HIS D 277 ASN D 305 GLN D 380 GLN D 442 GLN D 522 GLN D 531 GLN D 540 HIS D 552 GLN D 572 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.188774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.141652 restraints weight = 51151.933| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.84 r_work: 0.3544 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31780 Z= 0.165 Angle : 0.616 13.178 43372 Z= 0.306 Chirality : 0.047 0.647 5026 Planarity : 0.004 0.061 5477 Dihedral : 7.812 101.185 5612 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.88 % Allowed : 10.41 % Favored : 86.71 % 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: -1.12 (0.13), residues: 3761 helix: 1.26 (0.17), residues: 1021 sheet: -0.52 (0.18), residues: 668 loop : -1.95 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 190 TYR 0.021 0.001 TYR C 660 PHE 0.030 0.002 PHE C 192 TRP 0.021 0.001 TRP B 152 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00363 (31664) covalent geometry : angle 0.59049 (43069) SS BOND : bond 0.00577 ( 45) SS BOND : angle 2.55224 ( 90) hydrogen bonds : bond 0.04136 ( 1172) hydrogen bonds : angle 5.65112 ( 3312) link_BETA1-4 : bond 0.00347 ( 21) link_BETA1-4 : angle 0.98032 ( 63) link_NAG-ASN : bond 0.00473 ( 50) link_NAG-ASN : angle 2.32883 ( 150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 692 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 THR cc_start: 0.8644 (p) cc_final: 0.8389 (t) REVERT: C 42 VAL cc_start: 0.8503 (p) cc_final: 0.8046 (m) REVERT: C 104 TRP cc_start: 0.7174 (m-90) cc_final: 0.6754 (m-90) REVERT: C 128 ILE cc_start: 0.8381 (mt) cc_final: 0.8163 (mp) REVERT: C 129 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7369 (tppt) REVERT: C 130 VAL cc_start: 0.7175 (t) cc_final: 0.6899 (t) REVERT: C 192 PHE cc_start: 0.8251 (m-80) cc_final: 0.8048 (m-10) REVERT: C 228 ASP cc_start: 0.7258 (t0) cc_final: 0.6607 (t70) REVERT: C 237 ARG cc_start: 0.7954 (mtp-110) cc_final: 0.7535 (mtm110) REVERT: C 276 LEU cc_start: 0.8804 (tp) cc_final: 0.8586 (tt) REVERT: C 284 THR cc_start: 0.8493 (m) cc_final: 0.8127 (t) REVERT: C 305 SER cc_start: 0.8924 (t) cc_final: 0.8527 (p) REVERT: C 309 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6995 (mm-30) REVERT: C 313 TYR cc_start: 0.8360 (m-80) cc_final: 0.8089 (m-80) REVERT: C 353 TRP cc_start: 0.7554 (p-90) cc_final: 0.7316 (p-90) REVERT: C 378 LYS cc_start: 0.8045 (mttt) cc_final: 0.7609 (mttt) REVERT: C 424 LYS cc_start: 0.7324 (tttt) cc_final: 0.6714 (ttpt) REVERT: C 580 GLN cc_start: 0.7769 (mt0) cc_final: 0.7432 (mt0) REVERT: C 591 SER cc_start: 0.8701 (t) cc_final: 0.8245 (p) REVERT: C 740 MET cc_start: 0.8418 (tpp) cc_final: 0.8131 (tpp) REVERT: C 773 GLU cc_start: 0.7251 (tt0) cc_final: 0.6975 (tt0) REVERT: C 774 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7763 (mp10) REVERT: C 803 SER cc_start: 0.8623 (t) cc_final: 0.8340 (p) REVERT: C 804 GLN cc_start: 0.8233 (mt0) cc_final: 0.7981 (mt0) REVERT: C 868 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7294 (tp30) REVERT: C 870 ILE cc_start: 0.8319 (pt) cc_final: 0.8099 (mt) REVERT: C 886 TRP cc_start: 0.8164 (OUTLIER) cc_final: 0.7783 (p90) REVERT: C 900 MET cc_start: 0.8163 (mtm) cc_final: 0.7837 (mtm) REVERT: C 949 GLN cc_start: 0.8173 (tp40) cc_final: 0.7795 (tp40) REVERT: C 973 ILE cc_start: 0.8952 (mt) cc_final: 0.8620 (mm) REVERT: C 993 ILE cc_start: 0.8913 (mm) cc_final: 0.8693 (mt) REVERT: C 994 ASP cc_start: 0.7970 (t70) cc_final: 0.7660 (t0) REVERT: C 1029 MET cc_start: 0.8331 (tpp) cc_final: 0.8014 (tpp) REVERT: C 1072 GLU cc_start: 0.8029 (pm20) cc_final: 0.7825 (pm20) REVERT: C 1073 LYS cc_start: 0.7792 (mtpt) cc_final: 0.7511 (mmmm) REVERT: C 1103 PHE cc_start: 0.8351 (m-80) cc_final: 0.8006 (m-80) REVERT: C 1107 ARG cc_start: 0.8002 (mtt180) cc_final: 0.7086 (mtt90) REVERT: C 1139 ASP cc_start: 0.8170 (t0) cc_final: 0.7952 (t0) REVERT: B 65 PHE cc_start: 0.7827 (m-80) cc_final: 0.7607 (m-10) REVERT: B 132 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7581 (mp0) REVERT: B 204 TYR cc_start: 0.7507 (m-80) cc_final: 0.7132 (m-80) REVERT: B 206 LYS cc_start: 0.8417 (tptm) cc_final: 0.8019 (tptp) REVERT: B 270 LEU cc_start: 0.8060 (mt) cc_final: 0.7822 (mp) REVERT: B 275 PHE cc_start: 0.8239 (m-80) cc_final: 0.8038 (m-80) REVERT: B 296 LEU cc_start: 0.8216 (tp) cc_final: 0.7997 (tp) REVERT: B 324 GLU cc_start: 0.7916 (pm20) cc_final: 0.7629 (pm20) REVERT: B 358 ILE cc_start: 0.8311 (mm) cc_final: 0.7728 (tt) REVERT: B 392 PHE cc_start: 0.6226 (m-80) cc_final: 0.5861 (m-10) REVERT: B 394 ASN cc_start: 0.8395 (p0) cc_final: 0.8095 (p0) REVERT: B 448 ASN cc_start: 0.7926 (t0) cc_final: 0.6285 (p0) REVERT: B 576 VAL cc_start: 0.8875 (p) cc_final: 0.8527 (t) REVERT: B 580 GLN cc_start: 0.7457 (mm110) cc_final: 0.7112 (mm-40) REVERT: B 619 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7207 (mt-10) REVERT: B 764 ASN cc_start: 0.8208 (m-40) cc_final: 0.7996 (m110) REVERT: B 773 GLU cc_start: 0.7317 (pt0) cc_final: 0.6977 (pt0) REVERT: B 781 VAL cc_start: 0.8546 (t) cc_final: 0.8269 (p) REVERT: B 790 LYS cc_start: 0.8484 (ptmt) cc_final: 0.8183 (ptmt) REVERT: B 904 TYR cc_start: 0.7687 (m-10) cc_final: 0.7252 (m-10) REVERT: B 929 SER cc_start: 0.8276 (t) cc_final: 0.7884 (p) REVERT: B 953 ASN cc_start: 0.8289 (m-40) cc_final: 0.8047 (m-40) REVERT: B 968 SER cc_start: 0.8688 (m) cc_final: 0.8337 (t) REVERT: B 987 VAL cc_start: 0.8298 (t) cc_final: 0.8064 (p) REVERT: B 1086 LYS cc_start: 0.8423 (mppt) cc_final: 0.7966 (mtmm) REVERT: B 1117 THR cc_start: 0.8328 (m) cc_final: 0.8001 (t) REVERT: B 1136 THR cc_start: 0.8641 (t) cc_final: 0.8306 (p) REVERT: B 1141 LEU cc_start: 0.8668 (tt) cc_final: 0.8394 (tt) REVERT: A 28 TYR cc_start: 0.8004 (m-80) cc_final: 0.7795 (m-80) REVERT: A 48 LEU cc_start: 0.8135 (mp) cc_final: 0.7922 (mt) REVERT: A 117 LEU cc_start: 0.7953 (tp) cc_final: 0.7459 (mp) REVERT: A 120 VAL cc_start: 0.7874 (t) cc_final: 0.7504 (m) REVERT: A 191 GLU cc_start: 0.7425 (mp0) cc_final: 0.6924 (mt-10) REVERT: A 206 LYS cc_start: 0.8166 (tptm) cc_final: 0.7922 (tptm) REVERT: A 239 GLN cc_start: 0.8028 (tt0) cc_final: 0.7795 (tt0) REVERT: A 535 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8577 (mttp) REVERT: A 544 ASN cc_start: 0.7670 (t0) cc_final: 0.7357 (t0) REVERT: A 549 THR cc_start: 0.7939 (m) cc_final: 0.7590 (p) REVERT: A 551 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8415 (m) REVERT: A 569 ILE cc_start: 0.8652 (mp) cc_final: 0.8415 (mm) REVERT: A 580 GLN cc_start: 0.6912 (mt0) cc_final: 0.6548 (mm110) REVERT: A 596 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8435 (p) REVERT: A 605 SER cc_start: 0.8693 (t) cc_final: 0.8274 (m) REVERT: A 654 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8077 (tt0) REVERT: A 664 ILE cc_start: 0.8247 (mt) cc_final: 0.7876 (tt) REVERT: A 704 SER cc_start: 0.8491 (t) cc_final: 0.8080 (p) REVERT: A 755 GLN cc_start: 0.7714 (mt0) cc_final: 0.7276 (pt0) REVERT: A 758 SER cc_start: 0.8688 (m) cc_final: 0.8267 (p) REVERT: A 773 GLU cc_start: 0.7794 (tt0) cc_final: 0.7460 (tt0) REVERT: A 776 LYS cc_start: 0.8357 (tmmt) cc_final: 0.7984 (ttpp) REVERT: A 790 LYS cc_start: 0.8280 (ttpp) cc_final: 0.8007 (ttmm) REVERT: A 796 ASP cc_start: 0.6816 (p0) cc_final: 0.6397 (p0) REVERT: A 825 LYS cc_start: 0.8329 (mmmt) cc_final: 0.7991 (mmmm) REVERT: A 878 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8223 (mt) REVERT: A 921 LYS cc_start: 0.8062 (mmtp) cc_final: 0.7839 (mmtp) REVERT: A 935 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: A 950 ASP cc_start: 0.7579 (t0) cc_final: 0.7171 (t0) REVERT: A 1038 LYS cc_start: 0.8604 (mttt) cc_final: 0.8314 (mttm) REVERT: A 1045 LYS cc_start: 0.8405 (mttt) cc_final: 0.8116 (mttt) REVERT: A 1073 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8107 (mtpp) REVERT: A 1084 ASP cc_start: 0.7712 (p0) cc_final: 0.7336 (p0) REVERT: A 1139 ASP cc_start: 0.8148 (t0) cc_final: 0.7779 (t0) REVERT: A 1141 LEU cc_start: 0.8785 (tt) cc_final: 0.8567 (tt) REVERT: D 39 LEU cc_start: 0.8468 (mt) cc_final: 0.8259 (mt) REVERT: D 41 TYR cc_start: 0.8178 (t80) cc_final: 0.7266 (t80) REVERT: D 42 GLN cc_start: 0.8009 (tp40) cc_final: 0.7247 (tp40) REVERT: D 74 LYS cc_start: 0.8657 (tppp) cc_final: 0.8110 (tppp) REVERT: D 340 GLN cc_start: 0.1579 (tm-30) cc_final: 0.1250 (tm-30) REVERT: D 360 MET cc_start: 0.3810 (tmm) cc_final: 0.3133 (tmm) REVERT: D 369 PHE cc_start: 0.8766 (t80) cc_final: 0.8421 (t80) REVERT: D 376 MET cc_start: 0.0628 (ttm) cc_final: 0.0014 (mpp) REVERT: D 454 TYR cc_start: 0.5891 (t80) cc_final: 0.5285 (t80) REVERT: D 479 GLU cc_start: 0.7974 (pt0) cc_final: 0.7513 (pp20) REVERT: D 521 TYR cc_start: 0.5049 (m-10) cc_final: 0.4458 (m-80) REVERT: D 557 MET cc_start: 0.7415 (tmm) cc_final: 0.7053 (tmm) REVERT: D 560 LEU cc_start: 0.7717 (mt) cc_final: 0.7477 (mp) outliers start: 96 outliers final: 51 residues processed: 763 average time/residue: 0.2154 time to fit residues: 262.4927 Evaluate side-chains 701 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 643 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 522 GLN Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 0.0980 chunk 329 optimal weight: 30.0000 chunk 14 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 212 optimal weight: 0.7980 chunk 301 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 chunk 355 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN C 777 ASN C1119 ASN B 30 ASN B 394 ASN B 675 GLN B1002 GLN B1119 ASN A 207 HIS A 542 ASN A 658 ASN A 675 GLN A 919 ASN A 935 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN D 380 GLN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.184177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.136603 restraints weight = 50757.747| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.78 r_work: 0.3494 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 31780 Z= 0.261 Angle : 0.681 14.790 43372 Z= 0.338 Chirality : 0.048 0.621 5026 Planarity : 0.004 0.044 5477 Dihedral : 7.507 94.574 5603 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.48 % Allowed : 11.94 % Favored : 84.58 % 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: -0.92 (0.13), residues: 3761 helix: 1.33 (0.17), residues: 1036 sheet: -0.39 (0.19), residues: 659 loop : -1.80 (0.12), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1107 TYR 0.029 0.002 TYR D 183 PHE 0.023 0.002 PHE B 201 TRP 0.016 0.001 TRP B 104 HIS 0.009 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00579 (31664) covalent geometry : angle 0.64907 (43069) SS BOND : bond 0.00540 ( 45) SS BOND : angle 3.26896 ( 90) hydrogen bonds : bond 0.04588 ( 1172) hydrogen bonds : angle 5.51078 ( 3312) link_BETA1-4 : bond 0.00294 ( 21) link_BETA1-4 : angle 1.15933 ( 63) link_NAG-ASN : bond 0.00573 ( 50) link_NAG-ASN : angle 2.44830 ( 150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 667 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 THR cc_start: 0.8153 (t) cc_final: 0.6779 (p) REVERT: C 42 VAL cc_start: 0.8640 (p) cc_final: 0.8240 (m) REVERT: C 129 LYS cc_start: 0.8337 (mtmt) cc_final: 0.8128 (mtmm) REVERT: C 140 PHE cc_start: 0.8153 (p90) cc_final: 0.7934 (p90) REVERT: C 228 ASP cc_start: 0.7637 (t0) cc_final: 0.6961 (t70) REVERT: C 276 LEU cc_start: 0.8837 (tp) cc_final: 0.8632 (tt) REVERT: C 284 THR cc_start: 0.8690 (m) cc_final: 0.8279 (t) REVERT: C 289 VAL cc_start: 0.8770 (p) cc_final: 0.8481 (m) REVERT: C 305 SER cc_start: 0.8893 (t) cc_final: 0.8493 (p) REVERT: C 353 TRP cc_start: 0.7803 (p-90) cc_final: 0.7453 (p-90) REVERT: C 378 LYS cc_start: 0.8151 (mttt) cc_final: 0.7692 (mttt) REVERT: C 424 LYS cc_start: 0.7442 (tttt) cc_final: 0.6626 (ttpp) REVERT: C 704 SER cc_start: 0.8414 (m) cc_final: 0.7916 (t) REVERT: C 740 MET cc_start: 0.8575 (tpp) cc_final: 0.8299 (tpp) REVERT: C 773 GLU cc_start: 0.7703 (tt0) cc_final: 0.7452 (tt0) REVERT: C 774 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7982 (mp-120) REVERT: C 796 ASP cc_start: 0.7674 (t0) cc_final: 0.7400 (t0) REVERT: C 803 SER cc_start: 0.8846 (t) cc_final: 0.8560 (p) REVERT: C 804 GLN cc_start: 0.8443 (mt0) cc_final: 0.8199 (mt0) REVERT: C 868 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7603 (tp30) REVERT: C 870 ILE cc_start: 0.8395 (pt) cc_final: 0.8155 (mt) REVERT: C 886 TRP cc_start: 0.8354 (OUTLIER) cc_final: 0.7795 (p90) REVERT: C 900 MET cc_start: 0.8456 (mtm) cc_final: 0.8174 (mtm) REVERT: C 949 GLN cc_start: 0.8447 (tp40) cc_final: 0.7979 (tp40) REVERT: C 973 ILE cc_start: 0.9104 (mt) cc_final: 0.8869 (mm) REVERT: C 994 ASP cc_start: 0.8406 (t70) cc_final: 0.8101 (t0) REVERT: C 1010 GLN cc_start: 0.8107 (mm-40) cc_final: 0.7655 (mm-40) REVERT: C 1029 MET cc_start: 0.8503 (tpp) cc_final: 0.8202 (tpp) REVERT: C 1072 GLU cc_start: 0.8190 (pm20) cc_final: 0.7926 (pm20) REVERT: C 1073 LYS cc_start: 0.8039 (mtpt) cc_final: 0.7555 (mtpp) REVERT: C 1107 ARG cc_start: 0.8221 (mtt180) cc_final: 0.7302 (mtt90) REVERT: C 1139 ASP cc_start: 0.8360 (t0) cc_final: 0.7944 (t0) REVERT: B 47 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8141 (p) REVERT: B 65 PHE cc_start: 0.8090 (m-80) cc_final: 0.7860 (m-10) REVERT: B 132 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7654 (mp0) REVERT: B 159 VAL cc_start: 0.7509 (OUTLIER) cc_final: 0.7226 (m) REVERT: B 169 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7755 (tp30) REVERT: B 195 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7828 (ptpt) REVERT: B 206 LYS cc_start: 0.8603 (tptm) cc_final: 0.8203 (tptp) REVERT: B 226 LEU cc_start: 0.7464 (mt) cc_final: 0.7134 (mt) REVERT: B 324 GLU cc_start: 0.8271 (pm20) cc_final: 0.7716 (pm20) REVERT: B 355 ARG cc_start: 0.7590 (ttt180) cc_final: 0.7326 (ttt180) REVERT: B 386 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8199 (mmmm) REVERT: B 392 PHE cc_start: 0.6796 (m-80) cc_final: 0.6004 (m-10) REVERT: B 394 ASN cc_start: 0.8514 (p0) cc_final: 0.8218 (p0) REVERT: B 396 TYR cc_start: 0.7618 (m-80) cc_final: 0.7204 (m-80) REVERT: B 448 ASN cc_start: 0.8284 (t0) cc_final: 0.6269 (p0) REVERT: B 519 HIS cc_start: 0.4106 (OUTLIER) cc_final: 0.3867 (p-80) REVERT: B 576 VAL cc_start: 0.8974 (p) cc_final: 0.8600 (t) REVERT: B 619 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7581 (mt-10) REVERT: B 764 ASN cc_start: 0.8597 (m-40) cc_final: 0.8319 (m-40) REVERT: B 790 LYS cc_start: 0.8562 (ptmt) cc_final: 0.8274 (ptmt) REVERT: B 820 ASP cc_start: 0.7774 (t0) cc_final: 0.7397 (t0) REVERT: B 904 TYR cc_start: 0.7876 (m-10) cc_final: 0.7425 (m-10) REVERT: B 929 SER cc_start: 0.8577 (t) cc_final: 0.8230 (p) REVERT: B 950 ASP cc_start: 0.8028 (t0) cc_final: 0.7377 (t0) REVERT: B 953 ASN cc_start: 0.8532 (m-40) cc_final: 0.8315 (m110) REVERT: B 968 SER cc_start: 0.8875 (m) cc_final: 0.8549 (t) REVERT: B 987 VAL cc_start: 0.8465 (t) cc_final: 0.8227 (p) REVERT: B 994 ASP cc_start: 0.8234 (t70) cc_final: 0.8009 (t0) REVERT: B 1003 SER cc_start: 0.8632 (m) cc_final: 0.8302 (t) REVERT: B 1086 LYS cc_start: 0.8669 (mppt) cc_final: 0.8157 (mtmm) REVERT: B 1117 THR cc_start: 0.8394 (m) cc_final: 0.8046 (t) REVERT: B 1136 THR cc_start: 0.8786 (t) cc_final: 0.8468 (p) REVERT: A 28 TYR cc_start: 0.8336 (m-80) cc_final: 0.8102 (m-80) REVERT: A 117 LEU cc_start: 0.8307 (tp) cc_final: 0.7646 (mp) REVERT: A 120 VAL cc_start: 0.8057 (t) cc_final: 0.7757 (m) REVERT: A 191 GLU cc_start: 0.7834 (mp0) cc_final: 0.7314 (mt-10) REVERT: A 535 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8680 (mttm) REVERT: A 544 ASN cc_start: 0.8018 (t0) cc_final: 0.7702 (t0) REVERT: A 549 THR cc_start: 0.8108 (m) cc_final: 0.7835 (p) REVERT: A 569 ILE cc_start: 0.8719 (mp) cc_final: 0.8471 (mm) REVERT: A 580 GLN cc_start: 0.7367 (mt0) cc_final: 0.7098 (mm110) REVERT: A 586 ASP cc_start: 0.7997 (t0) cc_final: 0.7595 (m-30) REVERT: A 596 SER cc_start: 0.8921 (OUTLIER) cc_final: 0.8599 (p) REVERT: A 605 SER cc_start: 0.8761 (t) cc_final: 0.8385 (m) REVERT: A 654 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8327 (tt0) REVERT: A 660 TYR cc_start: 0.8911 (m-80) cc_final: 0.8034 (m-80) REVERT: A 704 SER cc_start: 0.8706 (t) cc_final: 0.8364 (p) REVERT: A 719 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8314 (p) REVERT: A 758 SER cc_start: 0.8747 (m) cc_final: 0.8349 (p) REVERT: A 790 LYS cc_start: 0.8519 (ttpp) cc_final: 0.8258 (ttmm) REVERT: A 796 ASP cc_start: 0.7030 (p0) cc_final: 0.6572 (p0) REVERT: A 825 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8163 (mmmm) REVERT: A 900 MET cc_start: 0.8482 (mtp) cc_final: 0.8039 (mtp) REVERT: A 921 LYS cc_start: 0.8363 (mmtp) cc_final: 0.8109 (mmtp) REVERT: A 935 GLN cc_start: 0.8405 (tt0) cc_final: 0.8140 (tt0) REVERT: A 950 ASP cc_start: 0.7951 (t0) cc_final: 0.7524 (t0) REVERT: A 1038 LYS cc_start: 0.8861 (mttt) cc_final: 0.8554 (mttm) REVERT: A 1045 LYS cc_start: 0.8616 (mttt) cc_final: 0.8301 (mttt) REVERT: A 1073 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8288 (mtpp) REVERT: A 1084 ASP cc_start: 0.8056 (p0) cc_final: 0.7814 (p0) REVERT: A 1126 CYS cc_start: 0.7325 (m) cc_final: 0.7048 (m) REVERT: A 1144 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7633 (mt-10) REVERT: D 26 LYS cc_start: 0.8280 (mtmm) cc_final: 0.8013 (mmtp) REVERT: D 41 TYR cc_start: 0.8333 (t80) cc_final: 0.7346 (t80) REVERT: D 42 GLN cc_start: 0.8187 (tp40) cc_final: 0.7383 (tp40) REVERT: D 64 ASN cc_start: 0.8806 (t0) cc_final: 0.7714 (m-40) REVERT: D 74 LYS cc_start: 0.8692 (tppp) cc_final: 0.8191 (tppp) REVERT: D 123 MET cc_start: 0.1300 (ptt) cc_final: 0.0952 (ptt) REVERT: D 309 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8461 (mmtt) REVERT: D 360 MET cc_start: 0.3868 (tmm) cc_final: 0.3575 (tmm) REVERT: D 369 PHE cc_start: 0.8830 (t80) cc_final: 0.8477 (t80) REVERT: D 407 ILE cc_start: 0.7515 (mm) cc_final: 0.7213 (mm) REVERT: D 408 MET cc_start: 0.7783 (mpm) cc_final: 0.7558 (mpm) REVERT: D 410 LEU cc_start: 0.8717 (mt) cc_final: 0.8245 (pp) REVERT: D 454 TYR cc_start: 0.5933 (t80) cc_final: 0.5389 (t80) REVERT: D 479 GLU cc_start: 0.7981 (pt0) cc_final: 0.7576 (pp20) REVERT: D 521 TYR cc_start: 0.5062 (m-10) cc_final: 0.4450 (m-80) REVERT: D 557 MET cc_start: 0.7574 (tmm) cc_final: 0.7177 (tmm) REVERT: D 560 LEU cc_start: 0.7598 (mt) cc_final: 0.7366 (mp) outliers start: 116 outliers final: 79 residues processed: 745 average time/residue: 0.2046 time to fit residues: 244.7953 Evaluate side-chains 721 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 633 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 522 GLN Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 51 optimal weight: 0.8980 chunk 242 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 270 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 327 optimal weight: 10.0000 chunk 173 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 804 GLN C1101 HIS B 30 ASN B 777 ASN B1011 GLN A 66 HIS A 207 HIS A 239 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 89 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.184670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.137465 restraints weight = 50461.433| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.76 r_work: 0.3501 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31780 Z= 0.193 Angle : 0.634 15.519 43372 Z= 0.312 Chirality : 0.046 0.364 5026 Planarity : 0.004 0.048 5477 Dihedral : 6.652 93.571 5599 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.75 % Allowed : 13.02 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.76 (0.13), residues: 3761 helix: 1.43 (0.17), residues: 1047 sheet: -0.40 (0.19), residues: 657 loop : -1.64 (0.12), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 190 TYR 0.035 0.001 TYR D 183 PHE 0.024 0.002 PHE C 192 TRP 0.014 0.001 TRP B 436 HIS 0.008 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00430 (31664) covalent geometry : angle 0.60559 (43069) SS BOND : bond 0.00508 ( 45) SS BOND : angle 2.76738 ( 90) hydrogen bonds : bond 0.04114 ( 1172) hydrogen bonds : angle 5.32358 ( 3312) link_BETA1-4 : bond 0.00327 ( 21) link_BETA1-4 : angle 1.08757 ( 63) link_NAG-ASN : bond 0.00519 ( 50) link_NAG-ASN : angle 2.39463 ( 150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 647 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 THR cc_start: 0.7947 (t) cc_final: 0.6619 (p) REVERT: C 42 VAL cc_start: 0.8490 (p) cc_final: 0.8130 (m) REVERT: C 64 TRP cc_start: 0.8149 (t60) cc_final: 0.7862 (t60) REVERT: C 99 ASN cc_start: 0.7916 (t0) cc_final: 0.7678 (t0) REVERT: C 129 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7687 (mtmm) REVERT: C 140 PHE cc_start: 0.7992 (p90) cc_final: 0.7776 (p90) REVERT: C 228 ASP cc_start: 0.7271 (t0) cc_final: 0.6550 (t70) REVERT: C 284 THR cc_start: 0.8586 (m) cc_final: 0.8209 (t) REVERT: C 287 ASP cc_start: 0.7877 (t0) cc_final: 0.7589 (m-30) REVERT: C 289 VAL cc_start: 0.8731 (p) cc_final: 0.8410 (m) REVERT: C 305 SER cc_start: 0.8895 (t) cc_final: 0.8502 (p) REVERT: C 353 TRP cc_start: 0.7755 (p-90) cc_final: 0.7330 (p-90) REVERT: C 362 VAL cc_start: 0.7974 (t) cc_final: 0.7702 (m) REVERT: C 378 LYS cc_start: 0.8075 (mttt) cc_final: 0.7647 (mttt) REVERT: C 398 ASP cc_start: 0.7165 (m-30) cc_final: 0.6894 (p0) REVERT: C 424 LYS cc_start: 0.7295 (tttt) cc_final: 0.6607 (ttpp) REVERT: C 537 LYS cc_start: 0.8247 (mtpt) cc_final: 0.8003 (ttpt) REVERT: C 646 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7516 (ttm170) REVERT: C 704 SER cc_start: 0.8430 (m) cc_final: 0.7855 (t) REVERT: C 773 GLU cc_start: 0.7453 (tt0) cc_final: 0.7173 (tt0) REVERT: C 774 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7773 (mp-120) REVERT: C 796 ASP cc_start: 0.7599 (t0) cc_final: 0.7148 (t0) REVERT: C 803 SER cc_start: 0.8760 (t) cc_final: 0.8468 (p) REVERT: C 804 GLN cc_start: 0.8208 (mt0) cc_final: 0.7935 (mt0) REVERT: C 868 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7297 (tp30) REVERT: C 870 ILE cc_start: 0.8226 (pt) cc_final: 0.7977 (mt) REVERT: C 886 TRP cc_start: 0.8302 (OUTLIER) cc_final: 0.7773 (p90) REVERT: C 900 MET cc_start: 0.8238 (mtm) cc_final: 0.8002 (mtm) REVERT: C 949 GLN cc_start: 0.8236 (tp40) cc_final: 0.7818 (tp40) REVERT: C 973 ILE cc_start: 0.8991 (mt) cc_final: 0.8777 (mm) REVERT: C 994 ASP cc_start: 0.8100 (t70) cc_final: 0.7752 (t0) REVERT: C 1073 LYS cc_start: 0.7848 (mtpt) cc_final: 0.7394 (mtpp) REVERT: C 1107 ARG cc_start: 0.7950 (mtt180) cc_final: 0.7683 (mtt90) REVERT: C 1139 ASP cc_start: 0.8261 (t0) cc_final: 0.8043 (t0) REVERT: B 47 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.8045 (p) REVERT: B 65 PHE cc_start: 0.7940 (m-80) cc_final: 0.7730 (m-10) REVERT: B 102 ARG cc_start: 0.7595 (mtt180) cc_final: 0.7243 (mmt-90) REVERT: B 132 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7535 (mp0) REVERT: B 159 VAL cc_start: 0.7292 (OUTLIER) cc_final: 0.7039 (m) REVERT: B 169 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: B 195 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7667 (ptpp) REVERT: B 226 LEU cc_start: 0.7424 (mt) cc_final: 0.7060 (mt) REVERT: B 294 ASP cc_start: 0.8174 (p0) cc_final: 0.7888 (p0) REVERT: B 296 LEU cc_start: 0.8341 (tp) cc_final: 0.8070 (tp) REVERT: B 355 ARG cc_start: 0.7356 (ttt180) cc_final: 0.7138 (ttt180) REVERT: B 392 PHE cc_start: 0.6592 (m-80) cc_final: 0.5667 (m-10) REVERT: B 394 ASN cc_start: 0.8336 (p0) cc_final: 0.8122 (p0) REVERT: B 414 GLN cc_start: 0.6207 (tm-30) cc_final: 0.5923 (tm-30) REVERT: B 448 ASN cc_start: 0.8090 (t0) cc_final: 0.6070 (p0) REVERT: B 513 LEU cc_start: 0.8284 (mt) cc_final: 0.7954 (mp) REVERT: B 523 THR cc_start: 0.7590 (OUTLIER) cc_final: 0.7340 (m) REVERT: B 524 VAL cc_start: 0.8807 (t) cc_final: 0.8603 (p) REVERT: B 580 GLN cc_start: 0.7342 (mm110) cc_final: 0.6935 (mm110) REVERT: B 599 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8055 (p) REVERT: B 619 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7037 (mt-10) REVERT: B 764 ASN cc_start: 0.8436 (m-40) cc_final: 0.8073 (m-40) REVERT: B 790 LYS cc_start: 0.8398 (ptmt) cc_final: 0.8133 (ptmt) REVERT: B 820 ASP cc_start: 0.7412 (t0) cc_final: 0.7069 (t0) REVERT: B 929 SER cc_start: 0.8410 (t) cc_final: 0.8083 (p) REVERT: B 950 ASP cc_start: 0.7753 (t0) cc_final: 0.7004 (t0) REVERT: B 968 SER cc_start: 0.8781 (m) cc_final: 0.8537 (m) REVERT: B 987 VAL cc_start: 0.8324 (t) cc_final: 0.8115 (p) REVERT: B 1003 SER cc_start: 0.8467 (m) cc_final: 0.8092 (t) REVERT: B 1073 LYS cc_start: 0.8531 (mttm) cc_final: 0.8317 (mtmt) REVERT: B 1101 HIS cc_start: 0.8513 (m90) cc_final: 0.8237 (m90) REVERT: B 1117 THR cc_start: 0.8305 (m) cc_final: 0.7965 (t) REVERT: B 1136 THR cc_start: 0.8632 (t) cc_final: 0.8328 (p) REVERT: A 28 TYR cc_start: 0.8159 (m-80) cc_final: 0.7830 (m-80) REVERT: A 120 VAL cc_start: 0.7879 (t) cc_final: 0.7631 (m) REVERT: A 191 GLU cc_start: 0.7487 (mp0) cc_final: 0.7007 (mt-10) REVERT: A 239 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: A 298 GLU cc_start: 0.7661 (tt0) cc_final: 0.7459 (tt0) REVERT: A 535 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8606 (mttm) REVERT: A 544 ASN cc_start: 0.7942 (t0) cc_final: 0.7652 (t0) REVERT: A 549 THR cc_start: 0.7947 (m) cc_final: 0.7675 (p) REVERT: A 557 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8143 (mttt) REVERT: A 586 ASP cc_start: 0.7673 (t0) cc_final: 0.7403 (t0) REVERT: A 596 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8439 (p) REVERT: A 605 SER cc_start: 0.8698 (t) cc_final: 0.8326 (m) REVERT: A 704 SER cc_start: 0.8556 (t) cc_final: 0.8223 (p) REVERT: A 719 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8211 (p) REVERT: A 758 SER cc_start: 0.8535 (m) cc_final: 0.8115 (p) REVERT: A 796 ASP cc_start: 0.6908 (p0) cc_final: 0.6423 (p0) REVERT: A 825 LYS cc_start: 0.8404 (mmmt) cc_final: 0.8025 (mmmm) REVERT: A 900 MET cc_start: 0.8301 (mtp) cc_final: 0.7673 (mtp) REVERT: A 921 LYS cc_start: 0.8169 (mmtp) cc_final: 0.7945 (mmtp) REVERT: A 950 ASP cc_start: 0.7618 (t0) cc_final: 0.7187 (t0) REVERT: A 986 LYS cc_start: 0.8082 (mttm) cc_final: 0.7526 (mttm) REVERT: A 987 VAL cc_start: 0.8455 (p) cc_final: 0.8015 (t) REVERT: A 990 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6989 (mp0) REVERT: A 1019 ARG cc_start: 0.7850 (ttm110) cc_final: 0.7483 (ttp80) REVERT: A 1038 LYS cc_start: 0.8710 (mttt) cc_final: 0.8367 (mmtm) REVERT: A 1045 LYS cc_start: 0.8409 (mttt) cc_final: 0.8104 (mttt) REVERT: A 1073 LYS cc_start: 0.8486 (mtpt) cc_final: 0.8171 (mtpp) REVERT: A 1084 ASP cc_start: 0.7825 (p0) cc_final: 0.7467 (p0) REVERT: A 1144 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7463 (mt-10) REVERT: D 26 LYS cc_start: 0.8292 (mtmm) cc_final: 0.8038 (mmtp) REVERT: D 41 TYR cc_start: 0.8048 (t80) cc_final: 0.7077 (t80) REVERT: D 42 GLN cc_start: 0.8047 (tp40) cc_final: 0.7251 (tp40) REVERT: D 72 PHE cc_start: 0.8059 (t80) cc_final: 0.7833 (t80) REVERT: D 74 LYS cc_start: 0.8607 (tppp) cc_final: 0.8101 (tppp) REVERT: D 308 PHE cc_start: 0.7982 (m-80) cc_final: 0.7432 (m-80) REVERT: D 309 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8552 (mmtt) REVERT: D 360 MET cc_start: 0.3867 (tmm) cc_final: 0.3497 (tmm) REVERT: D 369 PHE cc_start: 0.8762 (t80) cc_final: 0.8384 (t80) REVERT: D 380 GLN cc_start: 0.4429 (mm110) cc_final: 0.4208 (mm-40) REVERT: D 383 MET cc_start: 0.6778 (mpp) cc_final: 0.6186 (mpp) REVERT: D 391 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6390 (pp) REVERT: D 410 LEU cc_start: 0.8753 (mt) cc_final: 0.8257 (pp) REVERT: D 454 TYR cc_start: 0.5854 (t80) cc_final: 0.5299 (t80) REVERT: D 479 GLU cc_start: 0.7950 (pt0) cc_final: 0.7487 (pp20) REVERT: D 497 TYR cc_start: 0.6552 (m-80) cc_final: 0.6160 (m-80) REVERT: D 521 TYR cc_start: 0.5050 (m-10) cc_final: 0.4496 (m-80) REVERT: D 557 MET cc_start: 0.7474 (tmm) cc_final: 0.7109 (tmm) REVERT: D 570 LEU cc_start: 0.1869 (OUTLIER) cc_final: -0.0116 (mm) outliers start: 125 outliers final: 81 residues processed: 731 average time/residue: 0.2139 time to fit residues: 249.2048 Evaluate side-chains 714 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 618 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 185 optimal weight: 0.9980 chunk 214 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 242 optimal weight: 0.9990 chunk 287 optimal weight: 0.0670 chunk 56 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 311 optimal weight: 2.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN B 777 ASN B1119 ASN A 188 ASN A 239 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 935 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.184606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137289 restraints weight = 50361.827| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.77 r_work: 0.3495 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 31780 Z= 0.193 Angle : 0.626 11.893 43372 Z= 0.310 Chirality : 0.046 0.370 5026 Planarity : 0.004 0.052 5477 Dihedral : 6.425 87.510 5599 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.38 % Allowed : 13.47 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.64 (0.13), residues: 3761 helix: 1.51 (0.17), residues: 1045 sheet: -0.37 (0.19), residues: 667 loop : -1.54 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 190 TYR 0.021 0.001 TYR A 707 PHE 0.020 0.002 PHE C 192 TRP 0.026 0.001 TRP B 152 HIS 0.018 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00431 (31664) covalent geometry : angle 0.60132 (43069) SS BOND : bond 0.00518 ( 45) SS BOND : angle 2.72265 ( 90) hydrogen bonds : bond 0.04041 ( 1172) hydrogen bonds : angle 5.29177 ( 3312) link_BETA1-4 : bond 0.00270 ( 21) link_BETA1-4 : angle 1.09646 ( 63) link_NAG-ASN : bond 0.00442 ( 50) link_NAG-ASN : angle 2.10238 ( 150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 655 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 THR cc_start: 0.8154 (t) cc_final: 0.6753 (p) REVERT: C 42 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8245 (m) REVERT: C 99 ASN cc_start: 0.7899 (t0) cc_final: 0.7500 (t0) REVERT: C 267 VAL cc_start: 0.8620 (t) cc_final: 0.8335 (p) REVERT: C 284 THR cc_start: 0.8680 (m) cc_final: 0.8297 (t) REVERT: C 287 ASP cc_start: 0.8118 (t0) cc_final: 0.7681 (m-30) REVERT: C 289 VAL cc_start: 0.8860 (p) cc_final: 0.8596 (m) REVERT: C 305 SER cc_start: 0.8967 (t) cc_final: 0.8576 (p) REVERT: C 353 TRP cc_start: 0.7884 (p-90) cc_final: 0.7464 (p-90) REVERT: C 362 VAL cc_start: 0.8260 (t) cc_final: 0.7984 (m) REVERT: C 378 LYS cc_start: 0.8169 (mttt) cc_final: 0.7709 (mttt) REVERT: C 400 PHE cc_start: 0.7454 (p90) cc_final: 0.7002 (p90) REVERT: C 414 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7364 (mm-40) REVERT: C 424 LYS cc_start: 0.7396 (tttt) cc_final: 0.6742 (ttpp) REVERT: C 430 THR cc_start: 0.8481 (t) cc_final: 0.8113 (p) REVERT: C 495 TYR cc_start: 0.7267 (m-80) cc_final: 0.6397 (m-80) REVERT: C 537 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8215 (ttpt) REVERT: C 580 GLN cc_start: 0.8183 (mt0) cc_final: 0.7327 (mt0) REVERT: C 646 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7885 (ttm170) REVERT: C 704 SER cc_start: 0.8564 (m) cc_final: 0.8006 (t) REVERT: C 773 GLU cc_start: 0.7795 (tt0) cc_final: 0.7476 (tt0) REVERT: C 774 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7950 (mp-120) REVERT: C 796 ASP cc_start: 0.7788 (t0) cc_final: 0.7375 (t0) REVERT: C 803 SER cc_start: 0.8867 (t) cc_final: 0.8583 (p) REVERT: C 804 GLN cc_start: 0.8440 (mt0) cc_final: 0.8156 (mt0) REVERT: C 868 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7574 (tp30) REVERT: C 870 ILE cc_start: 0.8370 (pt) cc_final: 0.8133 (mt) REVERT: C 886 TRP cc_start: 0.8352 (OUTLIER) cc_final: 0.7786 (p90) REVERT: C 900 MET cc_start: 0.8450 (mtm) cc_final: 0.8219 (mtm) REVERT: C 949 GLN cc_start: 0.8422 (tp40) cc_final: 0.7963 (tp40) REVERT: C 994 ASP cc_start: 0.8402 (t70) cc_final: 0.8055 (t0) REVERT: C 1010 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7647 (mm-40) REVERT: C 1073 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7594 (mtpp) REVERT: C 1107 ARG cc_start: 0.8251 (mtt180) cc_final: 0.7990 (mtt90) REVERT: C 1139 ASP cc_start: 0.8408 (t0) cc_final: 0.8198 (t0) REVERT: B 90 VAL cc_start: 0.8707 (p) cc_final: 0.8359 (m) REVERT: B 159 VAL cc_start: 0.7452 (OUTLIER) cc_final: 0.7119 (m) REVERT: B 195 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7917 (ptpt) REVERT: B 206 LYS cc_start: 0.8601 (tptm) cc_final: 0.8273 (tptp) REVERT: B 294 ASP cc_start: 0.8422 (p0) cc_final: 0.8168 (p0) REVERT: B 360 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7999 (m110) REVERT: B 392 PHE cc_start: 0.6899 (m-80) cc_final: 0.6247 (m-80) REVERT: B 394 ASN cc_start: 0.8551 (p0) cc_final: 0.8323 (p0) REVERT: B 414 GLN cc_start: 0.6465 (tm-30) cc_final: 0.6103 (tm-30) REVERT: B 448 ASN cc_start: 0.8315 (t0) cc_final: 0.6087 (p0) REVERT: B 519 HIS cc_start: 0.4308 (OUTLIER) cc_final: 0.4101 (p-80) REVERT: B 523 THR cc_start: 0.7765 (OUTLIER) cc_final: 0.7481 (m) REVERT: B 543 PHE cc_start: 0.8491 (m-10) cc_final: 0.8276 (m-10) REVERT: B 580 GLN cc_start: 0.7559 (mm110) cc_final: 0.7105 (mm110) REVERT: B 619 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7397 (mt-10) REVERT: B 673 SER cc_start: 0.9019 (t) cc_final: 0.8561 (m) REVERT: B 733 LYS cc_start: 0.8328 (mttt) cc_final: 0.8060 (mtpp) REVERT: B 764 ASN cc_start: 0.8612 (m-40) cc_final: 0.8280 (m-40) REVERT: B 790 LYS cc_start: 0.8533 (ptmt) cc_final: 0.8299 (ptmt) REVERT: B 811 LYS cc_start: 0.7500 (mttt) cc_final: 0.7056 (mtpt) REVERT: B 820 ASP cc_start: 0.7688 (t0) cc_final: 0.7257 (t0) REVERT: B 929 SER cc_start: 0.8582 (t) cc_final: 0.8251 (p) REVERT: B 950 ASP cc_start: 0.8084 (t0) cc_final: 0.7539 (t0) REVERT: B 968 SER cc_start: 0.8854 (m) cc_final: 0.8624 (m) REVERT: B 1003 SER cc_start: 0.8659 (m) cc_final: 0.8328 (t) REVERT: B 1107 ARG cc_start: 0.8337 (mtt90) cc_final: 0.8113 (mtt90) REVERT: B 1117 THR cc_start: 0.8404 (m) cc_final: 0.8048 (t) REVERT: B 1136 THR cc_start: 0.8757 (t) cc_final: 0.8459 (p) REVERT: A 28 TYR cc_start: 0.8361 (m-80) cc_final: 0.8000 (m-80) REVERT: A 120 VAL cc_start: 0.8144 (t) cc_final: 0.7853 (m) REVERT: A 191 GLU cc_start: 0.7848 (mp0) cc_final: 0.7471 (mt-10) REVERT: A 239 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: A 298 GLU cc_start: 0.8052 (tt0) cc_final: 0.7851 (tt0) REVERT: A 535 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8655 (mttm) REVERT: A 546 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7209 (pt) REVERT: A 549 THR cc_start: 0.8040 (m) cc_final: 0.7772 (p) REVERT: A 557 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8328 (mttt) REVERT: A 596 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8556 (p) REVERT: A 605 SER cc_start: 0.8789 (t) cc_final: 0.8441 (m) REVERT: A 661 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7763 (tt0) REVERT: A 704 SER cc_start: 0.8708 (t) cc_final: 0.8396 (p) REVERT: A 719 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8322 (p) REVERT: A 758 SER cc_start: 0.8664 (m) cc_final: 0.8196 (p) REVERT: A 825 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8190 (mmmm) REVERT: A 878 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8272 (mt) REVERT: A 900 MET cc_start: 0.8586 (mtp) cc_final: 0.7897 (mtp) REVERT: A 921 LYS cc_start: 0.8369 (mmtp) cc_final: 0.8109 (mmtp) REVERT: A 950 ASP cc_start: 0.7823 (t0) cc_final: 0.7416 (t0) REVERT: A 963 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8639 (p) REVERT: A 987 VAL cc_start: 0.8582 (p) cc_final: 0.8333 (t) REVERT: A 1019 ARG cc_start: 0.8061 (ttm110) cc_final: 0.7689 (ttp80) REVERT: A 1038 LYS cc_start: 0.8796 (mttt) cc_final: 0.8468 (mmtm) REVERT: A 1045 LYS cc_start: 0.8471 (mttt) cc_final: 0.8146 (mttt) REVERT: A 1073 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8343 (mtpp) REVERT: A 1084 ASP cc_start: 0.8110 (p0) cc_final: 0.7561 (p0) REVERT: A 1144 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7712 (mt-10) REVERT: D 26 LYS cc_start: 0.8297 (mtmm) cc_final: 0.8048 (mmtp) REVERT: D 41 TYR cc_start: 0.8241 (t80) cc_final: 0.7263 (t80) REVERT: D 42 GLN cc_start: 0.8168 (tp40) cc_final: 0.7391 (tp40) REVERT: D 72 PHE cc_start: 0.8176 (t80) cc_final: 0.7898 (t80) REVERT: D 74 LYS cc_start: 0.8663 (tppp) cc_final: 0.8157 (tppp) REVERT: D 308 PHE cc_start: 0.8226 (m-80) cc_final: 0.7491 (m-80) REVERT: D 309 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8575 (mmtt) REVERT: D 312 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8235 (mm-30) REVERT: D 314 PHE cc_start: 0.9079 (t80) cc_final: 0.8523 (m-10) REVERT: D 324 THR cc_start: 0.5655 (p) cc_final: 0.5029 (t) REVERT: D 360 MET cc_start: 0.3958 (tmm) cc_final: 0.3411 (tmm) REVERT: D 369 PHE cc_start: 0.8840 (t80) cc_final: 0.8537 (t80) REVERT: D 380 GLN cc_start: 0.4527 (mm110) cc_final: 0.4182 (mm-40) REVERT: D 383 MET cc_start: 0.7143 (mpp) cc_final: 0.6476 (mpp) REVERT: D 391 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6441 (pp) REVERT: D 410 LEU cc_start: 0.8826 (mt) cc_final: 0.8193 (pp) REVERT: D 454 TYR cc_start: 0.5847 (t80) cc_final: 0.5340 (t80) REVERT: D 479 GLU cc_start: 0.7926 (pt0) cc_final: 0.7459 (pp20) REVERT: D 480 MET cc_start: 0.7726 (mtp) cc_final: 0.7327 (mtp) REVERT: D 497 TYR cc_start: 0.6680 (m-80) cc_final: 0.6275 (m-80) REVERT: D 521 TYR cc_start: 0.5203 (m-10) cc_final: 0.4742 (m-80) REVERT: D 557 MET cc_start: 0.7433 (tmm) cc_final: 0.7130 (tmm) REVERT: D 570 LEU cc_start: 0.1918 (OUTLIER) cc_final: -0.0071 (mm) outliers start: 146 outliers final: 94 residues processed: 751 average time/residue: 0.2128 time to fit residues: 255.8636 Evaluate side-chains 746 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 633 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 50 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 275 optimal weight: 1.9990 chunk 59 optimal weight: 0.0970 chunk 140 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 777 ASN B 460 ASN B 777 ASN B1119 ASN A 239 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 935 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.184466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.137062 restraints weight = 50360.934| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.80 r_work: 0.3498 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31780 Z= 0.173 Angle : 0.630 13.409 43372 Z= 0.309 Chirality : 0.046 0.575 5026 Planarity : 0.004 0.058 5477 Dihedral : 6.230 79.623 5599 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.90 % Allowed : 14.79 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.54 (0.13), residues: 3761 helix: 1.59 (0.17), residues: 1045 sheet: -0.31 (0.19), residues: 681 loop : -1.47 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 190 TYR 0.022 0.001 TYR A 707 PHE 0.032 0.002 PHE B 201 TRP 0.022 0.001 TRP C 64 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00388 (31664) covalent geometry : angle 0.60196 (43069) SS BOND : bond 0.00469 ( 45) SS BOND : angle 2.71771 ( 90) hydrogen bonds : bond 0.03881 ( 1172) hydrogen bonds : angle 5.21591 ( 3312) link_BETA1-4 : bond 0.00299 ( 21) link_BETA1-4 : angle 1.09036 ( 63) link_NAG-ASN : bond 0.00419 ( 50) link_NAG-ASN : angle 2.41594 ( 150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 637 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 THR cc_start: 0.7964 (t) cc_final: 0.6648 (p) REVERT: C 42 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8145 (m) REVERT: C 99 ASN cc_start: 0.7888 (t0) cc_final: 0.7503 (t0) REVERT: C 129 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7725 (mptt) REVERT: C 239 GLN cc_start: 0.8130 (tt0) cc_final: 0.7892 (tt0) REVERT: C 267 VAL cc_start: 0.8409 (t) cc_final: 0.8118 (p) REVERT: C 284 THR cc_start: 0.8593 (m) cc_final: 0.8193 (t) REVERT: C 289 VAL cc_start: 0.8828 (p) cc_final: 0.8563 (m) REVERT: C 305 SER cc_start: 0.8913 (t) cc_final: 0.8530 (p) REVERT: C 356 LYS cc_start: 0.8616 (ptpt) cc_final: 0.8219 (pttt) REVERT: C 362 VAL cc_start: 0.8024 (t) cc_final: 0.7808 (m) REVERT: C 378 LYS cc_start: 0.8060 (mttt) cc_final: 0.7604 (mttt) REVERT: C 400 PHE cc_start: 0.7401 (p90) cc_final: 0.6839 (p90) REVERT: C 414 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7357 (mm-40) REVERT: C 424 LYS cc_start: 0.7357 (tttt) cc_final: 0.6624 (ttpp) REVERT: C 430 THR cc_start: 0.8470 (t) cc_final: 0.8054 (p) REVERT: C 495 TYR cc_start: 0.6904 (m-80) cc_final: 0.6074 (m-80) REVERT: C 537 LYS cc_start: 0.8348 (mtpt) cc_final: 0.8074 (ttpt) REVERT: C 580 GLN cc_start: 0.7949 (mt0) cc_final: 0.7686 (mt0) REVERT: C 704 SER cc_start: 0.8523 (m) cc_final: 0.7925 (t) REVERT: C 773 GLU cc_start: 0.7549 (tt0) cc_final: 0.7210 (tt0) REVERT: C 774 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7746 (mp-120) REVERT: C 796 ASP cc_start: 0.7647 (t0) cc_final: 0.7166 (t0) REVERT: C 803 SER cc_start: 0.8778 (t) cc_final: 0.8498 (p) REVERT: C 804 GLN cc_start: 0.8231 (mt0) cc_final: 0.7941 (mt0) REVERT: C 868 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7185 (tp30) REVERT: C 870 ILE cc_start: 0.8185 (pt) cc_final: 0.7975 (mt) REVERT: C 886 TRP cc_start: 0.8302 (OUTLIER) cc_final: 0.7780 (p90) REVERT: C 900 MET cc_start: 0.8294 (mtm) cc_final: 0.8068 (mtm) REVERT: C 949 GLN cc_start: 0.8228 (tp40) cc_final: 0.7735 (tp40) REVERT: C 994 ASP cc_start: 0.8092 (t70) cc_final: 0.7710 (t0) REVERT: C 1010 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7380 (mm-40) REVERT: C 1045 LYS cc_start: 0.8410 (mttt) cc_final: 0.8101 (mttt) REVERT: C 1073 LYS cc_start: 0.7894 (mtpt) cc_final: 0.7590 (mmmm) REVERT: C 1107 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7700 (mtt90) REVERT: C 1139 ASP cc_start: 0.8341 (t0) cc_final: 0.8134 (t0) REVERT: B 90 VAL cc_start: 0.8517 (p) cc_final: 0.8100 (m) REVERT: B 132 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7436 (mp0) REVERT: B 159 VAL cc_start: 0.7249 (OUTLIER) cc_final: 0.6911 (m) REVERT: B 191 GLU cc_start: 0.7998 (mp0) cc_final: 0.7676 (mp0) REVERT: B 195 LYS cc_start: 0.7970 (mtmt) cc_final: 0.7747 (ptpt) REVERT: B 206 LYS cc_start: 0.8408 (tptm) cc_final: 0.8101 (tptp) REVERT: B 296 LEU cc_start: 0.8318 (tp) cc_final: 0.8103 (tp) REVERT: B 360 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7813 (m110) REVERT: B 392 PHE cc_start: 0.6749 (m-80) cc_final: 0.5973 (m-80) REVERT: B 414 GLN cc_start: 0.6224 (tm-30) cc_final: 0.5874 (tm-30) REVERT: B 448 ASN cc_start: 0.8343 (t0) cc_final: 0.6053 (p0) REVERT: B 523 THR cc_start: 0.7627 (OUTLIER) cc_final: 0.7334 (m) REVERT: B 576 VAL cc_start: 0.8974 (p) cc_final: 0.8538 (t) REVERT: B 599 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8097 (p) REVERT: B 673 SER cc_start: 0.8910 (t) cc_final: 0.8414 (m) REVERT: B 733 LYS cc_start: 0.8282 (mttt) cc_final: 0.8002 (mtpp) REVERT: B 764 ASN cc_start: 0.8457 (m-40) cc_final: 0.8058 (m-40) REVERT: B 790 LYS cc_start: 0.8377 (ptmt) cc_final: 0.8145 (ptmt) REVERT: B 811 LYS cc_start: 0.7405 (mttt) cc_final: 0.6692 (mtpt) REVERT: B 820 ASP cc_start: 0.7514 (t0) cc_final: 0.6811 (t0) REVERT: B 824 ASN cc_start: 0.7937 (m-40) cc_final: 0.7703 (m-40) REVERT: B 929 SER cc_start: 0.8419 (t) cc_final: 0.8073 (p) REVERT: B 950 ASP cc_start: 0.7847 (t0) cc_final: 0.7256 (t0) REVERT: B 968 SER cc_start: 0.8793 (m) cc_final: 0.8538 (m) REVERT: B 1003 SER cc_start: 0.8443 (m) cc_final: 0.8121 (t) REVERT: B 1073 LYS cc_start: 0.8533 (mtmt) cc_final: 0.8267 (mtmm) REVERT: B 1117 THR cc_start: 0.8322 (m) cc_final: 0.7982 (t) REVERT: A 28 TYR cc_start: 0.8202 (m-80) cc_final: 0.7720 (m-80) REVERT: A 117 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7826 (tt) REVERT: A 120 VAL cc_start: 0.7927 (t) cc_final: 0.7660 (m) REVERT: A 191 GLU cc_start: 0.7599 (mp0) cc_final: 0.7127 (mt-10) REVERT: A 270 LEU cc_start: 0.8774 (mp) cc_final: 0.8563 (mp) REVERT: A 535 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8617 (mttm) REVERT: A 546 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7016 (pt) REVERT: A 549 THR cc_start: 0.7900 (m) cc_final: 0.7624 (p) REVERT: A 557 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8232 (mttt) REVERT: A 586 ASP cc_start: 0.7705 (t0) cc_final: 0.7305 (m-30) REVERT: A 596 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8409 (p) REVERT: A 605 SER cc_start: 0.8731 (t) cc_final: 0.8374 (m) REVERT: A 719 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8226 (p) REVERT: A 758 SER cc_start: 0.8427 (m) cc_final: 0.7976 (p) REVERT: A 790 LYS cc_start: 0.8300 (ttmm) cc_final: 0.8086 (mtmm) REVERT: A 796 ASP cc_start: 0.6917 (p0) cc_final: 0.6714 (p0) REVERT: A 825 LYS cc_start: 0.8380 (mmmt) cc_final: 0.7981 (mmmm) REVERT: A 878 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8136 (mt) REVERT: A 900 MET cc_start: 0.8369 (mtp) cc_final: 0.7756 (mtp) REVERT: A 921 LYS cc_start: 0.8202 (mmtp) cc_final: 0.7945 (mmtp) REVERT: A 950 ASP cc_start: 0.7517 (t0) cc_final: 0.7099 (t0) REVERT: A 987 VAL cc_start: 0.8480 (p) cc_final: 0.8212 (t) REVERT: A 1019 ARG cc_start: 0.7864 (ttm110) cc_final: 0.7477 (ttp80) REVERT: A 1038 LYS cc_start: 0.8692 (mttt) cc_final: 0.8361 (mmtm) REVERT: A 1045 LYS cc_start: 0.8317 (mttt) cc_final: 0.7999 (mttt) REVERT: A 1073 LYS cc_start: 0.8479 (mtpt) cc_final: 0.8219 (mtpp) REVERT: A 1084 ASP cc_start: 0.7938 (p0) cc_final: 0.7348 (p0) REVERT: A 1144 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7521 (mt-10) REVERT: D 26 LYS cc_start: 0.8333 (mtmm) cc_final: 0.8064 (mmtp) REVERT: D 41 TYR cc_start: 0.8071 (t80) cc_final: 0.7109 (t80) REVERT: D 42 GLN cc_start: 0.8103 (tp40) cc_final: 0.7307 (tp40) REVERT: D 72 PHE cc_start: 0.8070 (t80) cc_final: 0.7777 (t80) REVERT: D 74 LYS cc_start: 0.8609 (tppp) cc_final: 0.8109 (tppp) REVERT: D 308 PHE cc_start: 0.8106 (m-80) cc_final: 0.7631 (m-80) REVERT: D 312 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8297 (mm-30) REVERT: D 314 PHE cc_start: 0.9061 (t80) cc_final: 0.8482 (m-10) REVERT: D 360 MET cc_start: 0.3437 (tmm) cc_final: 0.3040 (tmm) REVERT: D 380 GLN cc_start: 0.4473 (mm110) cc_final: 0.4093 (mm-40) REVERT: D 383 MET cc_start: 0.7151 (mpp) cc_final: 0.6278 (mpp) REVERT: D 410 LEU cc_start: 0.8844 (mt) cc_final: 0.8291 (pp) REVERT: D 454 TYR cc_start: 0.5850 (t80) cc_final: 0.5383 (t80) REVERT: D 479 GLU cc_start: 0.7981 (pt0) cc_final: 0.7516 (pp20) REVERT: D 480 MET cc_start: 0.7740 (mtp) cc_final: 0.7332 (mtp) REVERT: D 497 TYR cc_start: 0.6732 (m-80) cc_final: 0.6403 (m-80) REVERT: D 521 TYR cc_start: 0.5225 (m-10) cc_final: 0.4876 (m-80) REVERT: D 557 MET cc_start: 0.7412 (tmm) cc_final: 0.7089 (tmm) outliers start: 130 outliers final: 92 residues processed: 724 average time/residue: 0.2130 time to fit residues: 246.5223 Evaluate side-chains 724 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 617 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 271 optimal weight: 0.1980 chunk 209 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 248 optimal weight: 0.5980 chunk 250 optimal weight: 0.6980 chunk 194 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 340 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 356 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 777 ASN B1119 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 969 ASN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.185017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.137526 restraints weight = 50447.084| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.82 r_work: 0.3510 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31780 Z= 0.143 Angle : 0.621 12.973 43372 Z= 0.304 Chirality : 0.046 0.520 5026 Planarity : 0.004 0.068 5477 Dihedral : 5.966 77.014 5599 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.90 % Allowed : 15.42 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.42 (0.13), residues: 3761 helix: 1.68 (0.17), residues: 1038 sheet: -0.20 (0.19), residues: 663 loop : -1.39 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 190 TYR 0.023 0.001 TYR A 707 PHE 0.028 0.001 PHE B 201 TRP 0.021 0.001 TRP D 271 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00322 (31664) covalent geometry : angle 0.59498 (43069) SS BOND : bond 0.00459 ( 45) SS BOND : angle 2.56315 ( 90) hydrogen bonds : bond 0.03699 ( 1172) hydrogen bonds : angle 5.14245 ( 3312) link_BETA1-4 : bond 0.00301 ( 21) link_BETA1-4 : angle 1.06708 ( 63) link_NAG-ASN : bond 0.00436 ( 50) link_NAG-ASN : angle 2.32252 ( 150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 640 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 THR cc_start: 0.8100 (t) cc_final: 0.6706 (p) REVERT: C 42 VAL cc_start: 0.8614 (p) cc_final: 0.8250 (m) REVERT: C 99 ASN cc_start: 0.7964 (t0) cc_final: 0.7620 (t0) REVERT: C 267 VAL cc_start: 0.8543 (t) cc_final: 0.8262 (p) REVERT: C 284 THR cc_start: 0.8688 (m) cc_final: 0.8297 (t) REVERT: C 289 VAL cc_start: 0.8880 (p) cc_final: 0.8594 (m) REVERT: C 305 SER cc_start: 0.8958 (t) cc_final: 0.8566 (p) REVERT: C 353 TRP cc_start: 0.8035 (p-90) cc_final: 0.7796 (p-90) REVERT: C 356 LYS cc_start: 0.8776 (ptpt) cc_final: 0.8458 (pttt) REVERT: C 362 VAL cc_start: 0.8258 (t) cc_final: 0.8015 (m) REVERT: C 378 LYS cc_start: 0.8186 (mttt) cc_final: 0.7701 (mttt) REVERT: C 400 PHE cc_start: 0.7480 (p90) cc_final: 0.6926 (p90) REVERT: C 414 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7426 (mm-40) REVERT: C 424 LYS cc_start: 0.7509 (tttt) cc_final: 0.6781 (ttpp) REVERT: C 537 LYS cc_start: 0.8431 (mtpt) cc_final: 0.8201 (ttpt) REVERT: C 578 ASP cc_start: 0.7295 (t0) cc_final: 0.6964 (t0) REVERT: C 580 GLN cc_start: 0.8203 (mt0) cc_final: 0.7746 (mt0) REVERT: C 646 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7726 (ttm170) REVERT: C 704 SER cc_start: 0.8677 (m) cc_final: 0.8126 (t) REVERT: C 747 THR cc_start: 0.8225 (m) cc_final: 0.7831 (p) REVERT: C 773 GLU cc_start: 0.7781 (tt0) cc_final: 0.7431 (tt0) REVERT: C 774 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7842 (mp-120) REVERT: C 796 ASP cc_start: 0.7924 (t0) cc_final: 0.7409 (t0) REVERT: C 803 SER cc_start: 0.8841 (t) cc_final: 0.8587 (p) REVERT: C 804 GLN cc_start: 0.8453 (mt0) cc_final: 0.8179 (mt0) REVERT: C 868 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7467 (tp30) REVERT: C 870 ILE cc_start: 0.8371 (pt) cc_final: 0.8141 (mt) REVERT: C 886 TRP cc_start: 0.8335 (OUTLIER) cc_final: 0.7886 (p90) REVERT: C 949 GLN cc_start: 0.8414 (tp40) cc_final: 0.7934 (tp40) REVERT: C 994 ASP cc_start: 0.8337 (t70) cc_final: 0.7997 (t0) REVERT: C 1017 GLU cc_start: 0.8351 (tp30) cc_final: 0.7968 (tp30) REVERT: C 1045 LYS cc_start: 0.8580 (mttt) cc_final: 0.8282 (mttt) REVERT: C 1073 LYS cc_start: 0.8076 (mtpt) cc_final: 0.7766 (mmmm) REVERT: C 1107 ARG cc_start: 0.8273 (mtt180) cc_final: 0.8017 (mtt90) REVERT: C 1139 ASP cc_start: 0.8456 (t0) cc_final: 0.8253 (t0) REVERT: B 90 VAL cc_start: 0.8688 (p) cc_final: 0.8296 (m) REVERT: B 132 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7690 (mp0) REVERT: B 159 VAL cc_start: 0.7479 (OUTLIER) cc_final: 0.7176 (m) REVERT: B 191 GLU cc_start: 0.8303 (mp0) cc_final: 0.8012 (mp0) REVERT: B 195 LYS cc_start: 0.8239 (mtmt) cc_final: 0.7995 (ptpt) REVERT: B 206 LYS cc_start: 0.8597 (tptm) cc_final: 0.8320 (tptp) REVERT: B 296 LEU cc_start: 0.8361 (tp) cc_final: 0.8076 (tp) REVERT: B 360 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7917 (m110) REVERT: B 392 PHE cc_start: 0.6983 (m-80) cc_final: 0.6314 (m-80) REVERT: B 414 GLN cc_start: 0.6443 (tm-30) cc_final: 0.6095 (tm-30) REVERT: B 448 ASN cc_start: 0.8316 (t0) cc_final: 0.6099 (p0) REVERT: B 523 THR cc_start: 0.7720 (OUTLIER) cc_final: 0.7459 (m) REVERT: B 537 LYS cc_start: 0.8643 (ttpp) cc_final: 0.8397 (tttp) REVERT: B 565 PHE cc_start: 0.7188 (m-10) cc_final: 0.6458 (m-10) REVERT: B 576 VAL cc_start: 0.8976 (p) cc_final: 0.8562 (t) REVERT: B 599 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8195 (p) REVERT: B 673 SER cc_start: 0.9021 (t) cc_final: 0.8557 (m) REVERT: B 733 LYS cc_start: 0.8352 (mttt) cc_final: 0.8056 (mtpp) REVERT: B 764 ASN cc_start: 0.8594 (m-40) cc_final: 0.8239 (m-40) REVERT: B 790 LYS cc_start: 0.8502 (ptmt) cc_final: 0.8270 (ptmt) REVERT: B 811 LYS cc_start: 0.7407 (mttt) cc_final: 0.7011 (mtpt) REVERT: B 820 ASP cc_start: 0.7793 (t0) cc_final: 0.7123 (t0) REVERT: B 929 SER cc_start: 0.8566 (t) cc_final: 0.8228 (p) REVERT: B 950 ASP cc_start: 0.8088 (t0) cc_final: 0.7496 (t0) REVERT: B 968 SER cc_start: 0.8858 (m) cc_final: 0.8624 (m) REVERT: B 1003 SER cc_start: 0.8650 (m) cc_final: 0.8312 (t) REVERT: B 1073 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8441 (mtmm) REVERT: B 1117 THR cc_start: 0.8400 (m) cc_final: 0.8038 (t) REVERT: B 1136 THR cc_start: 0.8780 (t) cc_final: 0.8503 (p) REVERT: A 28 TYR cc_start: 0.8354 (m-80) cc_final: 0.7910 (m-80) REVERT: A 117 LEU cc_start: 0.8236 (tt) cc_final: 0.7463 (mp) REVERT: A 120 VAL cc_start: 0.8009 (t) cc_final: 0.7780 (m) REVERT: A 191 GLU cc_start: 0.7971 (mp0) cc_final: 0.7571 (mt-10) REVERT: A 535 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8693 (mttm) REVERT: A 549 THR cc_start: 0.7970 (m) cc_final: 0.7685 (p) REVERT: A 557 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8333 (mttm) REVERT: A 586 ASP cc_start: 0.8056 (t0) cc_final: 0.7557 (m-30) REVERT: A 596 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8510 (p) REVERT: A 605 SER cc_start: 0.8816 (t) cc_final: 0.8494 (m) REVERT: A 719 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8326 (p) REVERT: A 758 SER cc_start: 0.8520 (m) cc_final: 0.8042 (p) REVERT: A 790 LYS cc_start: 0.8519 (ttmm) cc_final: 0.8177 (mtmm) REVERT: A 825 LYS cc_start: 0.8502 (mmmt) cc_final: 0.8106 (mmmm) REVERT: A 878 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8241 (mt) REVERT: A 900 MET cc_start: 0.8531 (mtp) cc_final: 0.8303 (mtt) REVERT: A 921 LYS cc_start: 0.8346 (mmtp) cc_final: 0.8085 (mmtp) REVERT: A 950 ASP cc_start: 0.7816 (t0) cc_final: 0.7422 (t0) REVERT: A 963 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8655 (p) REVERT: A 987 VAL cc_start: 0.8548 (p) cc_final: 0.8309 (t) REVERT: A 1019 ARG cc_start: 0.8082 (ttm110) cc_final: 0.7732 (ttp80) REVERT: A 1038 LYS cc_start: 0.8791 (mttt) cc_final: 0.8558 (mmtm) REVERT: A 1073 LYS cc_start: 0.8580 (mtpt) cc_final: 0.8348 (mtpp) REVERT: A 1084 ASP cc_start: 0.8156 (p0) cc_final: 0.7586 (p0) REVERT: A 1144 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7634 (mt-10) REVERT: D 41 TYR cc_start: 0.8179 (t80) cc_final: 0.7246 (t80) REVERT: D 42 GLN cc_start: 0.8162 (tp40) cc_final: 0.7371 (tp40) REVERT: D 72 PHE cc_start: 0.8183 (t80) cc_final: 0.7885 (t80) REVERT: D 74 LYS cc_start: 0.8624 (tppp) cc_final: 0.8114 (tppp) REVERT: D 312 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8246 (mm-30) REVERT: D 314 PHE cc_start: 0.9088 (t80) cc_final: 0.8486 (m-10) REVERT: D 380 GLN cc_start: 0.4563 (mm110) cc_final: 0.4161 (mm-40) REVERT: D 383 MET cc_start: 0.7290 (mpp) cc_final: 0.6309 (mpp) REVERT: D 408 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7429 (mpm) REVERT: D 410 LEU cc_start: 0.8849 (mt) cc_final: 0.8341 (pp) REVERT: D 454 TYR cc_start: 0.5857 (t80) cc_final: 0.5390 (t80) REVERT: D 479 GLU cc_start: 0.7994 (pt0) cc_final: 0.7565 (pp20) REVERT: D 480 MET cc_start: 0.7730 (mtp) cc_final: 0.7294 (mtp) REVERT: D 481 LYS cc_start: 0.1700 (OUTLIER) cc_final: 0.1380 (ptmm) REVERT: D 497 TYR cc_start: 0.6723 (m-80) cc_final: 0.6476 (m-80) REVERT: D 521 TYR cc_start: 0.5298 (m-10) cc_final: 0.4897 (m-80) REVERT: D 557 MET cc_start: 0.7376 (tmm) cc_final: 0.7053 (tmm) outliers start: 130 outliers final: 94 residues processed: 734 average time/residue: 0.2134 time to fit residues: 250.5429 Evaluate side-chains 729 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 620 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 335 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 99 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 362 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN C 762 GLN B 394 ASN B 540 ASN B 777 ASN B 824 ASN B1119 ASN A 69 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.184364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.136861 restraints weight = 50262.001| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.81 r_work: 0.3497 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31780 Z= 0.176 Angle : 0.643 13.343 43372 Z= 0.315 Chirality : 0.047 0.586 5026 Planarity : 0.004 0.054 5477 Dihedral : 5.801 78.591 5599 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.96 % Allowed : 15.75 % Favored : 80.29 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.42 (0.13), residues: 3761 helix: 1.69 (0.17), residues: 1032 sheet: -0.21 (0.19), residues: 672 loop : -1.39 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 190 TYR 0.030 0.001 TYR A 904 PHE 0.025 0.002 PHE B 201 TRP 0.020 0.001 TRP D 271 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00397 (31664) covalent geometry : angle 0.61620 (43069) SS BOND : bond 0.00477 ( 45) SS BOND : angle 2.64982 ( 90) hydrogen bonds : bond 0.03861 ( 1172) hydrogen bonds : angle 5.16167 ( 3312) link_BETA1-4 : bond 0.00304 ( 21) link_BETA1-4 : angle 1.11146 ( 63) link_NAG-ASN : bond 0.00456 ( 50) link_NAG-ASN : angle 2.41290 ( 150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 638 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 THR cc_start: 0.8004 (t) cc_final: 0.6683 (p) REVERT: C 42 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8045 (m) REVERT: C 99 ASN cc_start: 0.7894 (t0) cc_final: 0.7553 (t0) REVERT: C 237 ARG cc_start: 0.7865 (mtm110) cc_final: 0.7567 (mtp-110) REVERT: C 239 GLN cc_start: 0.8041 (tt0) cc_final: 0.7592 (mt0) REVERT: C 267 VAL cc_start: 0.8369 (t) cc_final: 0.8076 (p) REVERT: C 284 THR cc_start: 0.8598 (m) cc_final: 0.8180 (t) REVERT: C 289 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8553 (m) REVERT: C 305 SER cc_start: 0.8931 (t) cc_final: 0.8550 (p) REVERT: C 353 TRP cc_start: 0.8117 (p-90) cc_final: 0.7903 (p-90) REVERT: C 356 LYS cc_start: 0.8610 (ptpt) cc_final: 0.8261 (pttt) REVERT: C 362 VAL cc_start: 0.8099 (t) cc_final: 0.7880 (m) REVERT: C 378 LYS cc_start: 0.8020 (mttt) cc_final: 0.7622 (mttt) REVERT: C 414 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7385 (mm-40) REVERT: C 424 LYS cc_start: 0.7335 (tttt) cc_final: 0.6628 (ttpp) REVERT: C 495 TYR cc_start: 0.6953 (m-80) cc_final: 0.6114 (m-80) REVERT: C 537 LYS cc_start: 0.8354 (mtpt) cc_final: 0.8107 (ttpt) REVERT: C 578 ASP cc_start: 0.6974 (t0) cc_final: 0.6656 (t0) REVERT: C 580 GLN cc_start: 0.7860 (mt0) cc_final: 0.7412 (mt0) REVERT: C 646 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7410 (ttm170) REVERT: C 703 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.8036 (m-40) REVERT: C 704 SER cc_start: 0.8617 (m) cc_final: 0.8033 (t) REVERT: C 747 THR cc_start: 0.8044 (m) cc_final: 0.7662 (p) REVERT: C 773 GLU cc_start: 0.7534 (tt0) cc_final: 0.7212 (tt0) REVERT: C 774 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7615 (mp-120) REVERT: C 796 ASP cc_start: 0.7749 (t0) cc_final: 0.7291 (t0) REVERT: C 803 SER cc_start: 0.8811 (t) cc_final: 0.8520 (p) REVERT: C 804 GLN cc_start: 0.8223 (mt0) cc_final: 0.7945 (mt0) REVERT: C 858 LEU cc_start: 0.8426 (mt) cc_final: 0.8210 (mp) REVERT: C 868 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7216 (tp30) REVERT: C 870 ILE cc_start: 0.8187 (pt) cc_final: 0.7985 (mt) REVERT: C 886 TRP cc_start: 0.8284 (OUTLIER) cc_final: 0.7796 (p90) REVERT: C 949 GLN cc_start: 0.8281 (tp40) cc_final: 0.7780 (tp40) REVERT: C 994 ASP cc_start: 0.8018 (t70) cc_final: 0.7659 (t0) REVERT: C 1010 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7389 (mm-40) REVERT: C 1017 GLU cc_start: 0.8029 (tp30) cc_final: 0.7580 (tp30) REVERT: C 1045 LYS cc_start: 0.8358 (mttt) cc_final: 0.8041 (mttt) REVERT: C 1073 LYS cc_start: 0.7860 (mtpt) cc_final: 0.7579 (mmmm) REVERT: C 1107 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7704 (mtt90) REVERT: C 1139 ASP cc_start: 0.8356 (t0) cc_final: 0.8144 (t0) REVERT: B 90 VAL cc_start: 0.8529 (p) cc_final: 0.8118 (m) REVERT: B 132 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7525 (mp0) REVERT: B 159 VAL cc_start: 0.7272 (OUTLIER) cc_final: 0.6982 (m) REVERT: B 195 LYS cc_start: 0.7994 (mtmt) cc_final: 0.7770 (ptpt) REVERT: B 206 LYS cc_start: 0.8409 (tptm) cc_final: 0.8127 (tptm) REVERT: B 296 LEU cc_start: 0.8247 (tp) cc_final: 0.8004 (tp) REVERT: B 324 GLU cc_start: 0.8183 (pm20) cc_final: 0.7744 (pm20) REVERT: B 360 ASN cc_start: 0.8023 (m110) cc_final: 0.7753 (m110) REVERT: B 414 GLN cc_start: 0.6343 (tm-30) cc_final: 0.5877 (tm-30) REVERT: B 537 LYS cc_start: 0.8480 (ttpp) cc_final: 0.7998 (tttp) REVERT: B 542 ASN cc_start: 0.8193 (t0) cc_final: 0.7954 (t0) REVERT: B 576 VAL cc_start: 0.8928 (p) cc_final: 0.8583 (t) REVERT: B 599 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8087 (p) REVERT: B 673 SER cc_start: 0.8930 (t) cc_final: 0.8432 (m) REVERT: B 764 ASN cc_start: 0.8424 (m-40) cc_final: 0.7999 (m-40) REVERT: B 779 GLN cc_start: 0.8061 (tt0) cc_final: 0.7847 (tt0) REVERT: B 790 LYS cc_start: 0.8348 (ptmt) cc_final: 0.8087 (ptmt) REVERT: B 811 LYS cc_start: 0.7414 (mttt) cc_final: 0.6994 (mtpt) REVERT: B 820 ASP cc_start: 0.7501 (t0) cc_final: 0.6956 (t0) REVERT: B 929 SER cc_start: 0.8418 (t) cc_final: 0.8077 (p) REVERT: B 950 ASP cc_start: 0.7838 (t0) cc_final: 0.7212 (t0) REVERT: B 968 SER cc_start: 0.8792 (m) cc_final: 0.8563 (m) REVERT: B 1003 SER cc_start: 0.8482 (m) cc_final: 0.8124 (t) REVERT: B 1073 LYS cc_start: 0.8527 (mtmt) cc_final: 0.8275 (mtmm) REVERT: B 1117 THR cc_start: 0.8303 (m) cc_final: 0.7942 (t) REVERT: B 1136 THR cc_start: 0.8634 (t) cc_final: 0.8357 (p) REVERT: B 1138 TYR cc_start: 0.7668 (t80) cc_final: 0.7420 (t80) REVERT: A 28 TYR cc_start: 0.8207 (m-80) cc_final: 0.7681 (m-80) REVERT: A 104 TRP cc_start: 0.7858 (m-90) cc_final: 0.7381 (m-90) REVERT: A 120 VAL cc_start: 0.7925 (t) cc_final: 0.7655 (m) REVERT: A 191 GLU cc_start: 0.7603 (mp0) cc_final: 0.7266 (mt-10) REVERT: A 535 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8612 (mttm) REVERT: A 546 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7114 (pt) REVERT: A 549 THR cc_start: 0.7883 (m) cc_final: 0.7619 (p) REVERT: A 596 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8398 (p) REVERT: A 605 SER cc_start: 0.8749 (t) cc_final: 0.8422 (m) REVERT: A 719 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8237 (p) REVERT: A 725 GLU cc_start: 0.7811 (tp30) cc_final: 0.7352 (tt0) REVERT: A 758 SER cc_start: 0.8404 (m) cc_final: 0.7951 (p) REVERT: A 790 LYS cc_start: 0.8328 (ttmm) cc_final: 0.7961 (mtmm) REVERT: A 825 LYS cc_start: 0.8367 (mmmt) cc_final: 0.7953 (mmmm) REVERT: A 878 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8124 (mt) REVERT: A 900 MET cc_start: 0.8250 (mtp) cc_final: 0.7826 (mtp) REVERT: A 921 LYS cc_start: 0.8155 (mmtp) cc_final: 0.7900 (mmtp) REVERT: A 950 ASP cc_start: 0.7514 (t0) cc_final: 0.7119 (t0) REVERT: A 963 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8580 (p) REVERT: A 986 LYS cc_start: 0.8183 (mttm) cc_final: 0.7788 (mttm) REVERT: A 987 VAL cc_start: 0.8495 (p) cc_final: 0.8153 (t) REVERT: A 1019 ARG cc_start: 0.7807 (ttm110) cc_final: 0.7429 (ttp80) REVERT: A 1045 LYS cc_start: 0.8417 (mttt) cc_final: 0.8155 (mttt) REVERT: A 1073 LYS cc_start: 0.8480 (mtpt) cc_final: 0.8221 (mtpp) REVERT: A 1144 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7510 (mt-10) REVERT: D 41 TYR cc_start: 0.8032 (t80) cc_final: 0.7096 (t80) REVERT: D 42 GLN cc_start: 0.8109 (tp40) cc_final: 0.7319 (tp40) REVERT: D 72 PHE cc_start: 0.8057 (t80) cc_final: 0.7741 (t80) REVERT: D 74 LYS cc_start: 0.8645 (tppp) cc_final: 0.8130 (tppp) REVERT: D 187 LYS cc_start: 0.6885 (mmtt) cc_final: 0.6077 (ptpp) REVERT: D 308 PHE cc_start: 0.8099 (m-80) cc_final: 0.7715 (m-80) REVERT: D 312 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8247 (mm-30) REVERT: D 314 PHE cc_start: 0.9054 (t80) cc_final: 0.8449 (m-10) REVERT: D 383 MET cc_start: 0.7156 (mpp) cc_final: 0.6683 (mpp) REVERT: D 408 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7315 (mpt) REVERT: D 410 LEU cc_start: 0.8832 (mt) cc_final: 0.8312 (pp) REVERT: D 454 TYR cc_start: 0.5822 (t80) cc_final: 0.5423 (t80) REVERT: D 479 GLU cc_start: 0.8023 (pt0) cc_final: 0.7527 (pp20) REVERT: D 480 MET cc_start: 0.7647 (mtp) cc_final: 0.7159 (mtp) REVERT: D 497 TYR cc_start: 0.6711 (m-80) cc_final: 0.6409 (m-80) REVERT: D 521 TYR cc_start: 0.5304 (m-10) cc_final: 0.4913 (m-80) REVERT: D 557 MET cc_start: 0.7374 (tmm) cc_final: 0.7035 (tmm) outliers start: 132 outliers final: 100 residues processed: 723 average time/residue: 0.2175 time to fit residues: 250.1451 Evaluate side-chains 735 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 620 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 267 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 369 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 chunk 189 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 655 HIS B 777 ASN B1119 ASN A 146 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 675 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.184718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.137515 restraints weight = 50387.945| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.78 r_work: 0.3487 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31780 Z= 0.167 Angle : 0.642 11.550 43372 Z= 0.317 Chirality : 0.046 0.452 5026 Planarity : 0.004 0.047 5477 Dihedral : 5.714 79.124 5599 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.75 % Allowed : 16.41 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.39 (0.13), residues: 3761 helix: 1.67 (0.17), residues: 1039 sheet: -0.21 (0.19), residues: 670 loop : -1.35 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 190 TYR 0.040 0.001 TYR A 904 PHE 0.029 0.002 PHE C 133 TRP 0.021 0.001 TRP D 328 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00376 (31664) covalent geometry : angle 0.61741 (43069) SS BOND : bond 0.00482 ( 45) SS BOND : angle 2.72596 ( 90) hydrogen bonds : bond 0.03821 ( 1172) hydrogen bonds : angle 5.13422 ( 3312) link_BETA1-4 : bond 0.00308 ( 21) link_BETA1-4 : angle 1.09624 ( 63) link_NAG-ASN : bond 0.00382 ( 50) link_NAG-ASN : angle 2.21519 ( 150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 622 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 THR cc_start: 0.7967 (t) cc_final: 0.6657 (p) REVERT: C 42 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8034 (m) REVERT: C 83 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8092 (t) REVERT: C 99 ASN cc_start: 0.7909 (t0) cc_final: 0.7578 (t0) REVERT: C 228 ASP cc_start: 0.7832 (m-30) cc_final: 0.7613 (m-30) REVERT: C 239 GLN cc_start: 0.8079 (tt0) cc_final: 0.7745 (tt0) REVERT: C 267 VAL cc_start: 0.8388 (t) cc_final: 0.8072 (p) REVERT: C 284 THR cc_start: 0.8588 (m) cc_final: 0.8166 (t) REVERT: C 289 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8548 (m) REVERT: C 305 SER cc_start: 0.8935 (t) cc_final: 0.8547 (p) REVERT: C 353 TRP cc_start: 0.8095 (p-90) cc_final: 0.7874 (p-90) REVERT: C 356 LYS cc_start: 0.8690 (ptpt) cc_final: 0.8307 (pttt) REVERT: C 362 VAL cc_start: 0.8112 (t) cc_final: 0.7717 (p) REVERT: C 378 LYS cc_start: 0.7988 (mttt) cc_final: 0.7585 (mttt) REVERT: C 396 TYR cc_start: 0.8401 (m-80) cc_final: 0.8113 (m-10) REVERT: C 398 ASP cc_start: 0.7537 (p0) cc_final: 0.6885 (p0) REVERT: C 400 PHE cc_start: 0.7414 (p90) cc_final: 0.6846 (p90) REVERT: C 424 LYS cc_start: 0.7361 (tttt) cc_final: 0.6644 (ttpp) REVERT: C 495 TYR cc_start: 0.6941 (m-80) cc_final: 0.6061 (m-80) REVERT: C 537 LYS cc_start: 0.8339 (mtpt) cc_final: 0.8093 (ttpt) REVERT: C 578 ASP cc_start: 0.6870 (t0) cc_final: 0.6559 (t0) REVERT: C 580 GLN cc_start: 0.7850 (mt0) cc_final: 0.7415 (mt0) REVERT: C 646 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7482 (ttm170) REVERT: C 703 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.8057 (m-40) REVERT: C 704 SER cc_start: 0.8491 (m) cc_final: 0.7917 (t) REVERT: C 747 THR cc_start: 0.8037 (m) cc_final: 0.7657 (p) REVERT: C 773 GLU cc_start: 0.7539 (tt0) cc_final: 0.7220 (tt0) REVERT: C 774 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7618 (mp-120) REVERT: C 796 ASP cc_start: 0.7755 (t0) cc_final: 0.7304 (t0) REVERT: C 803 SER cc_start: 0.8806 (t) cc_final: 0.8547 (p) REVERT: C 804 GLN cc_start: 0.8217 (mt0) cc_final: 0.7945 (mt0) REVERT: C 868 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7412 (tm-30) REVERT: C 870 ILE cc_start: 0.8196 (pt) cc_final: 0.7990 (mt) REVERT: C 886 TRP cc_start: 0.8278 (OUTLIER) cc_final: 0.7856 (p90) REVERT: C 949 GLN cc_start: 0.8246 (tp40) cc_final: 0.7762 (tp40) REVERT: C 994 ASP cc_start: 0.8026 (t70) cc_final: 0.7643 (t0) REVERT: C 1010 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7388 (mm-40) REVERT: C 1017 GLU cc_start: 0.8044 (tp30) cc_final: 0.7637 (tp30) REVERT: C 1045 LYS cc_start: 0.8415 (mttt) cc_final: 0.8097 (mttt) REVERT: C 1073 LYS cc_start: 0.7867 (mtpt) cc_final: 0.7585 (mmmm) REVERT: C 1107 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7680 (mtt90) REVERT: C 1139 ASP cc_start: 0.8344 (t0) cc_final: 0.7946 (t70) REVERT: B 90 VAL cc_start: 0.8524 (p) cc_final: 0.8118 (m) REVERT: B 159 VAL cc_start: 0.7174 (OUTLIER) cc_final: 0.6786 (m) REVERT: B 206 LYS cc_start: 0.8428 (tptm) cc_final: 0.8073 (tptm) REVERT: B 296 LEU cc_start: 0.8249 (tp) cc_final: 0.8003 (tp) REVERT: B 324 GLU cc_start: 0.8190 (pm20) cc_final: 0.7729 (pm20) REVERT: B 360 ASN cc_start: 0.7999 (m110) cc_final: 0.7745 (m110) REVERT: B 537 LYS cc_start: 0.8470 (ttpp) cc_final: 0.8025 (tttp) REVERT: B 542 ASN cc_start: 0.8170 (t0) cc_final: 0.7948 (t0) REVERT: B 576 VAL cc_start: 0.8921 (p) cc_final: 0.8613 (t) REVERT: B 599 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8085 (p) REVERT: B 673 SER cc_start: 0.8900 (t) cc_final: 0.8413 (m) REVERT: B 764 ASN cc_start: 0.8414 (m-40) cc_final: 0.7996 (m-40) REVERT: B 790 LYS cc_start: 0.8380 (ptmt) cc_final: 0.8150 (ptmt) REVERT: B 811 LYS cc_start: 0.7437 (mttt) cc_final: 0.6994 (mtpt) REVERT: B 820 ASP cc_start: 0.7515 (t0) cc_final: 0.6862 (t0) REVERT: B 929 SER cc_start: 0.8418 (t) cc_final: 0.8080 (p) REVERT: B 950 ASP cc_start: 0.7822 (t0) cc_final: 0.7316 (t0) REVERT: B 968 SER cc_start: 0.8789 (m) cc_final: 0.8542 (m) REVERT: B 1003 SER cc_start: 0.8465 (m) cc_final: 0.8151 (t) REVERT: B 1073 LYS cc_start: 0.8549 (mtmt) cc_final: 0.8296 (mtmm) REVERT: B 1117 THR cc_start: 0.8289 (m) cc_final: 0.7929 (t) REVERT: B 1136 THR cc_start: 0.8629 (t) cc_final: 0.8355 (p) REVERT: B 1138 TYR cc_start: 0.7647 (t80) cc_final: 0.7379 (t80) REVERT: A 28 TYR cc_start: 0.8204 (m-80) cc_final: 0.7682 (m-80) REVERT: A 104 TRP cc_start: 0.7838 (m-90) cc_final: 0.7364 (m-90) REVERT: A 120 VAL cc_start: 0.7890 (t) cc_final: 0.7616 (m) REVERT: A 191 GLU cc_start: 0.7621 (mp0) cc_final: 0.7208 (mt-10) REVERT: A 535 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8634 (mttm) REVERT: A 546 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7186 (pt) REVERT: A 549 THR cc_start: 0.7883 (m) cc_final: 0.7612 (p) REVERT: A 586 ASP cc_start: 0.7900 (t0) cc_final: 0.7467 (t0) REVERT: A 596 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8431 (p) REVERT: A 605 SER cc_start: 0.8753 (t) cc_final: 0.8427 (m) REVERT: A 719 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8260 (p) REVERT: A 725 GLU cc_start: 0.7790 (tp30) cc_final: 0.7379 (tt0) REVERT: A 758 SER cc_start: 0.8392 (m) cc_final: 0.7930 (p) REVERT: A 790 LYS cc_start: 0.8344 (ttmm) cc_final: 0.7974 (mtmm) REVERT: A 825 LYS cc_start: 0.8392 (mmmt) cc_final: 0.7975 (mmmm) REVERT: A 878 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8138 (mt) REVERT: A 900 MET cc_start: 0.8302 (mtp) cc_final: 0.7820 (mtp) REVERT: A 921 LYS cc_start: 0.8209 (mmtp) cc_final: 0.7946 (mmtp) REVERT: A 950 ASP cc_start: 0.7525 (t0) cc_final: 0.7134 (t0) REVERT: A 963 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8586 (p) REVERT: A 986 LYS cc_start: 0.8153 (mttm) cc_final: 0.7647 (mttm) REVERT: A 987 VAL cc_start: 0.8441 (p) cc_final: 0.7914 (t) REVERT: A 990 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6869 (mp0) REVERT: A 1019 ARG cc_start: 0.7815 (ttm110) cc_final: 0.7445 (ttp80) REVERT: A 1045 LYS cc_start: 0.8409 (mttt) cc_final: 0.8143 (mttt) REVERT: A 1073 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8218 (mtpp) REVERT: A 1144 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7532 (mt-10) REVERT: D 41 TYR cc_start: 0.8069 (t80) cc_final: 0.7134 (t80) REVERT: D 42 GLN cc_start: 0.8114 (tp40) cc_final: 0.7325 (tp40) REVERT: D 74 LYS cc_start: 0.8680 (tppp) cc_final: 0.8174 (tppp) REVERT: D 187 LYS cc_start: 0.6982 (mmtt) cc_final: 0.6186 (ptpp) REVERT: D 189 GLU cc_start: 0.6456 (tp30) cc_final: 0.6203 (tm-30) REVERT: D 308 PHE cc_start: 0.8263 (m-80) cc_final: 0.7867 (m-80) REVERT: D 312 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8243 (mm-30) REVERT: D 314 PHE cc_start: 0.9073 (t80) cc_final: 0.8445 (m-10) REVERT: D 328 TRP cc_start: 0.8550 (m-90) cc_final: 0.8199 (m-90) REVERT: D 369 PHE cc_start: 0.8667 (t80) cc_final: 0.8186 (m-80) REVERT: D 383 MET cc_start: 0.7146 (mpp) cc_final: 0.6652 (mpp) REVERT: D 408 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7334 (mpt) REVERT: D 410 LEU cc_start: 0.8830 (mt) cc_final: 0.8325 (pp) REVERT: D 454 TYR cc_start: 0.5806 (t80) cc_final: 0.5393 (t80) REVERT: D 479 GLU cc_start: 0.8104 (pt0) cc_final: 0.7726 (pp20) REVERT: D 497 TYR cc_start: 0.6703 (m-80) cc_final: 0.6403 (m-80) REVERT: D 521 TYR cc_start: 0.5309 (m-10) cc_final: 0.4911 (m-80) REVERT: D 557 MET cc_start: 0.7375 (tmm) cc_final: 0.7057 (tmm) REVERT: D 560 LEU cc_start: 0.7614 (mt) cc_final: 0.7375 (mp) outliers start: 125 outliers final: 90 residues processed: 704 average time/residue: 0.1973 time to fit residues: 221.4906 Evaluate side-chains 721 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 615 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 4 optimal weight: 0.5980 chunk 178 optimal weight: 0.9980 chunk 219 optimal weight: 0.6980 chunk 271 optimal weight: 0.8980 chunk 292 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 311 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 299 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 655 HIS C 762 GLN B 777 ASN B 824 ASN B1119 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.183840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136519 restraints weight = 50015.793| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.76 r_work: 0.3472 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31780 Z= 0.188 Angle : 0.663 14.856 43372 Z= 0.326 Chirality : 0.048 0.805 5026 Planarity : 0.004 0.046 5477 Dihedral : 5.528 78.964 5599 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.39 % Allowed : 16.59 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.39 (0.13), residues: 3761 helix: 1.68 (0.17), residues: 1035 sheet: -0.20 (0.19), residues: 669 loop : -1.35 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 815 TYR 0.037 0.001 TYR A 904 PHE 0.024 0.002 PHE C 133 TRP 0.019 0.001 TRP D 271 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00424 (31664) covalent geometry : angle 0.63663 (43069) SS BOND : bond 0.00469 ( 45) SS BOND : angle 2.67051 ( 90) hydrogen bonds : bond 0.03946 ( 1172) hydrogen bonds : angle 5.14849 ( 3312) link_BETA1-4 : bond 0.00273 ( 21) link_BETA1-4 : angle 1.13466 ( 63) link_NAG-ASN : bond 0.00458 ( 50) link_NAG-ASN : angle 2.42493 ( 150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 621 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 THR cc_start: 0.8191 (t) cc_final: 0.6816 (p) REVERT: C 42 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8158 (m) REVERT: C 83 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8327 (t) REVERT: C 99 ASN cc_start: 0.8010 (t0) cc_final: 0.7715 (t0) REVERT: C 207 HIS cc_start: 0.8326 (t-170) cc_final: 0.7987 (t70) REVERT: C 239 GLN cc_start: 0.8238 (tt0) cc_final: 0.8014 (tt0) REVERT: C 267 VAL cc_start: 0.8536 (t) cc_final: 0.8241 (p) REVERT: C 284 THR cc_start: 0.8700 (m) cc_final: 0.8282 (t) REVERT: C 289 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8578 (m) REVERT: C 305 SER cc_start: 0.8964 (t) cc_final: 0.8588 (p) REVERT: C 326 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8412 (pt) REVERT: C 356 LYS cc_start: 0.8841 (ptpt) cc_final: 0.8526 (pttt) REVERT: C 362 VAL cc_start: 0.8373 (t) cc_final: 0.8033 (p) REVERT: C 378 LYS cc_start: 0.8139 (mttt) cc_final: 0.7738 (mttt) REVERT: C 398 ASP cc_start: 0.7624 (p0) cc_final: 0.7092 (p0) REVERT: C 400 PHE cc_start: 0.7487 (p90) cc_final: 0.6974 (p90) REVERT: C 424 LYS cc_start: 0.7523 (tttt) cc_final: 0.6779 (ttpp) REVERT: C 495 TYR cc_start: 0.7179 (m-80) cc_final: 0.6283 (m-80) REVERT: C 537 LYS cc_start: 0.8494 (mtpt) cc_final: 0.8291 (ttpt) REVERT: C 578 ASP cc_start: 0.7212 (t0) cc_final: 0.6896 (t0) REVERT: C 580 GLN cc_start: 0.8149 (mt0) cc_final: 0.7738 (mt0) REVERT: C 703 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8216 (m-40) REVERT: C 704 SER cc_start: 0.8564 (m) cc_final: 0.8040 (t) REVERT: C 747 THR cc_start: 0.8225 (m) cc_final: 0.7817 (p) REVERT: C 773 GLU cc_start: 0.7824 (tt0) cc_final: 0.7480 (tt0) REVERT: C 774 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7824 (mp-120) REVERT: C 796 ASP cc_start: 0.7961 (t0) cc_final: 0.7521 (t0) REVERT: C 803 SER cc_start: 0.8875 (t) cc_final: 0.8655 (p) REVERT: C 804 GLN cc_start: 0.8440 (mt0) cc_final: 0.8102 (mt0) REVERT: C 816 SER cc_start: 0.8626 (p) cc_final: 0.8303 (t) REVERT: C 823 PHE cc_start: 0.8091 (m-10) cc_final: 0.7627 (m-10) REVERT: C 858 LEU cc_start: 0.8500 (mt) cc_final: 0.8287 (mp) REVERT: C 868 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7653 (tm-30) REVERT: C 870 ILE cc_start: 0.8396 (pt) cc_final: 0.8158 (mt) REVERT: C 886 TRP cc_start: 0.8333 (OUTLIER) cc_final: 0.7879 (p90) REVERT: C 949 GLN cc_start: 0.8429 (tp40) cc_final: 0.7952 (tp40) REVERT: C 994 ASP cc_start: 0.8375 (t70) cc_final: 0.8048 (t0) REVERT: C 1010 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7707 (mm-40) REVERT: C 1045 LYS cc_start: 0.8558 (mttt) cc_final: 0.8261 (mttt) REVERT: C 1073 LYS cc_start: 0.8097 (mtpt) cc_final: 0.7798 (mmmm) REVERT: C 1107 ARG cc_start: 0.8241 (mtt180) cc_final: 0.7991 (mtt90) REVERT: C 1139 ASP cc_start: 0.8461 (t0) cc_final: 0.8134 (t0) REVERT: B 90 VAL cc_start: 0.8683 (p) cc_final: 0.8298 (m) REVERT: B 115 GLN cc_start: 0.8539 (mp10) cc_final: 0.8120 (mm-40) REVERT: B 159 VAL cc_start: 0.7459 (OUTLIER) cc_final: 0.7120 (m) REVERT: B 206 LYS cc_start: 0.8615 (tptm) cc_final: 0.8291 (tptm) REVERT: B 296 LEU cc_start: 0.8422 (tp) cc_final: 0.8186 (tp) REVERT: B 300 LYS cc_start: 0.8492 (mtmt) cc_final: 0.8221 (mttt) REVERT: B 310 LYS cc_start: 0.9051 (ttpp) cc_final: 0.8805 (ttpp) REVERT: B 324 GLU cc_start: 0.8364 (pm20) cc_final: 0.7910 (pm20) REVERT: B 360 ASN cc_start: 0.8144 (m110) cc_final: 0.7903 (m110) REVERT: B 386 LYS cc_start: 0.8566 (mmmt) cc_final: 0.8273 (mmmm) REVERT: B 414 GLN cc_start: 0.6554 (tm-30) cc_final: 0.6104 (tm-30) REVERT: B 537 LYS cc_start: 0.8632 (ttpp) cc_final: 0.8210 (tttp) REVERT: B 576 VAL cc_start: 0.8939 (p) cc_final: 0.8627 (t) REVERT: B 599 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8172 (p) REVERT: B 673 SER cc_start: 0.8991 (t) cc_final: 0.8547 (m) REVERT: B 764 ASN cc_start: 0.8600 (m-40) cc_final: 0.8244 (m-40) REVERT: B 779 GLN cc_start: 0.8300 (tt0) cc_final: 0.8017 (tp40) REVERT: B 790 LYS cc_start: 0.8501 (ptmt) cc_final: 0.8282 (ptmt) REVERT: B 811 LYS cc_start: 0.7518 (mttt) cc_final: 0.7046 (mtpt) REVERT: B 820 ASP cc_start: 0.7800 (t0) cc_final: 0.7224 (t0) REVERT: B 856 ASN cc_start: 0.8413 (t0) cc_final: 0.8127 (t0) REVERT: B 929 SER cc_start: 0.8605 (t) cc_final: 0.8280 (p) REVERT: B 950 ASP cc_start: 0.8105 (t0) cc_final: 0.7624 (t0) REVERT: B 1003 SER cc_start: 0.8633 (m) cc_final: 0.8354 (t) REVERT: B 1073 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8459 (mtmm) REVERT: B 1117 THR cc_start: 0.8404 (m) cc_final: 0.8032 (t) REVERT: B 1136 THR cc_start: 0.8759 (t) cc_final: 0.8491 (p) REVERT: B 1138 TYR cc_start: 0.7887 (t80) cc_final: 0.7589 (t80) REVERT: A 21 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7710 (ptm-80) REVERT: A 28 TYR cc_start: 0.8390 (m-80) cc_final: 0.7902 (m-80) REVERT: A 120 VAL cc_start: 0.8123 (t) cc_final: 0.7882 (m) REVERT: A 191 GLU cc_start: 0.7936 (mp0) cc_final: 0.7523 (mt-10) REVERT: A 535 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8692 (mttm) REVERT: A 546 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7419 (pt) REVERT: A 549 THR cc_start: 0.7974 (m) cc_final: 0.7710 (p) REVERT: A 586 ASP cc_start: 0.8187 (t0) cc_final: 0.7805 (t0) REVERT: A 596 SER cc_start: 0.8803 (OUTLIER) cc_final: 0.8564 (p) REVERT: A 605 SER cc_start: 0.8826 (t) cc_final: 0.8534 (m) REVERT: A 719 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8354 (p) REVERT: A 725 GLU cc_start: 0.8136 (tp30) cc_final: 0.7637 (tt0) REVERT: A 758 SER cc_start: 0.8582 (m) cc_final: 0.8105 (p) REVERT: A 790 LYS cc_start: 0.8515 (ttmm) cc_final: 0.8138 (mtmm) REVERT: A 804 GLN cc_start: 0.8492 (mt0) cc_final: 0.8079 (mt0) REVERT: A 825 LYS cc_start: 0.8486 (mmmt) cc_final: 0.8078 (mmmm) REVERT: A 878 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8260 (mt) REVERT: A 900 MET cc_start: 0.8527 (mtp) cc_final: 0.8319 (mtt) REVERT: A 902 MET cc_start: 0.8421 (mmm) cc_final: 0.8191 (tpt) REVERT: A 904 TYR cc_start: 0.7818 (m-10) cc_final: 0.7495 (m-10) REVERT: A 921 LYS cc_start: 0.8404 (mmtp) cc_final: 0.8127 (mmtp) REVERT: A 950 ASP cc_start: 0.7847 (t0) cc_final: 0.7462 (t0) REVERT: A 963 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8669 (p) REVERT: A 986 LYS cc_start: 0.8347 (mttm) cc_final: 0.7737 (mttm) REVERT: A 987 VAL cc_start: 0.8584 (p) cc_final: 0.8095 (t) REVERT: A 990 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7224 (mp0) REVERT: A 1019 ARG cc_start: 0.8049 (ttm110) cc_final: 0.7708 (ttp80) REVERT: A 1045 LYS cc_start: 0.8529 (mttt) cc_final: 0.8277 (mttt) REVERT: A 1073 LYS cc_start: 0.8619 (mtpt) cc_final: 0.8413 (mtpp) REVERT: A 1123 SER cc_start: 0.8893 (t) cc_final: 0.8543 (p) REVERT: A 1139 ASP cc_start: 0.8478 (t0) cc_final: 0.8189 (t0) REVERT: A 1144 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7790 (mt-10) REVERT: D 41 TYR cc_start: 0.8146 (t80) cc_final: 0.7221 (t80) REVERT: D 42 GLN cc_start: 0.8189 (tp40) cc_final: 0.7383 (tp40) REVERT: D 74 LYS cc_start: 0.8700 (tppp) cc_final: 0.8192 (tppp) REVERT: D 189 GLU cc_start: 0.6556 (tp30) cc_final: 0.6282 (tm-30) REVERT: D 312 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8184 (mm-30) REVERT: D 314 PHE cc_start: 0.9079 (t80) cc_final: 0.8468 (m-10) REVERT: D 369 PHE cc_start: 0.8717 (t80) cc_final: 0.8308 (m-80) REVERT: D 383 MET cc_start: 0.7184 (mpp) cc_final: 0.6689 (mpp) REVERT: D 408 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7407 (mpm) REVERT: D 410 LEU cc_start: 0.8881 (mt) cc_final: 0.8389 (pp) REVERT: D 454 TYR cc_start: 0.5808 (t80) cc_final: 0.5407 (t80) REVERT: D 479 GLU cc_start: 0.8149 (pt0) cc_final: 0.7795 (pp20) REVERT: D 497 TYR cc_start: 0.6624 (m-80) cc_final: 0.6340 (m-80) REVERT: D 521 TYR cc_start: 0.5261 (m-10) cc_final: 0.4812 (m-80) REVERT: D 557 MET cc_start: 0.7331 (tmm) cc_final: 0.6931 (tmm) REVERT: D 560 LEU cc_start: 0.7520 (mt) cc_final: 0.7214 (mp) outliers start: 113 outliers final: 86 residues processed: 697 average time/residue: 0.1872 time to fit residues: 209.4546 Evaluate side-chains 713 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 610 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 247 optimal weight: 1.9990 chunk 282 optimal weight: 0.5980 chunk 180 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 237 optimal weight: 0.6980 chunk 365 optimal weight: 2.9990 chunk 334 optimal weight: 10.0000 chunk 361 optimal weight: 10.0000 chunk 179 optimal weight: 0.7980 chunk 376 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN C 655 HIS C 762 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B1119 ASN B1135 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.183753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.136278 restraints weight = 50239.918| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.83 r_work: 0.3459 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31780 Z= 0.192 Angle : 0.667 11.936 43372 Z= 0.329 Chirality : 0.047 0.518 5026 Planarity : 0.004 0.044 5477 Dihedral : 5.430 78.920 5599 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.36 % Allowed : 16.86 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.42 (0.13), residues: 3761 helix: 1.65 (0.17), residues: 1036 sheet: -0.27 (0.19), residues: 661 loop : -1.34 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 190 TYR 0.035 0.001 TYR A 904 PHE 0.023 0.002 PHE A 140 TRP 0.025 0.001 TRP C 353 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00431 (31664) covalent geometry : angle 0.64113 (43069) SS BOND : bond 0.00467 ( 45) SS BOND : angle 2.61662 ( 90) hydrogen bonds : bond 0.03985 ( 1172) hydrogen bonds : angle 5.16492 ( 3312) link_BETA1-4 : bond 0.00290 ( 21) link_BETA1-4 : angle 1.14732 ( 63) link_NAG-ASN : bond 0.00444 ( 50) link_NAG-ASN : angle 2.45032 ( 150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10671.03 seconds wall clock time: 183 minutes 4.46 seconds (10984.46 seconds total)