Starting phenix.real_space_refine on Wed May 28 18:28:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z3w_39756/05_2025/8z3w_39756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z3w_39756/05_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_39756/05_2025/8z3w_39756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z3w_39756/05_2025/8z3w_39756.map" model { file = "/net/cci-nas-00/data/ceres_data/8z3w_39756/05_2025/8z3w_39756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z3w_39756/05_2025/8z3w_39756.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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): 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 18.10, per 1000 atoms: 0.58 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: 8.21 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 4.17 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: 13.12 Time building geometry restraints manager: 9.46 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 1148 or resid 1301 through 1309)) selection = (chain 'B' and (resid 14 through 177 or resid 185 through 260 or resid 264 throu \ gh 621 or resid 640 through 1148 or resid 1301 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 1148 or resid 1301 through 13 \ 09)) } 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: 3.400 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: 0.030 Extract box with map and model: 1.530 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 68.980 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.310 ------------------------------------------------------------------------------- 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 : 5.22 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (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 TRP 0.005 0.000 TRP B 152 HIS 0.001 0.000 HIS B1048 PHE 0.005 0.001 PHE B1095 TYR 0.006 0.001 TYR A1067 ARG 0.002 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 50) link_NAG-ASN : angle 1.61322 ( 150) link_BETA1-4 : bond 0.00345 ( 21) link_BETA1-4 : angle 0.80980 ( 63) hydrogen bonds : bond 0.19831 ( 1172) hydrogen bonds : angle 7.60595 ( 3312) SS BOND : bond 0.00104 ( 45) SS BOND : angle 0.47313 ( 90) covalent geometry : bond 0.00270 (31664) covalent geometry : angle 0.44627 (43069) *********************** 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 : 2.963 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: 0.8265 (t) REVERT: C 40 ASP cc_start: 0.7549 (p0) cc_final: 0.7296 (p0) REVERT: C 117 LEU cc_start: 0.7384 (tp) cc_final: 0.7178 (tt) REVERT: C 128 ILE cc_start: 0.8106 (mt) cc_final: 0.7886 (mp) REVERT: C 129 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7584 (tppt) REVERT: C 202 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.7086 (mtpp) REVERT: C 228 ASP cc_start: 0.6817 (t0) cc_final: 0.5989 (t70) REVERT: C 240 THR cc_start: 0.8170 (m) cc_final: 0.7918 (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: 0.8369 (tt) REVERT: C 278 LYS cc_start: 0.8216 (ttmt) cc_final: 0.7883 (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: 0.6877 (t) REVERT: C 305 SER cc_start: 0.8883 (t) cc_final: 0.8440 (p) REVERT: C 307 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.7151 (p) REVERT: C 312 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7885 (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: 0.6194 (t0) REVERT: C 774 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7318 (mp10) REVERT: C 803 SER cc_start: 0.8333 (t) cc_final: 0.8072 (p) REVERT: C 870 ILE cc_start: 0.8096 (pt) cc_final: 0.7830 (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: 0.7356 (tp40) REVERT: C 994 ASP cc_start: 0.7259 (t70) cc_final: 0.6990 (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: 0.8189 (tt) REVERT: B 132 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6943 (mt-10) REVERT: B 195 LYS cc_start: 0.7365 (mtmt) cc_final: 0.6994 (ttmt) REVERT: B 204 TYR cc_start: 0.7028 (m-80) cc_final: 0.6568 (m-80) REVERT: B 206 LYS cc_start: 0.8090 (tptm) cc_final: 0.7575 (tptp) REVERT: B 226 LEU cc_start: 0.7542 (tp) cc_final: 0.7329 (mt) REVERT: B 275 PHE cc_start: 0.8089 (m-80) cc_final: 0.7788 (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: 0.8118 (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: 0.8452 (t) REVERT: B 587 ILE cc_start: 0.7708 (mt) cc_final: 0.7353 (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: 0.6901 (tp-100) REVERT: B 664 ILE cc_start: 0.8567 (mt) cc_final: 0.8338 (mt) REVERT: B 773 GLU cc_start: 0.6711 (pt0) cc_final: 0.6396 (pt0) REVERT: B 781 VAL cc_start: 0.8562 (t) cc_final: 0.8320 (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: 0.7930 (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: 0.8090 (t) REVERT: B 1086 LYS cc_start: 0.8349 (mppt) cc_final: 0.7398 (mtmm) REVERT: B 1101 HIS cc_start: 0.8029 (m90) cc_final: 0.7673 (m170) REVERT: B 1117 THR cc_start: 0.8183 (m) cc_final: 0.7850 (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: 0.7068 (t80) REVERT: B 1141 LEU cc_start: 0.8371 (tt) cc_final: 0.8146 (tt) REVERT: A 54 LEU cc_start: 0.8035 (mt) cc_final: 0.7834 (mt) REVERT: A 120 VAL cc_start: 0.7969 (t) cc_final: 0.7628 (m) REVERT: A 206 LYS cc_start: 0.7883 (tptm) cc_final: 0.7655 (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: 0.6043 (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: 0.7016 (t0) REVERT: A 549 THR cc_start: 0.7766 (m) cc_final: 0.7507 (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: 0.7905 (mt) REVERT: A 721 SER cc_start: 0.7956 (t) cc_final: 0.7424 (p) REVERT: A 758 SER cc_start: 0.8553 (m) cc_final: 0.8228 (p) REVERT: A 819 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7233 (mt-10) REVERT: A 855 PHE cc_start: 0.7733 (m-10) cc_final: 0.7522 (m-80) REVERT: A 866 THR cc_start: 0.8423 (p) cc_final: 0.7860 (p) REVERT: A 868 GLU cc_start: 0.6901 (mp0) cc_final: 0.6195 (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: 0.6414 (t0) REVERT: A 986 LYS cc_start: 0.7751 (mttt) cc_final: 0.6893 (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: 0.6665 (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: 0.8189 (mt) REVERT: D 41 TYR cc_start: 0.7927 (t80) cc_final: 0.7065 (t80) REVERT: D 42 GLN cc_start: 0.7905 (tp40) cc_final: 0.7127 (tp40) REVERT: D 74 LYS cc_start: 0.8615 (tppp) cc_final: 0.8076 (tppp) REVERT: D 312 GLU cc_start: 0.8738 (tt0) cc_final: 0.8482 (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: -0.1160 (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: 0.7477 (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: 0.5944 (p) REVERT: D 521 TYR cc_start: 0.5107 (m-10) cc_final: 0.4452 (m-80) REVERT: D 557 MET cc_start: 0.7331 (tmm) cc_final: 0.7026 (tmm) outliers start: 52 outliers final: 14 residues processed: 901 average time/residue: 0.4175 time to fit residues: 588.9495 Evaluate side-chains 689 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 669 time to evaluate : 2.973 ------------------------------------------------------------------------------- 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 319 optimal weight: 9.9990 chunk 286 optimal weight: 0.0050 chunk 158 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 180 optimal weight: 0.3980 chunk 220 optimal weight: 2.9990 chunk 343 optimal weight: 10.0000 overall best weight: 1.2800 ------------------------------------------------------------------------------- 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 388 ASN C 474 GLN C 564 GLN C 703 ASN C 777 ASN C 856 ASN C 926 GLN C 955 ASN C 957 GLN C1011 GLN C1071 GLN B 134 GLN B 165 ASN B 188 ASN B 474 GLN B 501 ASN B 563 GLN B 613 GLN B 787 GLN B 804 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 542 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 690 GLN A 755 GLN A 762 GLN A 926 GLN A1005 GLN A1011 GLN A1071 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN 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: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.185983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.138034 restraints weight = 50563.509| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.82 r_work: 0.3493 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 31780 Z= 0.287 Angle : 0.696 12.782 43372 Z= 0.349 Chirality : 0.050 0.586 5026 Planarity : 0.004 0.061 5477 Dihedral : 8.015 99.124 5612 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.21 % Allowed : 10.11 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 3761 helix: 1.07 (0.16), residues: 1028 sheet: -0.59 (0.18), residues: 668 loop : -2.02 (0.12), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 152 HIS 0.008 0.001 HIS A1064 PHE 0.034 0.002 PHE C 192 TYR 0.023 0.002 TYR C 660 ARG 0.006 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00632 ( 50) link_NAG-ASN : angle 2.59217 ( 150) link_BETA1-4 : bond 0.00353 ( 21) link_BETA1-4 : angle 1.11954 ( 63) hydrogen bonds : bond 0.04744 ( 1172) hydrogen bonds : angle 5.69789 ( 3312) SS BOND : bond 0.00559 ( 45) SS BOND : angle 2.52049 ( 90) covalent geometry : bond 0.00637 (31664) covalent geometry : angle 0.67048 (43069) *********************** 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 805 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 698 time to evaluate : 3.101 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 42 VAL cc_start: 0.8458 (p) cc_final: 0.7997 (m) REVERT: C 129 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7901 (mtmm) REVERT: C 228 ASP cc_start: 0.7209 (t0) cc_final: 0.6604 (t70) REVERT: C 284 THR cc_start: 0.8575 (m) cc_final: 0.8160 (t) REVERT: C 289 VAL cc_start: 0.8752 (p) cc_final: 0.8446 (m) REVERT: C 290 ASP cc_start: 0.7312 (p0) cc_final: 0.7093 (p0) REVERT: C 305 SER cc_start: 0.8888 (t) cc_final: 0.8486 (p) REVERT: C 309 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7066 (mt-10) REVERT: C 313 TYR cc_start: 0.8376 (m-80) cc_final: 0.8118 (m-80) REVERT: C 353 TRP cc_start: 0.7656 (p-90) cc_final: 0.7317 (p-90) REVERT: C 378 LYS cc_start: 0.8110 (mttt) cc_final: 0.7673 (mttt) REVERT: C 424 LYS cc_start: 0.7356 (tttt) cc_final: 0.6665 (ttpp) REVERT: C 591 SER cc_start: 0.8816 (t) cc_final: 0.8415 (p) REVERT: C 704 SER cc_start: 0.8317 (m) cc_final: 0.7808 (t) REVERT: C 773 GLU cc_start: 0.7417 (tt0) cc_final: 0.7121 (tt0) REVERT: C 774 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7812 (mp-120) REVERT: C 803 SER cc_start: 0.8758 (t) cc_final: 0.8509 (p) REVERT: C 868 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7329 (tp30) REVERT: C 870 ILE cc_start: 0.8357 (pt) cc_final: 0.8135 (mt) REVERT: C 886 TRP cc_start: 0.8262 (OUTLIER) cc_final: 0.7708 (p90) REVERT: C 900 MET cc_start: 0.8342 (mtm) cc_final: 0.8089 (mtm) REVERT: C 935 GLN cc_start: 0.8422 (tt0) cc_final: 0.8023 (tt0) REVERT: C 949 GLN cc_start: 0.8301 (tp40) cc_final: 0.7868 (tp40) REVERT: C 973 ILE cc_start: 0.9000 (mt) cc_final: 0.8734 (mm) REVERT: C 993 ILE cc_start: 0.8966 (mm) cc_final: 0.8704 (mt) REVERT: C 994 ASP cc_start: 0.8107 (t70) cc_final: 0.7824 (t0) REVERT: C 1010 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7394 (mm-40) REVERT: C 1029 MET cc_start: 0.8458 (tpp) cc_final: 0.8111 (tpp) REVERT: C 1072 GLU cc_start: 0.8023 (pm20) cc_final: 0.7787 (pm20) REVERT: C 1073 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7591 (mmmm) REVERT: C 1107 ARG cc_start: 0.7928 (mtt180) cc_final: 0.7725 (mtt90) REVERT: C 1139 ASP cc_start: 0.8264 (t0) cc_final: 0.7873 (t0) REVERT: B 65 PHE cc_start: 0.7952 (m-80) cc_final: 0.7685 (m-80) REVERT: B 132 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7704 (mp0) REVERT: B 195 LYS cc_start: 0.7887 (mtmt) cc_final: 0.7596 (ptpp) REVERT: B 206 LYS cc_start: 0.8436 (tptm) cc_final: 0.8006 (tttm) REVERT: B 302 THR cc_start: 0.8259 (t) cc_final: 0.8059 (m) REVERT: B 303 LEU cc_start: 0.8242 (tt) cc_final: 0.7967 (pp) REVERT: B 313 TYR cc_start: 0.8139 (m-10) cc_final: 0.7840 (m-80) REVERT: B 324 GLU cc_start: 0.8031 (pm20) cc_final: 0.7499 (pm20) REVERT: B 385 THR cc_start: 0.8719 (p) cc_final: 0.8518 (p) REVERT: B 386 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8080 (mmmm) REVERT: B 392 PHE cc_start: 0.6449 (m-80) cc_final: 0.5858 (m-10) REVERT: B 394 ASN cc_start: 0.8340 (p0) cc_final: 0.8060 (p0) REVERT: B 430 THR cc_start: 0.8382 (m) cc_final: 0.8171 (p) REVERT: B 448 ASN cc_start: 0.8104 (t0) cc_final: 0.6383 (p0) REVERT: B 576 VAL cc_start: 0.8924 (p) cc_final: 0.8563 (t) REVERT: B 580 GLN cc_start: 0.7518 (mm110) cc_final: 0.7119 (mm-40) REVERT: B 619 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7271 (mt-10) REVERT: B 764 ASN cc_start: 0.8353 (m110) cc_final: 0.8113 (m-40) REVERT: B 790 LYS cc_start: 0.8442 (ptmt) cc_final: 0.8152 (ptmt) REVERT: B 811 LYS cc_start: 0.7529 (mttt) cc_final: 0.7313 (mttt) REVERT: B 870 ILE cc_start: 0.8411 (mm) cc_final: 0.8207 (mt) REVERT: B 929 SER cc_start: 0.8400 (t) cc_final: 0.8055 (p) REVERT: B 950 ASP cc_start: 0.7734 (t0) cc_final: 0.7134 (t0) REVERT: B 953 ASN cc_start: 0.8351 (m-40) cc_final: 0.8116 (m110) REVERT: B 954 GLN cc_start: 0.8000 (mt0) cc_final: 0.7535 (mt0) REVERT: B 968 SER cc_start: 0.8782 (m) cc_final: 0.8476 (t) REVERT: B 987 VAL cc_start: 0.8345 (t) cc_final: 0.8123 (p) REVERT: B 1086 LYS cc_start: 0.8479 (mppt) cc_final: 0.8008 (mtmm) REVERT: B 1101 HIS cc_start: 0.8553 (m90) cc_final: 0.8314 (m90) REVERT: B 1117 THR cc_start: 0.8333 (m) cc_final: 0.8002 (t) REVERT: B 1136 THR cc_start: 0.8655 (t) cc_final: 0.8322 (p) REVERT: B 1141 LEU cc_start: 0.8741 (tt) cc_final: 0.8491 (tt) REVERT: A 28 TYR cc_start: 0.8127 (m-80) cc_final: 0.7822 (m-80) REVERT: A 48 LEU cc_start: 0.8259 (mp) cc_final: 0.8046 (mt) REVERT: A 117 LEU cc_start: 0.7959 (tp) cc_final: 0.7451 (mp) REVERT: A 120 VAL cc_start: 0.8120 (t) cc_final: 0.7784 (m) REVERT: A 191 GLU cc_start: 0.7442 (mp0) cc_final: 0.6992 (mt-10) REVERT: A 206 LYS cc_start: 0.8177 (tptm) cc_final: 0.7908 (tptm) REVERT: A 239 GLN cc_start: 0.8155 (tt0) cc_final: 0.7911 (tt0) REVERT: A 535 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8624 (mttm) REVERT: A 544 ASN cc_start: 0.7794 (t0) cc_final: 0.7499 (t0) REVERT: A 549 THR cc_start: 0.7963 (m) cc_final: 0.7666 (p) REVERT: A 551 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8416 (m) REVERT: A 558 LYS cc_start: 0.8373 (mmtm) cc_final: 0.8075 (mmtt) REVERT: A 596 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8540 (p) REVERT: A 605 SER cc_start: 0.8647 (t) cc_final: 0.8256 (m) REVERT: A 704 SER cc_start: 0.8567 (t) cc_final: 0.8158 (p) REVERT: A 758 SER cc_start: 0.8777 (m) cc_final: 0.8311 (p) REVERT: A 773 GLU cc_start: 0.7848 (tt0) cc_final: 0.7614 (tt0) REVERT: A 776 LYS cc_start: 0.8418 (tmmt) cc_final: 0.8195 (ttpp) REVERT: A 796 ASP cc_start: 0.6854 (p0) cc_final: 0.6444 (p0) REVERT: A 825 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8060 (mmmm) REVERT: A 878 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8240 (mt) REVERT: A 900 MET cc_start: 0.8238 (mtp) cc_final: 0.7729 (mtp) REVERT: A 921 LYS cc_start: 0.8155 (mmtp) cc_final: 0.7938 (mmtp) REVERT: A 933 LYS cc_start: 0.8344 (mtmm) cc_final: 0.8080 (mttp) REVERT: A 950 ASP cc_start: 0.7682 (t0) cc_final: 0.7279 (t0) REVERT: A 1038 LYS cc_start: 0.8647 (mttt) cc_final: 0.8340 (mttm) REVERT: A 1045 LYS cc_start: 0.8398 (mttt) cc_final: 0.8118 (mttt) REVERT: A 1073 LYS cc_start: 0.8444 (mtpt) cc_final: 0.8143 (mtpp) REVERT: A 1084 ASP cc_start: 0.7790 (p0) cc_final: 0.7397 (p0) REVERT: A 1122 VAL cc_start: 0.8803 (t) cc_final: 0.8595 (p) REVERT: D 41 TYR cc_start: 0.8267 (t80) cc_final: 0.7283 (t80) REVERT: D 42 GLN cc_start: 0.8079 (tp40) cc_final: 0.7293 (tp40) REVERT: D 64 ASN cc_start: 0.8796 (t0) cc_final: 0.7697 (m-40) REVERT: D 74 LYS cc_start: 0.8705 (tppp) cc_final: 0.8160 (tppp) REVERT: D 309 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8570 (mmtt) REVERT: D 340 GLN cc_start: 0.1693 (tm-30) cc_final: 0.1339 (tm-30) REVERT: D 360 MET cc_start: 0.3878 (tmm) cc_final: 0.3224 (tmm) REVERT: D 369 PHE cc_start: 0.8818 (t80) cc_final: 0.8408 (t80) REVERT: D 376 MET cc_start: 0.0766 (ttm) cc_final: 0.0242 (mpp) REVERT: D 378 HIS cc_start: 0.3202 (OUTLIER) cc_final: 0.2919 (m90) REVERT: D 408 MET cc_start: 0.7562 (mpm) cc_final: 0.7355 (mpm) REVERT: D 410 LEU cc_start: 0.8609 (mt) cc_final: 0.7762 (pp) REVERT: D 454 TYR cc_start: 0.5966 (t80) cc_final: 0.5387 (t80) REVERT: D 479 GLU cc_start: 0.7962 (pt0) cc_final: 0.7544 (pp20) REVERT: D 498 CYS cc_start: 0.6187 (t) cc_final: 0.5880 (p) REVERT: D 521 TYR cc_start: 0.5241 (m-10) cc_final: 0.4625 (m-80) REVERT: D 557 MET cc_start: 0.7444 (tmm) cc_final: 0.7079 (tmm) REVERT: D 560 LEU cc_start: 0.7739 (mt) cc_final: 0.7500 (mp) outliers start: 107 outliers final: 57 residues processed: 776 average time/residue: 0.4120 time to fit residues: 511.7011 Evaluate side-chains 704 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 640 time to evaluate : 3.053 ------------------------------------------------------------------------------- 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 238 PHE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE 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 588 THR 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 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain B residue 127 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 391 CYS 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 547 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 803 SER 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 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 193 VAL Chi-restraints excluded: chain A residue 289 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 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 878 LEU 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 378 HIS 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 97 optimal weight: 0.4980 chunk 191 optimal weight: 0.6980 chunk 151 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 346 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 242 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 228 optimal weight: 0.0070 chunk 204 optimal weight: 0.3980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 777 ASN C 965 GLN C1101 HIS C1119 ASN B 493 GLN B 675 GLN B 777 ASN B 901 GLN B1011 GLN A 66 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 675 GLN A 919 ASN A 935 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 76 GLN D 89 GLN D 380 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.186863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.140326 restraints weight = 50729.094| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.09 r_work: 0.3518 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31780 Z= 0.128 Angle : 0.604 12.566 43372 Z= 0.296 Chirality : 0.046 0.604 5026 Planarity : 0.004 0.051 5477 Dihedral : 7.342 94.139 5604 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.00 % Allowed : 12.36 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.13), residues: 3761 helix: 1.43 (0.17), residues: 1048 sheet: -0.47 (0.18), residues: 671 loop : -1.76 (0.12), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 104 HIS 0.003 0.001 HIS A1064 PHE 0.024 0.001 PHE C 192 TYR 0.024 0.001 TYR D 183 ARG 0.010 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 50) link_NAG-ASN : angle 2.32278 ( 150) link_BETA1-4 : bond 0.00318 ( 21) link_BETA1-4 : angle 1.03467 ( 63) hydrogen bonds : bond 0.03894 ( 1172) hydrogen bonds : angle 5.35381 ( 3312) SS BOND : bond 0.00419 ( 45) SS BOND : angle 2.54329 ( 90) covalent geometry : bond 0.00284 (31664) covalent geometry : angle 0.57793 (43069) *********************** 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 775 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 675 time to evaluate : 3.095 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 33 THR cc_start: 0.8613 (p) cc_final: 0.8403 (t) REVERT: C 42 VAL cc_start: 0.8495 (p) cc_final: 0.8086 (m) REVERT: C 64 TRP cc_start: 0.8147 (t60) cc_final: 0.7932 (t60) REVERT: C 129 LYS cc_start: 0.8109 (mtmt) cc_final: 0.7736 (mtmm) REVERT: C 207 HIS cc_start: 0.8275 (t-170) cc_final: 0.7960 (t70) REVERT: C 228 ASP cc_start: 0.7287 (t0) cc_final: 0.6570 (t70) REVERT: C 276 LEU cc_start: 0.8728 (tt) cc_final: 0.8510 (tp) REVERT: C 284 THR cc_start: 0.8570 (m) cc_final: 0.8217 (t) REVERT: C 289 VAL cc_start: 0.8714 (p) cc_final: 0.8305 (m) REVERT: C 290 ASP cc_start: 0.7404 (p0) cc_final: 0.7154 (p0) REVERT: C 305 SER cc_start: 0.8902 (t) cc_final: 0.8537 (p) REVERT: C 309 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7091 (mm-30) REVERT: C 313 TYR cc_start: 0.8379 (m-80) cc_final: 0.8140 (m-80) REVERT: C 353 TRP cc_start: 0.7733 (p-90) cc_final: 0.7290 (p-90) REVERT: C 362 VAL cc_start: 0.8045 (t) cc_final: 0.7757 (m) REVERT: C 378 LYS cc_start: 0.8060 (mttt) cc_final: 0.7616 (mttt) REVERT: C 424 LYS cc_start: 0.7311 (tttt) cc_final: 0.6507 (ttpp) REVERT: C 619 GLU cc_start: 0.7899 (pm20) cc_final: 0.7653 (pm20) REVERT: C 658 ASN cc_start: 0.8062 (p0) cc_final: 0.7673 (p0) REVERT: C 660 TYR cc_start: 0.8754 (m-10) cc_final: 0.8296 (m-10) REVERT: C 704 SER cc_start: 0.8304 (m) cc_final: 0.7793 (t) REVERT: C 740 MET cc_start: 0.8289 (tpp) cc_final: 0.7990 (tpp) REVERT: C 773 GLU cc_start: 0.7399 (tt0) cc_final: 0.7127 (tt0) REVERT: C 774 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7924 (mp10) REVERT: C 803 SER cc_start: 0.8659 (t) cc_final: 0.8389 (p) REVERT: C 804 GLN cc_start: 0.8294 (mt0) cc_final: 0.8000 (mt0) REVERT: C 868 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7275 (tp30) REVERT: C 870 ILE cc_start: 0.8297 (pt) cc_final: 0.8096 (mt) REVERT: C 886 TRP cc_start: 0.8229 (OUTLIER) cc_final: 0.7763 (p90) REVERT: C 900 MET cc_start: 0.8210 (mtm) cc_final: 0.7919 (mtp) REVERT: C 949 GLN cc_start: 0.8259 (tp40) cc_final: 0.7813 (tp40) REVERT: C 973 ILE cc_start: 0.8962 (mt) cc_final: 0.8733 (mm) REVERT: C 994 ASP cc_start: 0.8058 (t70) cc_final: 0.7717 (t0) REVERT: C 1010 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7484 (mm-40) REVERT: C 1029 MET cc_start: 0.8340 (tpp) cc_final: 0.8096 (tpp) REVERT: C 1073 LYS cc_start: 0.7869 (mtpt) cc_final: 0.7566 (mmmm) REVERT: C 1107 ARG cc_start: 0.7903 (mtt180) cc_final: 0.6928 (mtt90) REVERT: C 1139 ASP cc_start: 0.8267 (t0) cc_final: 0.7884 (t0) REVERT: B 47 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8053 (p) REVERT: B 65 PHE cc_start: 0.7957 (m-80) cc_final: 0.7726 (m-10) REVERT: B 132 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7572 (mp0) REVERT: B 195 LYS cc_start: 0.7920 (mtmt) cc_final: 0.7627 (ptpt) REVERT: B 206 LYS cc_start: 0.8530 (tptm) cc_final: 0.8109 (tptp) REVERT: B 294 ASP cc_start: 0.8124 (p0) cc_final: 0.7867 (p0) REVERT: B 296 LEU cc_start: 0.8244 (tp) cc_final: 0.7967 (tp) REVERT: B 302 THR cc_start: 0.8122 (t) cc_final: 0.7918 (m) REVERT: B 313 TYR cc_start: 0.8036 (m-10) cc_final: 0.7754 (m-80) REVERT: B 392 PHE cc_start: 0.6284 (m-80) cc_final: 0.5545 (m-80) REVERT: B 394 ASN cc_start: 0.8291 (p0) cc_final: 0.8090 (p0) REVERT: B 400 PHE cc_start: 0.6458 (p90) cc_final: 0.6245 (p90) REVERT: B 430 THR cc_start: 0.8332 (m) cc_final: 0.8094 (p) REVERT: B 448 ASN cc_start: 0.7923 (t0) cc_final: 0.6241 (p0) REVERT: B 523 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7520 (m) REVERT: B 524 VAL cc_start: 0.8660 (t) cc_final: 0.8427 (p) REVERT: B 532 ASN cc_start: 0.8357 (t0) cc_final: 0.8080 (t0) REVERT: B 576 VAL cc_start: 0.8956 (p) cc_final: 0.8544 (t) REVERT: B 580 GLN cc_start: 0.7329 (mm110) cc_final: 0.6936 (mm-40) REVERT: B 582 LEU cc_start: 0.8506 (mt) cc_final: 0.8251 (mt) REVERT: B 619 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7261 (mt-10) REVERT: B 644 GLN cc_start: 0.8568 (tp40) cc_final: 0.8006 (tp40) REVERT: B 764 ASN cc_start: 0.8288 (m110) cc_final: 0.8031 (m110) REVERT: B 790 LYS cc_start: 0.8504 (ptmt) cc_final: 0.8175 (ptmt) REVERT: B 811 LYS cc_start: 0.7536 (mttt) cc_final: 0.7284 (mttt) REVERT: B 820 ASP cc_start: 0.7407 (t0) cc_final: 0.6880 (t0) REVERT: B 904 TYR cc_start: 0.7726 (m-10) cc_final: 0.7267 (m-10) REVERT: B 929 SER cc_start: 0.8349 (t) cc_final: 0.7999 (p) REVERT: B 950 ASP cc_start: 0.7674 (t0) cc_final: 0.7027 (t0) REVERT: B 953 ASN cc_start: 0.8310 (m-40) cc_final: 0.8105 (m110) REVERT: B 954 GLN cc_start: 0.8000 (mt0) cc_final: 0.7454 (mt0) REVERT: B 968 SER cc_start: 0.8793 (m) cc_final: 0.8434 (t) REVERT: B 982 SER cc_start: 0.8280 (m) cc_final: 0.8074 (p) REVERT: B 987 VAL cc_start: 0.8283 (t) cc_final: 0.8080 (p) REVERT: B 1086 LYS cc_start: 0.8511 (mppt) cc_final: 0.8006 (mtmm) REVERT: B 1117 THR cc_start: 0.8283 (m) cc_final: 0.7961 (t) REVERT: B 1136 THR cc_start: 0.8635 (t) cc_final: 0.8329 (p) REVERT: A 28 TYR cc_start: 0.8095 (m-80) cc_final: 0.7817 (m-80) REVERT: A 117 LEU cc_start: 0.8004 (tp) cc_final: 0.7419 (mp) REVERT: A 120 VAL cc_start: 0.7899 (t) cc_final: 0.7547 (m) REVERT: A 191 GLU cc_start: 0.7528 (mp0) cc_final: 0.7116 (mt-10) REVERT: A 206 LYS cc_start: 0.8212 (tptm) cc_final: 0.7897 (tptm) REVERT: A 239 GLN cc_start: 0.8134 (tt0) cc_final: 0.7813 (tt0) REVERT: A 535 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8596 (mttm) REVERT: A 544 ASN cc_start: 0.7787 (t0) cc_final: 0.7477 (t0) REVERT: A 549 THR cc_start: 0.7966 (m) cc_final: 0.7707 (p) REVERT: A 557 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7657 (mttt) REVERT: A 558 LYS cc_start: 0.8337 (mmtm) cc_final: 0.8054 (mmmt) REVERT: A 586 ASP cc_start: 0.7692 (t0) cc_final: 0.7383 (m-30) REVERT: A 605 SER cc_start: 0.8681 (t) cc_final: 0.8291 (m) REVERT: A 660 TYR cc_start: 0.8702 (m-80) cc_final: 0.7855 (m-80) REVERT: A 661 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: A 704 SER cc_start: 0.8557 (t) cc_final: 0.8173 (p) REVERT: A 719 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8260 (p) REVERT: A 758 SER cc_start: 0.8671 (m) cc_final: 0.8239 (p) REVERT: A 790 LYS cc_start: 0.8322 (ttpp) cc_final: 0.8007 (ttmm) REVERT: A 796 ASP cc_start: 0.6958 (p0) cc_final: 0.6479 (p0) REVERT: A 825 LYS cc_start: 0.8439 (mmmt) cc_final: 0.8078 (mmmm) REVERT: A 900 MET cc_start: 0.8206 (mtp) cc_final: 0.7744 (mtp) REVERT: A 921 LYS cc_start: 0.8140 (mmtp) cc_final: 0.7900 (mmtp) REVERT: A 933 LYS cc_start: 0.8240 (mtmm) cc_final: 0.7988 (mttp) REVERT: A 950 ASP cc_start: 0.7610 (t0) cc_final: 0.7190 (t0) REVERT: A 963 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8527 (p) REVERT: A 1019 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7362 (ttp80) REVERT: A 1038 LYS cc_start: 0.8695 (mttt) cc_final: 0.8377 (mmtm) REVERT: A 1045 LYS cc_start: 0.8444 (mttt) cc_final: 0.8135 (mttt) REVERT: A 1073 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8128 (mtpp) REVERT: A 1084 ASP cc_start: 0.7827 (p0) cc_final: 0.7507 (p0) REVERT: A 1122 VAL cc_start: 0.8825 (t) cc_final: 0.8624 (p) REVERT: A 1139 ASP cc_start: 0.8243 (t0) cc_final: 0.7927 (t0) REVERT: A 1141 LEU cc_start: 0.8852 (tt) cc_final: 0.8546 (tt) REVERT: D 26 LYS cc_start: 0.8288 (mtmm) cc_final: 0.8024 (mmtp) REVERT: D 39 LEU cc_start: 0.8368 (mt) cc_final: 0.8118 (tp) REVERT: D 41 TYR cc_start: 0.8189 (t80) cc_final: 0.7266 (t80) REVERT: D 42 GLN cc_start: 0.8023 (tp40) cc_final: 0.7206 (tp40) REVERT: D 74 LYS cc_start: 0.8561 (tppp) cc_final: 0.8058 (tppp) REVERT: D 123 MET cc_start: 0.1120 (ptt) cc_final: 0.0768 (ptt) REVERT: D 187 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7482 (ptpp) REVERT: D 309 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8575 (mmtt) REVERT: D 312 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8197 (mm-30) REVERT: D 323 MET cc_start: 0.4098 (tpp) cc_final: 0.2549 (tpp) REVERT: D 360 MET cc_start: 0.3753 (tmm) cc_final: 0.3171 (tmm) REVERT: D 369 PHE cc_start: 0.8777 (t80) cc_final: 0.8573 (t80) REVERT: D 454 TYR cc_start: 0.5913 (t80) cc_final: 0.5351 (t80) REVERT: D 474 MET cc_start: -0.1501 (mpp) cc_final: -0.1754 (ptp) REVERT: D 479 GLU cc_start: 0.7968 (pt0) cc_final: 0.7540 (pp20) REVERT: D 498 CYS cc_start: 0.6198 (t) cc_final: 0.5859 (p) REVERT: D 521 TYR cc_start: 0.5381 (m-10) cc_final: 0.4711 (m-80) REVERT: D 557 MET cc_start: 0.7570 (tmm) cc_final: 0.7185 (tmm) REVERT: D 560 LEU cc_start: 0.7555 (mt) cc_final: 0.7326 (mp) outliers start: 100 outliers final: 59 residues processed: 745 average time/residue: 0.4209 time to fit residues: 496.9298 Evaluate side-chains 705 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 637 time to evaluate : 3.206 ------------------------------------------------------------------------------- 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 238 PHE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 326 ILE 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 646 ARG 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 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 391 CYS 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 620 VAL 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 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 B residue 1122 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 127 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 220 PHE 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 661 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 963 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 35 optimal weight: 2.9990 chunk 167 optimal weight: 0.3980 chunk 166 optimal weight: 0.5980 chunk 210 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 309 optimal weight: 0.8980 chunk 272 optimal weight: 0.6980 chunk 299 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 HIS C 777 ASN B 613 GLN B 777 ASN B1119 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** 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 = 0.4281 r_free = 0.4281 target = 0.185445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.138026 restraints weight = 50922.678| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.78 r_work: 0.3513 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31780 Z= 0.173 Angle : 0.615 14.748 43372 Z= 0.301 Chirality : 0.046 0.531 5026 Planarity : 0.004 0.040 5477 Dihedral : 6.554 92.284 5600 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.81 % Allowed : 12.51 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.13), residues: 3761 helix: 1.50 (0.17), residues: 1049 sheet: -0.33 (0.19), residues: 648 loop : -1.65 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.006 0.001 HIS A1064 PHE 0.031 0.001 PHE B 201 TYR 0.017 0.001 TYR B 660 ARG 0.007 0.000 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 50) link_NAG-ASN : angle 2.62503 ( 150) link_BETA1-4 : bond 0.00293 ( 21) link_BETA1-4 : angle 1.08765 ( 63) hydrogen bonds : bond 0.03923 ( 1172) hydrogen bonds : angle 5.24987 ( 3312) SS BOND : bond 0.00421 ( 45) SS BOND : angle 2.23329 ( 90) covalent geometry : bond 0.00387 (31664) covalent geometry : angle 0.58699 (43069) *********************** 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 785 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 658 time to evaluate : 3.130 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: 0.7936 (t) cc_final: 0.6621 (p) REVERT: C 42 VAL cc_start: 0.8472 (p) cc_final: 0.8093 (m) REVERT: C 64 TRP cc_start: 0.8128 (t60) cc_final: 0.7859 (t60) REVERT: C 99 ASN cc_start: 0.7824 (t0) cc_final: 0.7619 (t0) REVERT: C 228 ASP cc_start: 0.7281 (t0) cc_final: 0.6566 (t70) REVERT: C 276 LEU cc_start: 0.8720 (tt) cc_final: 0.8458 (tp) REVERT: C 284 THR cc_start: 0.8579 (m) cc_final: 0.8207 (t) REVERT: C 289 VAL cc_start: 0.8785 (OUTLIER) cc_final: 0.8440 (m) REVERT: C 290 ASP cc_start: 0.7451 (p0) cc_final: 0.7230 (p0) REVERT: C 305 SER cc_start: 0.8902 (t) cc_final: 0.8531 (p) REVERT: C 309 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7103 (mm-30) REVERT: C 313 TYR cc_start: 0.8377 (m-80) cc_final: 0.8162 (m-80) REVERT: C 353 TRP cc_start: 0.7762 (p-90) cc_final: 0.7321 (p-90) REVERT: C 362 VAL cc_start: 0.7985 (t) cc_final: 0.7711 (m) REVERT: C 378 LYS cc_start: 0.8086 (mttt) cc_final: 0.7672 (mttt) REVERT: C 424 LYS cc_start: 0.7341 (tttt) cc_final: 0.6538 (ttpp) REVERT: C 619 GLU cc_start: 0.7845 (pm20) cc_final: 0.7532 (pm20) REVERT: C 646 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7657 (ttm170) REVERT: C 704 SER cc_start: 0.8399 (m) cc_final: 0.7828 (t) REVERT: C 773 GLU cc_start: 0.7420 (tt0) cc_final: 0.7098 (tt0) REVERT: C 774 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: C 803 SER cc_start: 0.8710 (t) cc_final: 0.8456 (p) REVERT: C 804 GLN cc_start: 0.8263 (mt0) cc_final: 0.7965 (mt0) REVERT: C 868 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7266 (tp30) REVERT: C 870 ILE cc_start: 0.8373 (pt) cc_final: 0.8161 (mt) REVERT: C 886 TRP cc_start: 0.8259 (OUTLIER) cc_final: 0.7750 (p90) REVERT: C 900 MET cc_start: 0.8228 (mtm) cc_final: 0.7970 (mtm) REVERT: C 949 GLN cc_start: 0.8211 (tp40) cc_final: 0.7760 (tp40) REVERT: C 973 ILE cc_start: 0.8979 (mt) cc_final: 0.8768 (mm) REVERT: C 994 ASP cc_start: 0.8040 (t70) cc_final: 0.7679 (t0) REVERT: C 1029 MET cc_start: 0.8377 (tpp) cc_final: 0.8163 (tpp) REVERT: C 1073 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7591 (mmmm) REVERT: C 1107 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7024 (mtt90) REVERT: C 1139 ASP cc_start: 0.8290 (t0) cc_final: 0.8032 (t0) REVERT: B 102 ARG cc_start: 0.7605 (mtt180) cc_final: 0.7223 (mmt-90) REVERT: B 132 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7649 (mp0) REVERT: B 206 LYS cc_start: 0.8508 (tptm) cc_final: 0.8033 (tptp) REVERT: B 294 ASP cc_start: 0.8135 (p0) cc_final: 0.7843 (p0) REVERT: B 296 LEU cc_start: 0.8336 (tp) cc_final: 0.8045 (tp) REVERT: B 313 TYR cc_start: 0.8029 (m-10) cc_final: 0.7692 (m-80) REVERT: B 324 GLU cc_start: 0.8031 (pm20) cc_final: 0.7796 (pm20) REVERT: B 392 PHE cc_start: 0.6208 (m-80) cc_final: 0.5455 (m-10) REVERT: B 394 ASN cc_start: 0.8319 (p0) cc_final: 0.7977 (p0) REVERT: B 430 THR cc_start: 0.8315 (m) cc_final: 0.8110 (p) REVERT: B 448 ASN cc_start: 0.8193 (t0) cc_final: 0.6249 (p0) REVERT: B 513 LEU cc_start: 0.8275 (mt) cc_final: 0.7970 (mp) REVERT: B 516 GLU cc_start: 0.6806 (tm-30) cc_final: 0.6546 (tm-30) REVERT: B 524 VAL cc_start: 0.8792 (t) cc_final: 0.8556 (p) REVERT: B 532 ASN cc_start: 0.8321 (t0) cc_final: 0.8025 (t0) REVERT: B 576 VAL cc_start: 0.8953 (p) cc_final: 0.8559 (t) REVERT: B 580 GLN cc_start: 0.7276 (mm110) cc_final: 0.6914 (mm110) REVERT: B 599 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8067 (p) REVERT: B 619 GLU cc_start: 0.7258 (mt-10) cc_final: 0.7010 (mt-10) REVERT: B 764 ASN cc_start: 0.8308 (m110) cc_final: 0.8024 (m110) REVERT: B 788 ILE cc_start: 0.8579 (mm) cc_final: 0.8341 (mm) REVERT: B 790 LYS cc_start: 0.8463 (ptmt) cc_final: 0.8145 (ptmt) REVERT: B 811 LYS cc_start: 0.7437 (mttt) cc_final: 0.7175 (mttt) REVERT: B 820 ASP cc_start: 0.7387 (t0) cc_final: 0.6875 (t0) REVERT: B 904 TYR cc_start: 0.7676 (m-10) cc_final: 0.7240 (m-10) REVERT: B 929 SER cc_start: 0.8372 (t) cc_final: 0.8031 (p) REVERT: B 950 ASP cc_start: 0.7720 (t0) cc_final: 0.7031 (t0) REVERT: B 954 GLN cc_start: 0.7953 (mt0) cc_final: 0.7409 (mt0) REVERT: B 964 LYS cc_start: 0.8468 (ttmm) cc_final: 0.8119 (mtmm) REVERT: B 968 SER cc_start: 0.8800 (m) cc_final: 0.8461 (t) REVERT: B 982 SER cc_start: 0.8397 (m) cc_final: 0.8154 (p) REVERT: B 1003 SER cc_start: 0.8454 (m) cc_final: 0.8100 (t) REVERT: B 1073 LYS cc_start: 0.8536 (mttm) cc_final: 0.8324 (mtmt) REVERT: B 1086 LYS cc_start: 0.8538 (mppt) cc_final: 0.8009 (mtmm) REVERT: B 1101 HIS cc_start: 0.8452 (m90) cc_final: 0.8223 (m90) REVERT: B 1117 THR cc_start: 0.8286 (m) cc_final: 0.7953 (t) REVERT: B 1136 THR cc_start: 0.8614 (t) cc_final: 0.8324 (p) REVERT: A 28 TYR cc_start: 0.8154 (m-80) cc_final: 0.7775 (m-80) REVERT: A 120 VAL cc_start: 0.7919 (t) cc_final: 0.7596 (m) REVERT: A 191 GLU cc_start: 0.7360 (mp0) cc_final: 0.6963 (mt-10) REVERT: A 239 GLN cc_start: 0.8155 (tt0) cc_final: 0.7837 (tt0) REVERT: A 535 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8621 (mttm) REVERT: A 544 ASN cc_start: 0.7866 (t0) cc_final: 0.7568 (t0) REVERT: A 549 THR cc_start: 0.7975 (m) cc_final: 0.7679 (p) REVERT: A 557 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7745 (mttt) REVERT: A 558 LYS cc_start: 0.8438 (mmtm) cc_final: 0.8027 (mmmt) REVERT: A 586 ASP cc_start: 0.7640 (t0) cc_final: 0.7362 (t0) REVERT: A 605 SER cc_start: 0.8678 (t) cc_final: 0.8320 (m) REVERT: A 661 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7347 (tt0) REVERT: A 704 SER cc_start: 0.8558 (t) cc_final: 0.8208 (p) REVERT: A 719 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8232 (p) REVERT: A 758 SER cc_start: 0.8712 (m) cc_final: 0.8309 (p) REVERT: A 796 ASP cc_start: 0.6924 (p0) cc_final: 0.6442 (p0) REVERT: A 825 LYS cc_start: 0.8424 (mmmt) cc_final: 0.8054 (mmmm) REVERT: A 878 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8221 (mt) REVERT: A 900 MET cc_start: 0.8210 (mtp) cc_final: 0.7701 (mtp) REVERT: A 902 MET cc_start: 0.8274 (mmm) cc_final: 0.8041 (mmt) REVERT: A 921 LYS cc_start: 0.8176 (mmtp) cc_final: 0.7955 (mmtp) REVERT: A 933 LYS cc_start: 0.8284 (mtmm) cc_final: 0.8027 (mttp) REVERT: A 950 ASP cc_start: 0.7475 (t0) cc_final: 0.7062 (t0) REVERT: A 963 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8522 (p) REVERT: A 1019 ARG cc_start: 0.7730 (ttm110) cc_final: 0.7295 (ttp80) REVERT: A 1038 LYS cc_start: 0.8647 (mttt) cc_final: 0.8329 (mmtm) REVERT: A 1045 LYS cc_start: 0.8442 (mttt) cc_final: 0.8148 (mttt) REVERT: A 1073 LYS cc_start: 0.8497 (mtpt) cc_final: 0.8216 (mtpp) REVERT: A 1084 ASP cc_start: 0.7865 (p0) cc_final: 0.7485 (p0) REVERT: A 1101 HIS cc_start: 0.8202 (m90) cc_final: 0.7929 (m90) REVERT: D 26 LYS cc_start: 0.8318 (mtmm) cc_final: 0.8074 (mmtp) REVERT: D 41 TYR cc_start: 0.8111 (t80) cc_final: 0.7209 (t80) REVERT: D 42 GLN cc_start: 0.8101 (tp40) cc_final: 0.7298 (tp40) REVERT: D 61 ASN cc_start: 0.8762 (t0) cc_final: 0.8497 (t0) REVERT: D 74 LYS cc_start: 0.8627 (tppp) cc_final: 0.8123 (tppp) REVERT: D 76 GLN cc_start: 0.8269 (mm-40) cc_final: 0.8002 (mm110) REVERT: D 187 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7912 (ptpp) REVERT: D 309 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8585 (mmtt) REVERT: D 340 GLN cc_start: 0.1688 (tm-30) cc_final: 0.1438 (tm-30) REVERT: D 360 MET cc_start: 0.3761 (tmm) cc_final: 0.3114 (tmm) REVERT: D 369 PHE cc_start: 0.8894 (t80) cc_final: 0.8551 (t80) REVERT: D 383 MET cc_start: 0.6789 (mpp) cc_final: 0.6459 (mpp) REVERT: D 408 MET cc_start: 0.7673 (mpm) cc_final: 0.7466 (mpm) REVERT: D 410 LEU cc_start: 0.8586 (mt) cc_final: 0.8100 (pp) REVERT: D 454 TYR cc_start: 0.5852 (t80) cc_final: 0.5310 (t80) REVERT: D 479 GLU cc_start: 0.7941 (pt0) cc_final: 0.7481 (pp20) REVERT: D 487 VAL cc_start: 0.6017 (p) cc_final: 0.5677 (t) REVERT: D 521 TYR cc_start: 0.5256 (m-10) cc_final: 0.4695 (m-80) REVERT: D 557 MET cc_start: 0.7472 (tmm) cc_final: 0.7107 (tmm) REVERT: D 560 LEU cc_start: 0.7539 (mt) cc_final: 0.7317 (mp) REVERT: D 570 LEU cc_start: 0.1809 (OUTLIER) cc_final: -0.0185 (mm) outliers start: 127 outliers final: 87 residues processed: 746 average time/residue: 0.4235 time to fit residues: 504.2986 Evaluate side-chains 728 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 629 time to evaluate : 3.121 ------------------------------------------------------------------------------- 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 131 CYS 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 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 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 922 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 127 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 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 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 646 ARG 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 966 LEU 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 127 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 304 LYS 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 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 661 GLU 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 823 PHE 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 963 VAL Chi-restraints excluded: chain D residue 58 ASN 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 116 LEU 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 242 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 350 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 315 optimal weight: 0.9990 chunk 164 optimal weight: 0.5980 chunk 244 optimal weight: 8.9990 chunk 299 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 777 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 613 GLN B 644 GLN B 777 ASN B1119 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 340 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.184946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.137725 restraints weight = 50314.510| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.76 r_work: 0.3505 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31780 Z= 0.177 Angle : 0.611 12.522 43372 Z= 0.300 Chirality : 0.046 0.582 5026 Planarity : 0.004 0.044 5477 Dihedral : 6.313 85.817 5600 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.99 % Allowed : 13.44 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 3761 helix: 1.58 (0.17), residues: 1039 sheet: -0.37 (0.19), residues: 661 loop : -1.56 (0.12), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 271 HIS 0.006 0.001 HIS A1064 PHE 0.021 0.001 PHE C 192 TYR 0.016 0.001 TYR C 265 ARG 0.010 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 50) link_NAG-ASN : angle 2.46369 ( 150) link_BETA1-4 : bond 0.00296 ( 21) link_BETA1-4 : angle 1.08958 ( 63) hydrogen bonds : bond 0.03879 ( 1172) hydrogen bonds : angle 5.18242 ( 3312) SS BOND : bond 0.00451 ( 45) SS BOND : angle 2.30686 ( 90) covalent geometry : bond 0.00399 (31664) covalent geometry : angle 0.58463 (43069) *********************** 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 784 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 651 time to evaluate : 3.244 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 THR cc_start: 0.7978 (t) cc_final: 0.6650 (p) REVERT: C 42 VAL cc_start: 0.8485 (p) cc_final: 0.8105 (m) REVERT: C 64 TRP cc_start: 0.8146 (t60) cc_final: 0.7862 (t60) REVERT: C 99 ASN cc_start: 0.7869 (t0) cc_final: 0.7452 (t0) REVERT: C 228 ASP cc_start: 0.7261 (t0) cc_final: 0.6560 (t0) REVERT: C 267 VAL cc_start: 0.8456 (t) cc_final: 0.8135 (p) REVERT: C 276 LEU cc_start: 0.8714 (tt) cc_final: 0.8469 (tp) REVERT: C 284 THR cc_start: 0.8587 (m) cc_final: 0.8216 (t) REVERT: C 289 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8496 (m) REVERT: C 305 SER cc_start: 0.8902 (t) cc_final: 0.8526 (p) REVERT: C 309 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7114 (mm-30) REVERT: C 313 TYR cc_start: 0.8376 (m-80) cc_final: 0.8141 (m-80) REVERT: C 353 TRP cc_start: 0.7887 (p-90) cc_final: 0.7352 (p-90) REVERT: C 362 VAL cc_start: 0.8038 (t) cc_final: 0.7776 (m) REVERT: C 378 LYS cc_start: 0.8025 (mttt) cc_final: 0.7596 (mttt) REVERT: C 424 LYS cc_start: 0.7296 (tttt) cc_final: 0.6573 (ttpp) REVERT: C 495 TYR cc_start: 0.7086 (m-80) cc_final: 0.6251 (m-80) REVERT: C 619 GLU cc_start: 0.7887 (pm20) cc_final: 0.7552 (pm20) REVERT: C 646 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7589 (ttm170) REVERT: C 704 SER cc_start: 0.8468 (m) cc_final: 0.7912 (t) REVERT: C 773 GLU cc_start: 0.7476 (tt0) cc_final: 0.7168 (tt0) REVERT: C 774 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7773 (mp-120) REVERT: C 803 SER cc_start: 0.8728 (t) cc_final: 0.8460 (p) REVERT: C 804 GLN cc_start: 0.8248 (mt0) cc_final: 0.7908 (mt0) REVERT: C 868 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7325 (tp30) REVERT: C 870 ILE cc_start: 0.8369 (pt) cc_final: 0.8154 (mt) REVERT: C 886 TRP cc_start: 0.8275 (OUTLIER) cc_final: 0.7758 (p90) REVERT: C 900 MET cc_start: 0.8240 (mtm) cc_final: 0.8001 (mtm) REVERT: C 949 GLN cc_start: 0.8233 (tp40) cc_final: 0.7802 (tp40) REVERT: C 994 ASP cc_start: 0.8049 (t70) cc_final: 0.7689 (t0) REVERT: C 1010 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7286 (mm-40) REVERT: C 1017 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: C 1073 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7590 (mmmm) REVERT: C 1107 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7682 (mtt90) REVERT: C 1139 ASP cc_start: 0.8271 (t0) cc_final: 0.8068 (t0) REVERT: B 132 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7489 (mp0) REVERT: B 195 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7673 (ptpp) REVERT: B 294 ASP cc_start: 0.8172 (p0) cc_final: 0.7873 (p0) REVERT: B 296 LEU cc_start: 0.8337 (tp) cc_final: 0.8092 (tp) REVERT: B 313 TYR cc_start: 0.8003 (m-10) cc_final: 0.7605 (m-80) REVERT: B 360 ASN cc_start: 0.8103 (m110) cc_final: 0.7859 (m110) REVERT: B 392 PHE cc_start: 0.6284 (m-80) cc_final: 0.5465 (m-10) REVERT: B 394 ASN cc_start: 0.8332 (p0) cc_final: 0.8013 (p0) REVERT: B 448 ASN cc_start: 0.8192 (t0) cc_final: 0.6070 (p0) REVERT: B 523 THR cc_start: 0.7764 (OUTLIER) cc_final: 0.7499 (m) REVERT: B 524 VAL cc_start: 0.8757 (t) cc_final: 0.8520 (p) REVERT: B 532 ASN cc_start: 0.8286 (t0) cc_final: 0.7978 (t0) REVERT: B 576 VAL cc_start: 0.8861 (p) cc_final: 0.8494 (t) REVERT: B 580 GLN cc_start: 0.7202 (mm110) cc_final: 0.6938 (mm110) REVERT: B 599 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8073 (p) REVERT: B 619 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6995 (mt-10) REVERT: B 673 SER cc_start: 0.8886 (t) cc_final: 0.8442 (m) REVERT: B 764 ASN cc_start: 0.8352 (m110) cc_final: 0.8039 (m-40) REVERT: B 788 ILE cc_start: 0.8577 (mm) cc_final: 0.8344 (mm) REVERT: B 790 LYS cc_start: 0.8435 (ptmt) cc_final: 0.8148 (ptmt) REVERT: B 811 LYS cc_start: 0.7562 (mttt) cc_final: 0.7280 (mttt) REVERT: B 820 ASP cc_start: 0.7456 (t0) cc_final: 0.6903 (t0) REVERT: B 929 SER cc_start: 0.8403 (t) cc_final: 0.8073 (p) REVERT: B 950 ASP cc_start: 0.7766 (t0) cc_final: 0.6981 (t0) REVERT: B 954 GLN cc_start: 0.7990 (mt0) cc_final: 0.7341 (mt0) REVERT: B 968 SER cc_start: 0.8801 (m) cc_final: 0.8452 (t) REVERT: B 982 SER cc_start: 0.8387 (m) cc_final: 0.8184 (p) REVERT: B 1003 SER cc_start: 0.8376 (m) cc_final: 0.8099 (t) REVERT: B 1073 LYS cc_start: 0.8532 (mttm) cc_final: 0.8322 (mtmt) REVERT: B 1117 THR cc_start: 0.8297 (m) cc_final: 0.7968 (t) REVERT: B 1136 THR cc_start: 0.8637 (t) cc_final: 0.8355 (p) REVERT: A 28 TYR cc_start: 0.8189 (m-80) cc_final: 0.7806 (m-80) REVERT: A 117 LEU cc_start: 0.8053 (tp) cc_final: 0.7453 (mp) REVERT: A 120 VAL cc_start: 0.8015 (t) cc_final: 0.7675 (m) REVERT: A 191 GLU cc_start: 0.7358 (mp0) cc_final: 0.6948 (mt-10) REVERT: A 239 GLN cc_start: 0.8167 (tt0) cc_final: 0.7860 (tt0) REVERT: A 535 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8579 (mttm) REVERT: A 544 ASN cc_start: 0.7897 (t0) cc_final: 0.7693 (t0) REVERT: A 549 THR cc_start: 0.7951 (m) cc_final: 0.7663 (p) REVERT: A 557 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7730 (mttt) REVERT: A 558 LYS cc_start: 0.8466 (mmtm) cc_final: 0.7993 (mmmt) REVERT: A 605 SER cc_start: 0.8705 (t) cc_final: 0.8347 (m) REVERT: A 661 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: A 719 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8247 (p) REVERT: A 758 SER cc_start: 0.8709 (m) cc_final: 0.8283 (p) REVERT: A 790 LYS cc_start: 0.8329 (ttpp) cc_final: 0.8118 (ttmm) REVERT: A 796 ASP cc_start: 0.6971 (p0) cc_final: 0.6477 (p0) REVERT: A 825 LYS cc_start: 0.8505 (mmmt) cc_final: 0.8121 (mmmm) REVERT: A 866 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8252 (t) REVERT: A 878 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8225 (mt) REVERT: A 900 MET cc_start: 0.8343 (mtp) cc_final: 0.7595 (mtp) REVERT: A 902 MET cc_start: 0.8296 (mmm) cc_final: 0.8057 (tpt) REVERT: A 921 LYS cc_start: 0.8209 (mmtp) cc_final: 0.7968 (mmtp) REVERT: A 933 LYS cc_start: 0.8320 (mtmm) cc_final: 0.8072 (mttp) REVERT: A 950 ASP cc_start: 0.7514 (t0) cc_final: 0.7068 (t0) REVERT: A 963 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8535 (p) REVERT: A 987 VAL cc_start: 0.8436 (p) cc_final: 0.8198 (t) REVERT: A 1019 ARG cc_start: 0.7727 (ttm110) cc_final: 0.7279 (ttp80) REVERT: A 1038 LYS cc_start: 0.8690 (mttt) cc_final: 0.8351 (mmtm) REVERT: A 1045 LYS cc_start: 0.8369 (mttt) cc_final: 0.8062 (mttt) REVERT: A 1073 LYS cc_start: 0.8494 (mtpt) cc_final: 0.8215 (mtpp) REVERT: A 1084 ASP cc_start: 0.7894 (p0) cc_final: 0.7322 (p0) REVERT: A 1101 HIS cc_start: 0.8266 (m90) cc_final: 0.8020 (m90) REVERT: D 42 GLN cc_start: 0.8076 (tp40) cc_final: 0.7290 (tp40) REVERT: D 74 LYS cc_start: 0.8592 (tppp) cc_final: 0.8088 (tppp) REVERT: D 187 LYS cc_start: 0.8325 (mmtt) cc_final: 0.7955 (ptpp) REVERT: D 309 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8570 (mmtt) REVERT: D 312 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8521 (mm-30) REVERT: D 314 PHE cc_start: 0.9027 (t80) cc_final: 0.8565 (m-10) REVERT: D 340 GLN cc_start: 0.1834 (tm-30) cc_final: 0.1538 (tm-30) REVERT: D 360 MET cc_start: 0.3479 (tmm) cc_final: 0.2770 (tmm) REVERT: D 369 PHE cc_start: 0.8902 (t80) cc_final: 0.8613 (t80) REVERT: D 383 MET cc_start: 0.7080 (mpp) cc_final: 0.6508 (mpp) REVERT: D 410 LEU cc_start: 0.8628 (mt) cc_final: 0.8179 (pp) REVERT: D 454 TYR cc_start: 0.5864 (t80) cc_final: 0.5359 (t80) REVERT: D 479 GLU cc_start: 0.7917 (pt0) cc_final: 0.7462 (pp20) REVERT: D 487 VAL cc_start: 0.6065 (p) cc_final: 0.5659 (t) REVERT: D 497 TYR cc_start: 0.6801 (m-80) cc_final: 0.6473 (m-80) REVERT: D 521 TYR cc_start: 0.5284 (m-10) cc_final: 0.4872 (m-80) REVERT: D 557 MET cc_start: 0.7424 (tmm) cc_final: 0.7168 (tmm) REVERT: D 560 LEU cc_start: 0.7537 (mt) cc_final: 0.7302 (mp) outliers start: 133 outliers final: 93 residues processed: 743 average time/residue: 0.4391 time to fit residues: 523.3048 Evaluate side-chains 729 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 622 time to evaluate : 3.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE 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 289 VAL 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 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 821 LEU 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 981 LEU Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 127 VAL 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 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 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS 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 966 LEU 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 118 LEU Chi-restraints excluded: chain A residue 127 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 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 599 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 662 CYS 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 896 ILE 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 116 LEU Chi-restraints excluded: chain D residue 118 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 474 MET 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 203 optimal weight: 0.7980 chunk 212 optimal weight: 3.9990 chunk 316 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 336 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 chunk 189 optimal weight: 0.6980 chunk 299 optimal weight: 0.9980 chunk 324 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 777 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B1119 ASN A 218 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 340 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.184113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136590 restraints weight = 50516.824| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.80 r_work: 0.3491 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31780 Z= 0.204 Angle : 0.636 11.941 43372 Z= 0.314 Chirality : 0.047 0.505 5026 Planarity : 0.004 0.055 5477 Dihedral : 6.146 76.684 5600 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.81 % Allowed : 14.34 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 3761 helix: 1.50 (0.17), residues: 1046 sheet: -0.34 (0.19), residues: 677 loop : -1.52 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D 271 HIS 0.009 0.001 HIS D 373 PHE 0.032 0.002 PHE B 201 TYR 0.019 0.001 TYR A1067 ARG 0.011 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 50) link_NAG-ASN : angle 2.42271 ( 150) link_BETA1-4 : bond 0.00294 ( 21) link_BETA1-4 : angle 1.13650 ( 63) hydrogen bonds : bond 0.04085 ( 1172) hydrogen bonds : angle 5.20648 ( 3312) SS BOND : bond 0.00393 ( 45) SS BOND : angle 2.54765 ( 90) covalent geometry : bond 0.00457 (31664) covalent geometry : angle 0.60977 (43069) *********************** 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 771 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 644 time to evaluate : 3.321 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: symmetry clash REVERT: C 29 THR cc_start: 0.8171 (t) cc_final: 0.6767 (p) REVERT: C 42 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8256 (m) REVERT: C 99 ASN cc_start: 0.7957 (t0) cc_final: 0.7575 (t0) REVERT: C 170 TYR cc_start: 0.8434 (t80) cc_final: 0.8207 (t80) REVERT: C 267 VAL cc_start: 0.8571 (t) cc_final: 0.8282 (p) REVERT: C 276 LEU cc_start: 0.8769 (tt) cc_final: 0.8516 (tp) REVERT: C 284 THR cc_start: 0.8675 (m) cc_final: 0.8284 (t) REVERT: C 289 VAL cc_start: 0.8927 (OUTLIER) cc_final: 0.8633 (m) REVERT: C 305 SER cc_start: 0.8943 (t) cc_final: 0.8602 (p) REVERT: C 309 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7467 (mm-30) REVERT: C 313 TYR cc_start: 0.8513 (m-80) cc_final: 0.8200 (m-80) REVERT: C 353 TRP cc_start: 0.8005 (p-90) cc_final: 0.7736 (p-90) REVERT: C 356 LYS cc_start: 0.8720 (ptpt) cc_final: 0.8505 (pttt) REVERT: C 362 VAL cc_start: 0.8238 (t) cc_final: 0.8005 (m) REVERT: C 378 LYS cc_start: 0.8156 (mttt) cc_final: 0.7701 (mttt) REVERT: C 398 ASP cc_start: 0.7744 (p0) cc_final: 0.7040 (p0) REVERT: C 414 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7429 (mm-40) REVERT: C 424 LYS cc_start: 0.7455 (tttt) cc_final: 0.6723 (ttpp) REVERT: C 430 THR cc_start: 0.8500 (t) cc_final: 0.8084 (p) REVERT: C 495 TYR cc_start: 0.7341 (m-80) cc_final: 0.6435 (m-80) REVERT: C 580 GLN cc_start: 0.8122 (mt0) cc_final: 0.7546 (mt0) REVERT: C 619 GLU cc_start: 0.8109 (pm20) cc_final: 0.7841 (pm20) REVERT: C 646 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7880 (ttm170) REVERT: C 704 SER cc_start: 0.8605 (m) cc_final: 0.8056 (t) REVERT: C 773 GLU cc_start: 0.7813 (tt0) cc_final: 0.7495 (tt0) REVERT: C 774 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7942 (mp-120) REVERT: C 803 SER cc_start: 0.8846 (t) cc_final: 0.8620 (p) REVERT: C 804 GLN cc_start: 0.8489 (mt0) cc_final: 0.8250 (mt0) REVERT: C 868 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7547 (tp30) REVERT: C 870 ILE cc_start: 0.8373 (pt) cc_final: 0.8161 (mt) REVERT: C 886 TRP cc_start: 0.8361 (OUTLIER) cc_final: 0.7775 (p90) REVERT: C 900 MET cc_start: 0.8465 (mtm) cc_final: 0.8231 (mtm) REVERT: C 949 GLN cc_start: 0.8455 (tp40) cc_final: 0.7945 (tp40) REVERT: C 1010 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7606 (mm-40) REVERT: C 1017 GLU cc_start: 0.8665 (tt0) cc_final: 0.8135 (tp30) REVERT: C 1073 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7752 (mmmm) REVERT: C 1107 ARG cc_start: 0.8224 (mtt180) cc_final: 0.7960 (mtt90) REVERT: C 1139 ASP cc_start: 0.8426 (t0) cc_final: 0.8057 (t70) REVERT: B 42 VAL cc_start: 0.8271 (t) cc_final: 0.7928 (m) REVERT: B 90 VAL cc_start: 0.8698 (p) cc_final: 0.8391 (t) REVERT: B 132 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7657 (mp0) REVERT: B 195 LYS cc_start: 0.8203 (mtmt) cc_final: 0.7911 (ptpp) REVERT: B 206 LYS cc_start: 0.8729 (tptm) cc_final: 0.8380 (tptp) REVERT: B 294 ASP cc_start: 0.8441 (p0) cc_final: 0.8163 (p0) REVERT: B 296 LEU cc_start: 0.8499 (tp) cc_final: 0.8222 (tp) REVERT: B 360 ASN cc_start: 0.8237 (m110) cc_final: 0.7987 (m110) REVERT: B 394 ASN cc_start: 0.8479 (p0) cc_final: 0.8134 (p0) REVERT: B 448 ASN cc_start: 0.8393 (t0) cc_final: 0.6174 (p0) REVERT: B 523 THR cc_start: 0.7892 (OUTLIER) cc_final: 0.7616 (m) REVERT: B 524 VAL cc_start: 0.8681 (t) cc_final: 0.8464 (p) REVERT: B 532 ASN cc_start: 0.8563 (t0) cc_final: 0.8271 (t0) REVERT: B 576 VAL cc_start: 0.8859 (p) cc_final: 0.8536 (t) REVERT: B 673 SER cc_start: 0.9028 (t) cc_final: 0.8558 (m) REVERT: B 764 ASN cc_start: 0.8516 (m110) cc_final: 0.8187 (m-40) REVERT: B 788 ILE cc_start: 0.8630 (mm) cc_final: 0.8367 (mm) REVERT: B 790 LYS cc_start: 0.8541 (ptmt) cc_final: 0.8296 (ptmt) REVERT: B 820 ASP cc_start: 0.7795 (t0) cc_final: 0.7474 (t0) REVERT: B 929 SER cc_start: 0.8605 (t) cc_final: 0.8269 (p) REVERT: B 950 ASP cc_start: 0.8095 (t0) cc_final: 0.7343 (t0) REVERT: B 954 GLN cc_start: 0.8242 (mt0) cc_final: 0.7670 (mt0) REVERT: B 1003 SER cc_start: 0.8571 (m) cc_final: 0.8302 (t) REVERT: B 1073 LYS cc_start: 0.8668 (mttm) cc_final: 0.8464 (mtmt) REVERT: B 1117 THR cc_start: 0.8415 (m) cc_final: 0.8074 (t) REVERT: A 28 TYR cc_start: 0.8377 (m-80) cc_final: 0.7925 (m-80) REVERT: A 41 LYS cc_start: 0.8090 (mttt) cc_final: 0.7621 (mttm) REVERT: A 120 VAL cc_start: 0.8107 (t) cc_final: 0.7805 (m) REVERT: A 191 GLU cc_start: 0.7729 (mp0) cc_final: 0.7222 (mt-10) REVERT: A 239 GLN cc_start: 0.8432 (tt0) cc_final: 0.8108 (tt0) REVERT: A 535 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8662 (mttm) REVERT: A 544 ASN cc_start: 0.8168 (t0) cc_final: 0.7958 (t0) REVERT: A 546 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7110 (pt) REVERT: A 549 THR cc_start: 0.7971 (m) cc_final: 0.7669 (p) REVERT: A 557 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7840 (mttt) REVERT: A 558 LYS cc_start: 0.8604 (mmtm) cc_final: 0.8093 (mmmt) REVERT: A 586 ASP cc_start: 0.7998 (t0) cc_final: 0.7640 (t0) REVERT: A 605 SER cc_start: 0.8808 (t) cc_final: 0.8466 (m) REVERT: A 661 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: A 697 MET cc_start: 0.8672 (ptm) cc_final: 0.8458 (ptm) REVERT: A 719 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8342 (p) REVERT: A 758 SER cc_start: 0.8652 (m) cc_final: 0.8164 (p) REVERT: A 825 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8125 (mmmm) REVERT: A 866 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8331 (t) REVERT: A 878 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8306 (mt) REVERT: A 900 MET cc_start: 0.8620 (mtp) cc_final: 0.8122 (mtp) REVERT: A 902 MET cc_start: 0.8449 (mmm) cc_final: 0.8239 (mmt) REVERT: A 921 LYS cc_start: 0.8372 (mmtp) cc_final: 0.8095 (mmtp) REVERT: A 933 LYS cc_start: 0.8437 (mtmm) cc_final: 0.8177 (mttp) REVERT: A 950 ASP cc_start: 0.7850 (t0) cc_final: 0.7431 (t0) REVERT: A 963 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8657 (p) REVERT: A 985 ASP cc_start: 0.7894 (p0) cc_final: 0.7631 (p0) REVERT: A 1038 LYS cc_start: 0.8804 (mttt) cc_final: 0.8565 (mmtm) REVERT: A 1045 LYS cc_start: 0.8494 (mttt) cc_final: 0.8163 (mttt) REVERT: A 1073 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8337 (mtpp) REVERT: D 42 GLN cc_start: 0.8179 (tp40) cc_final: 0.7401 (tp40) REVERT: D 74 LYS cc_start: 0.8629 (tppp) cc_final: 0.8124 (tppp) REVERT: D 187 LYS cc_start: 0.8273 (mmtt) cc_final: 0.7938 (ptpp) REVERT: D 309 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8569 (mmtt) REVERT: D 314 PHE cc_start: 0.8974 (t80) cc_final: 0.8550 (m-10) REVERT: D 340 GLN cc_start: 0.2263 (tm-30) cc_final: 0.1894 (tm-30) REVERT: D 360 MET cc_start: 0.3585 (tmm) cc_final: 0.3044 (tmm) REVERT: D 383 MET cc_start: 0.7249 (mpp) cc_final: 0.6430 (mpp) REVERT: D 454 TYR cc_start: 0.5864 (t80) cc_final: 0.5356 (t80) REVERT: D 479 GLU cc_start: 0.7979 (pt0) cc_final: 0.7551 (pp20) REVERT: D 481 LYS cc_start: 0.1570 (OUTLIER) cc_final: 0.1152 (pttp) REVERT: D 487 VAL cc_start: 0.6308 (p) cc_final: 0.6094 (t) REVERT: D 497 TYR cc_start: 0.6840 (m-80) cc_final: 0.6499 (m-80) REVERT: D 521 TYR cc_start: 0.5349 (m-10) cc_final: 0.5029 (m-80) REVERT: D 557 MET cc_start: 0.7460 (tmm) cc_final: 0.7153 (tmm) REVERT: D 560 LEU cc_start: 0.7624 (mt) cc_final: 0.7339 (mp) outliers start: 127 outliers final: 92 residues processed: 729 average time/residue: 0.4192 time to fit residues: 487.3311 Evaluate side-chains 729 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 622 time to evaluate : 3.159 ------------------------------------------------------------------------------- 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 129 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 226 LEU 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 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 935 GLN Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 223 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 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 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 547 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 649 CYS 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 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 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 118 LEU 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 557 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 CYS 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 661 GLU Chi-restraints excluded: chain A residue 662 CYS 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 58 ASN Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 474 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 266 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 337 optimal weight: 20.0000 chunk 313 optimal weight: 0.6980 chunk 306 optimal weight: 1.9990 chunk 372 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 289 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 777 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 340 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.184540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137093 restraints weight = 50496.604| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.78 r_work: 0.3497 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 31780 Z= 0.182 Angle : 0.636 12.824 43372 Z= 0.313 Chirality : 0.047 0.508 5026 Planarity : 0.004 0.051 5477 Dihedral : 5.935 76.258 5600 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.84 % Allowed : 14.94 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 3761 helix: 1.54 (0.17), residues: 1041 sheet: -0.26 (0.19), residues: 675 loop : -1.48 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 328 HIS 0.007 0.001 HIS D 374 PHE 0.026 0.002 PHE B 201 TYR 0.020 0.001 TYR A1067 ARG 0.011 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 50) link_NAG-ASN : angle 2.35295 ( 150) link_BETA1-4 : bond 0.00324 ( 21) link_BETA1-4 : angle 1.09352 ( 63) hydrogen bonds : bond 0.03912 ( 1172) hydrogen bonds : angle 5.16479 ( 3312) SS BOND : bond 0.00387 ( 45) SS BOND : angle 2.64730 ( 90) covalent geometry : bond 0.00408 (31664) covalent geometry : angle 0.60937 (43069) *********************** 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 760 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 632 time to evaluate : 3.225 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: symmetry clash REVERT: C 29 THR cc_start: 0.8148 (t) cc_final: 0.6790 (p) REVERT: C 42 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8169 (m) REVERT: C 99 ASN cc_start: 0.7974 (t0) cc_final: 0.7627 (t0) REVERT: C 170 TYR cc_start: 0.8426 (t80) cc_final: 0.8189 (t80) REVERT: C 237 ARG cc_start: 0.8136 (mtm110) cc_final: 0.7824 (mtm110) REVERT: C 267 VAL cc_start: 0.8523 (t) cc_final: 0.8260 (p) REVERT: C 276 LEU cc_start: 0.8789 (tt) cc_final: 0.8546 (tp) REVERT: C 284 THR cc_start: 0.8698 (m) cc_final: 0.8290 (t) REVERT: C 289 VAL cc_start: 0.8904 (OUTLIER) cc_final: 0.8611 (m) REVERT: C 305 SER cc_start: 0.8947 (t) cc_final: 0.8598 (p) REVERT: C 309 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7504 (mm-30) REVERT: C 313 TYR cc_start: 0.8500 (m-80) cc_final: 0.8273 (m-80) REVERT: C 353 TRP cc_start: 0.8014 (p-90) cc_final: 0.7791 (p-90) REVERT: C 356 LYS cc_start: 0.8797 (ptpt) cc_final: 0.8422 (pttt) REVERT: C 362 VAL cc_start: 0.8277 (t) cc_final: 0.8054 (m) REVERT: C 378 LYS cc_start: 0.8168 (mttt) cc_final: 0.7732 (mttt) REVERT: C 398 ASP cc_start: 0.7694 (p0) cc_final: 0.7034 (p0) REVERT: C 414 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7436 (mm-40) REVERT: C 424 LYS cc_start: 0.7498 (tttt) cc_final: 0.6769 (ttpp) REVERT: C 495 TYR cc_start: 0.7356 (m-80) cc_final: 0.6493 (m-80) REVERT: C 580 GLN cc_start: 0.8116 (mt0) cc_final: 0.7912 (mt0) REVERT: C 619 GLU cc_start: 0.8036 (pm20) cc_final: 0.7797 (pm20) REVERT: C 703 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7705 (m-40) REVERT: C 704 SER cc_start: 0.8711 (m) cc_final: 0.8156 (t) REVERT: C 747 THR cc_start: 0.8307 (m) cc_final: 0.7874 (p) REVERT: C 773 GLU cc_start: 0.7837 (tt0) cc_final: 0.7529 (tt0) REVERT: C 774 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7858 (mp-120) REVERT: C 803 SER cc_start: 0.8824 (t) cc_final: 0.8597 (p) REVERT: C 804 GLN cc_start: 0.8487 (mt0) cc_final: 0.8245 (mt0) REVERT: C 868 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7528 (tp30) REVERT: C 870 ILE cc_start: 0.8349 (pt) cc_final: 0.8134 (mt) REVERT: C 886 TRP cc_start: 0.8337 (OUTLIER) cc_final: 0.7838 (p90) REVERT: C 949 GLN cc_start: 0.8443 (tp40) cc_final: 0.7945 (tp40) REVERT: C 994 ASP cc_start: 0.8399 (t70) cc_final: 0.8080 (t0) REVERT: C 1010 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7606 (mm-40) REVERT: C 1017 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8121 (tp30) REVERT: C 1073 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7760 (mmmm) REVERT: C 1107 ARG cc_start: 0.8260 (mtt180) cc_final: 0.7993 (mtt90) REVERT: B 42 VAL cc_start: 0.8243 (t) cc_final: 0.7892 (m) REVERT: B 90 VAL cc_start: 0.8683 (p) cc_final: 0.8286 (m) REVERT: B 132 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7700 (mp0) REVERT: B 195 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7957 (ptpt) REVERT: B 206 LYS cc_start: 0.8706 (tptm) cc_final: 0.8308 (tptp) REVERT: B 294 ASP cc_start: 0.8432 (p0) cc_final: 0.8136 (p0) REVERT: B 296 LEU cc_start: 0.8495 (tp) cc_final: 0.8258 (tp) REVERT: B 360 ASN cc_start: 0.8177 (m110) cc_final: 0.7945 (m110) REVERT: B 392 PHE cc_start: 0.6492 (m-80) cc_final: 0.5638 (m-10) REVERT: B 394 ASN cc_start: 0.8420 (p0) cc_final: 0.8058 (p0) REVERT: B 448 ASN cc_start: 0.8363 (t0) cc_final: 0.5961 (p0) REVERT: B 523 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7594 (m) REVERT: B 532 ASN cc_start: 0.8552 (t0) cc_final: 0.8285 (t0) REVERT: B 576 VAL cc_start: 0.8860 (p) cc_final: 0.8539 (t) REVERT: B 599 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8168 (p) REVERT: B 673 SER cc_start: 0.9002 (t) cc_final: 0.8538 (m) REVERT: B 764 ASN cc_start: 0.8531 (m110) cc_final: 0.8198 (m-40) REVERT: B 790 LYS cc_start: 0.8578 (ptmt) cc_final: 0.8356 (ptmt) REVERT: B 820 ASP cc_start: 0.7822 (t0) cc_final: 0.7315 (t0) REVERT: B 824 ASN cc_start: 0.8057 (m-40) cc_final: 0.7856 (m-40) REVERT: B 900 MET cc_start: 0.8332 (mmm) cc_final: 0.8029 (mtp) REVERT: B 929 SER cc_start: 0.8594 (t) cc_final: 0.8262 (p) REVERT: B 950 ASP cc_start: 0.8128 (t0) cc_final: 0.7368 (t0) REVERT: B 954 GLN cc_start: 0.8249 (mt0) cc_final: 0.7692 (mt0) REVERT: B 964 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8358 (mtmm) REVERT: B 1003 SER cc_start: 0.8561 (m) cc_final: 0.8295 (t) REVERT: B 1117 THR cc_start: 0.8405 (m) cc_final: 0.8053 (t) REVERT: B 1136 THR cc_start: 0.8742 (t) cc_final: 0.8459 (p) REVERT: A 28 TYR cc_start: 0.8367 (m-80) cc_final: 0.7876 (m-80) REVERT: A 41 LYS cc_start: 0.7977 (mttt) cc_final: 0.7587 (mttm) REVERT: A 120 VAL cc_start: 0.8106 (t) cc_final: 0.7809 (m) REVERT: A 191 GLU cc_start: 0.7832 (mp0) cc_final: 0.7342 (mt-10) REVERT: A 239 GLN cc_start: 0.8411 (tt0) cc_final: 0.8086 (tt0) REVERT: A 535 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8678 (mttm) REVERT: A 544 ASN cc_start: 0.8173 (t0) cc_final: 0.7942 (t0) REVERT: A 546 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7090 (pt) REVERT: A 549 THR cc_start: 0.7949 (m) cc_final: 0.7645 (p) REVERT: A 557 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7929 (mttt) REVERT: A 558 LYS cc_start: 0.8599 (mmtm) cc_final: 0.8097 (mmmt) REVERT: A 586 ASP cc_start: 0.8004 (t0) cc_final: 0.7731 (t0) REVERT: A 605 SER cc_start: 0.8806 (t) cc_final: 0.8474 (m) REVERT: A 661 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: A 697 MET cc_start: 0.8655 (ptm) cc_final: 0.8451 (ptm) REVERT: A 719 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8346 (p) REVERT: A 725 GLU cc_start: 0.7972 (tp30) cc_final: 0.7607 (tt0) REVERT: A 758 SER cc_start: 0.8567 (m) cc_final: 0.8066 (p) REVERT: A 825 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8124 (mmmm) REVERT: A 866 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8311 (t) REVERT: A 878 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8297 (mt) REVERT: A 900 MET cc_start: 0.8569 (mtp) cc_final: 0.8228 (mtt) REVERT: A 921 LYS cc_start: 0.8349 (mmtp) cc_final: 0.8071 (mmtp) REVERT: A 933 LYS cc_start: 0.8497 (mtmm) cc_final: 0.8243 (mttp) REVERT: A 950 ASP cc_start: 0.7869 (t0) cc_final: 0.7483 (t0) REVERT: A 963 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8628 (p) REVERT: A 986 LYS cc_start: 0.8386 (mttm) cc_final: 0.7636 (mttm) REVERT: A 990 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7278 (mm-30) REVERT: A 1019 ARG cc_start: 0.8019 (ttm110) cc_final: 0.7667 (ttp80) REVERT: A 1073 LYS cc_start: 0.8582 (mtpt) cc_final: 0.8358 (mtpp) REVERT: D 74 LYS cc_start: 0.8602 (tppp) cc_final: 0.8087 (tppp) REVERT: D 309 LYS cc_start: 0.9035 (mmtt) cc_final: 0.8600 (mmtt) REVERT: D 314 PHE cc_start: 0.8917 (t80) cc_final: 0.8519 (m-10) REVERT: D 340 GLN cc_start: 0.2274 (tm-30) cc_final: 0.1830 (tm-30) REVERT: D 360 MET cc_start: 0.3615 (tmm) cc_final: 0.3217 (tmm) REVERT: D 380 GLN cc_start: 0.5025 (mm110) cc_final: 0.4700 (mm-40) REVERT: D 383 MET cc_start: 0.7239 (mpp) cc_final: 0.6261 (mpp) REVERT: D 454 TYR cc_start: 0.5850 (t80) cc_final: 0.5364 (t80) REVERT: D 479 GLU cc_start: 0.8022 (pt0) cc_final: 0.7629 (pp20) REVERT: D 481 LYS cc_start: 0.1687 (OUTLIER) cc_final: 0.1140 (ptmm) REVERT: D 487 VAL cc_start: 0.6294 (p) cc_final: 0.5949 (t) REVERT: D 497 TYR cc_start: 0.6811 (m-80) cc_final: 0.6454 (m-80) REVERT: D 521 TYR cc_start: 0.5502 (m-10) cc_final: 0.5098 (m-80) REVERT: D 557 MET cc_start: 0.7379 (tmm) cc_final: 0.7012 (tmm) REVERT: D 560 LEU cc_start: 0.7510 (mt) cc_final: 0.7175 (mp) outliers start: 128 outliers final: 92 residues processed: 718 average time/residue: 0.4264 time to fit residues: 485.7584 Evaluate side-chains 716 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 607 time to evaluate : 3.092 ------------------------------------------------------------------------------- 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 68 ILE Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER 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 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 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 935 GLN 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 991 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 127 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 346 ARG 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 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 547 THR Chi-restraints excluded: chain B residue 599 THR 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 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 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 599 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 662 CYS 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 960 ASN 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 A residue 1141 LEU 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 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 246 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 272 optimal weight: 0.7980 chunk 185 optimal weight: 0.0170 chunk 258 optimal weight: 0.0570 chunk 218 optimal weight: 0.6980 chunk 263 optimal weight: 0.3980 chunk 47 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 199 optimal weight: 0.7980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN C 777 ASN B 30 ASN B 777 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 76 GLN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 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 = 0.4282 r_free = 0.4282 target = 0.185670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138350 restraints weight = 50622.348| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.79 r_work: 0.3496 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31780 Z= 0.125 Angle : 0.611 10.674 43372 Z= 0.300 Chirality : 0.045 0.421 5026 Planarity : 0.004 0.055 5477 Dihedral : 5.722 78.030 5600 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.33 % Allowed : 16.11 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.13), residues: 3761 helix: 1.75 (0.17), residues: 1022 sheet: -0.30 (0.18), residues: 699 loop : -1.38 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 328 HIS 0.004 0.001 HIS D 374 PHE 0.025 0.001 PHE B 201 TYR 0.017 0.001 TYR A1067 ARG 0.012 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 50) link_NAG-ASN : angle 2.14598 ( 150) link_BETA1-4 : bond 0.00336 ( 21) link_BETA1-4 : angle 1.07302 ( 63) hydrogen bonds : bond 0.03587 ( 1172) hydrogen bonds : angle 5.05121 ( 3312) SS BOND : bond 0.00362 ( 45) SS BOND : angle 2.31247 ( 90) covalent geometry : bond 0.00281 (31664) covalent geometry : angle 0.58901 (43069) *********************** 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 740 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 629 time to evaluate : 3.085 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 THR cc_start: 0.7949 (t) cc_final: 0.6550 (p) REVERT: C 42 VAL cc_start: 0.8426 (p) cc_final: 0.8071 (m) REVERT: C 99 ASN cc_start: 0.7880 (t0) cc_final: 0.7541 (t0) REVERT: C 170 TYR cc_start: 0.8259 (t80) cc_final: 0.8026 (t80) REVERT: C 237 ARG cc_start: 0.7915 (mtm110) cc_final: 0.7685 (mtm110) REVERT: C 267 VAL cc_start: 0.8337 (t) cc_final: 0.8012 (p) REVERT: C 276 LEU cc_start: 0.8714 (tt) cc_final: 0.8477 (tp) REVERT: C 284 THR cc_start: 0.8594 (m) cc_final: 0.8190 (t) REVERT: C 289 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8520 (m) REVERT: C 305 SER cc_start: 0.8919 (t) cc_final: 0.8553 (p) REVERT: C 309 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7220 (mm-30) REVERT: C 313 TYR cc_start: 0.8344 (m-80) cc_final: 0.8114 (m-80) REVERT: C 353 TRP cc_start: 0.8047 (p-90) cc_final: 0.7762 (p-90) REVERT: C 356 LYS cc_start: 0.8599 (ptpt) cc_final: 0.8271 (pttt) REVERT: C 362 VAL cc_start: 0.8100 (t) cc_final: 0.7882 (m) REVERT: C 378 LYS cc_start: 0.7982 (mttt) cc_final: 0.7561 (mttt) REVERT: C 398 ASP cc_start: 0.7566 (p0) cc_final: 0.6797 (p0) REVERT: C 400 PHE cc_start: 0.7448 (p90) cc_final: 0.6957 (p90) REVERT: C 414 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7369 (mm-40) REVERT: C 424 LYS cc_start: 0.7357 (tttt) cc_final: 0.6612 (ttpp) REVERT: C 495 TYR cc_start: 0.7113 (m-80) cc_final: 0.6286 (m-80) REVERT: C 554 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7510 (pp20) REVERT: C 588 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8196 (p) REVERT: C 703 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7566 (m-40) REVERT: C 704 SER cc_start: 0.8503 (m) cc_final: 0.7955 (t) REVERT: C 747 THR cc_start: 0.8058 (m) cc_final: 0.7751 (p) REVERT: C 773 GLU cc_start: 0.7519 (tt0) cc_final: 0.7174 (tt0) REVERT: C 774 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7583 (mp-120) REVERT: C 803 SER cc_start: 0.8743 (t) cc_final: 0.8497 (p) REVERT: C 804 GLN cc_start: 0.8221 (mt0) cc_final: 0.7910 (mt0) REVERT: C 868 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7258 (tp30) REVERT: C 886 TRP cc_start: 0.8258 (OUTLIER) cc_final: 0.7835 (p90) REVERT: C 949 GLN cc_start: 0.8248 (tp40) cc_final: 0.7716 (tp40) REVERT: C 994 ASP cc_start: 0.8008 (t70) cc_final: 0.7633 (t0) REVERT: C 1010 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7368 (mm-40) REVERT: C 1017 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7971 (tp30) REVERT: C 1073 LYS cc_start: 0.7866 (mtpt) cc_final: 0.7645 (mmmm) REVERT: C 1119 ASN cc_start: 0.8345 (m-40) cc_final: 0.7884 (m110) REVERT: C 1139 ASP cc_start: 0.8275 (t0) cc_final: 0.7870 (t70) REVERT: B 79 PHE cc_start: 0.7190 (t80) cc_final: 0.6824 (t80) REVERT: B 90 VAL cc_start: 0.8509 (p) cc_final: 0.8102 (m) REVERT: B 195 LYS cc_start: 0.7945 (mtmt) cc_final: 0.7687 (ptpp) REVERT: B 294 ASP cc_start: 0.8132 (p0) cc_final: 0.7800 (p0) REVERT: B 296 LEU cc_start: 0.8346 (tp) cc_final: 0.8104 (tp) REVERT: B 360 ASN cc_start: 0.8012 (m110) cc_final: 0.7790 (m110) REVERT: B 394 ASN cc_start: 0.8361 (p0) cc_final: 0.8006 (p0) REVERT: B 532 ASN cc_start: 0.8273 (t0) cc_final: 0.7999 (t0) REVERT: B 537 LYS cc_start: 0.8457 (ttpp) cc_final: 0.8062 (tttp) REVERT: B 576 VAL cc_start: 0.8822 (p) cc_final: 0.8502 (t) REVERT: B 599 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8086 (p) REVERT: B 673 SER cc_start: 0.8900 (t) cc_final: 0.8408 (m) REVERT: B 764 ASN cc_start: 0.8331 (m110) cc_final: 0.7981 (m-40) REVERT: B 790 LYS cc_start: 0.8483 (ptmt) cc_final: 0.8245 (ptmt) REVERT: B 900 MET cc_start: 0.8081 (mmm) cc_final: 0.7788 (mtp) REVERT: B 929 SER cc_start: 0.8394 (t) cc_final: 0.8052 (p) REVERT: B 950 ASP cc_start: 0.7807 (t0) cc_final: 0.7062 (t0) REVERT: B 954 GLN cc_start: 0.8004 (mt0) cc_final: 0.7399 (mt0) REVERT: B 964 LYS cc_start: 0.8548 (ttmm) cc_final: 0.8203 (mtmm) REVERT: B 982 SER cc_start: 0.8449 (m) cc_final: 0.8201 (p) REVERT: B 1003 SER cc_start: 0.8400 (m) cc_final: 0.8126 (t) REVERT: B 1073 LYS cc_start: 0.8532 (mtmt) cc_final: 0.8275 (mtmm) REVERT: B 1117 THR cc_start: 0.8319 (m) cc_final: 0.7973 (t) REVERT: A 28 TYR cc_start: 0.8175 (m-80) cc_final: 0.7674 (m-80) REVERT: A 41 LYS cc_start: 0.7848 (mttt) cc_final: 0.7482 (mttm) REVERT: A 117 LEU cc_start: 0.7915 (tt) cc_final: 0.7218 (mp) REVERT: A 120 VAL cc_start: 0.7906 (t) cc_final: 0.7580 (m) REVERT: A 191 GLU cc_start: 0.7448 (mp0) cc_final: 0.6984 (mt-10) REVERT: A 239 GLN cc_start: 0.8198 (tt0) cc_final: 0.7876 (tt0) REVERT: A 535 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8580 (mttm) REVERT: A 544 ASN cc_start: 0.8016 (t0) cc_final: 0.7782 (t0) REVERT: A 549 THR cc_start: 0.7836 (m) cc_final: 0.7528 (p) REVERT: A 557 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7880 (mttt) REVERT: A 558 LYS cc_start: 0.8505 (mmtm) cc_final: 0.8022 (mmmt) REVERT: A 586 ASP cc_start: 0.7704 (t0) cc_final: 0.7457 (t0) REVERT: A 605 SER cc_start: 0.8738 (t) cc_final: 0.8399 (m) REVERT: A 697 MET cc_start: 0.8534 (ptm) cc_final: 0.8329 (ptm) REVERT: A 719 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8257 (p) REVERT: A 758 SER cc_start: 0.8381 (m) cc_final: 0.7892 (p) REVERT: A 825 LYS cc_start: 0.8424 (mmmt) cc_final: 0.8010 (mmmm) REVERT: A 866 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8157 (t) REVERT: A 878 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8141 (mt) REVERT: A 900 MET cc_start: 0.8328 (mtp) cc_final: 0.7977 (mtt) REVERT: A 921 LYS cc_start: 0.8186 (mmtp) cc_final: 0.7931 (mmtp) REVERT: A 933 LYS cc_start: 0.8308 (mtmm) cc_final: 0.8063 (mttp) REVERT: A 950 ASP cc_start: 0.7519 (t0) cc_final: 0.7116 (t0) REVERT: A 963 VAL cc_start: 0.8785 (OUTLIER) cc_final: 0.8550 (p) REVERT: A 986 LYS cc_start: 0.8150 (mttm) cc_final: 0.7789 (mttm) REVERT: A 990 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6744 (mp0) REVERT: A 1019 ARG cc_start: 0.7726 (ttm110) cc_final: 0.7348 (ttp80) REVERT: A 1045 LYS cc_start: 0.8392 (mttt) cc_final: 0.8118 (mttt) REVERT: A 1073 LYS cc_start: 0.8468 (mtpt) cc_final: 0.8216 (mtpp) REVERT: D 42 GLN cc_start: 0.8145 (tp40) cc_final: 0.7368 (tp40) REVERT: D 74 LYS cc_start: 0.8586 (tppp) cc_final: 0.8078 (tppp) REVERT: D 189 GLU cc_start: 0.5941 (tm-30) cc_final: 0.5705 (tm-30) REVERT: D 309 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8641 (mmtt) REVERT: D 312 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8386 (mm-30) REVERT: D 314 PHE cc_start: 0.8907 (t80) cc_final: 0.8493 (m-10) REVERT: D 315 PHE cc_start: 0.7528 (m-10) cc_final: 0.7128 (m-10) REVERT: D 340 GLN cc_start: 0.2128 (tm-30) cc_final: 0.1696 (tm-30) REVERT: D 360 MET cc_start: 0.2844 (tmm) cc_final: 0.2518 (tmm) REVERT: D 383 MET cc_start: 0.7179 (mpp) cc_final: 0.6817 (mpp) REVERT: D 454 TYR cc_start: 0.5861 (t80) cc_final: 0.5417 (t80) REVERT: D 479 GLU cc_start: 0.8024 (pt0) cc_final: 0.7667 (pp20) REVERT: D 481 LYS cc_start: 0.1849 (OUTLIER) cc_final: 0.1242 (ptmm) REVERT: D 487 VAL cc_start: 0.6208 (p) cc_final: 0.5867 (t) REVERT: D 497 TYR cc_start: 0.6826 (m-80) cc_final: 0.6518 (m-80) REVERT: D 521 TYR cc_start: 0.5400 (m-10) cc_final: 0.5059 (m-80) REVERT: D 555 PHE cc_start: 0.6195 (m-10) cc_final: 0.5761 (m-80) REVERT: D 557 MET cc_start: 0.7398 (tmm) cc_final: 0.6839 (tmm) outliers start: 111 outliers final: 79 residues processed: 709 average time/residue: 0.4164 time to fit residues: 466.6045 Evaluate side-chains 707 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 613 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER 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 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 553 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR 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 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 1017 GLU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 127 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 346 ARG Chi-restraints excluded: chain B residue 391 CYS 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 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS 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 966 LEU Chi-restraints excluded: chain B residue 981 LEU 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 118 LEU Chi-restraints excluded: chain A residue 127 VAL 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 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 823 PHE 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 114 LYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 474 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 343 optimal weight: 2.9990 chunk 280 optimal weight: 0.8980 chunk 231 optimal weight: 0.0980 chunk 110 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 337 optimal weight: 30.0000 chunk 249 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 107 optimal weight: 0.0040 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN B 777 ASN B 824 ASN B1119 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 787 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.184709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.137218 restraints weight = 50745.898| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.87 r_work: 0.3507 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 31780 Z= 0.151 Angle : 0.625 13.139 43372 Z= 0.307 Chirality : 0.046 0.680 5026 Planarity : 0.004 0.045 5477 Dihedral : 5.529 79.208 5600 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.27 % Allowed : 16.32 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.13), residues: 3761 helix: 1.77 (0.17), residues: 1023 sheet: -0.19 (0.19), residues: 673 loop : -1.37 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 328 HIS 0.005 0.001 HIS A1064 PHE 0.023 0.001 PHE B 201 TYR 0.018 0.001 TYR A1067 ARG 0.010 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 50) link_NAG-ASN : angle 2.28225 ( 150) link_BETA1-4 : bond 0.00319 ( 21) link_BETA1-4 : angle 1.09771 ( 63) hydrogen bonds : bond 0.03679 ( 1172) hydrogen bonds : angle 5.06780 ( 3312) SS BOND : bond 0.00359 ( 45) SS BOND : angle 2.35901 ( 90) covalent geometry : bond 0.00340 (31664) covalent geometry : angle 0.60162 (43069) *********************** 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 735 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 626 time to evaluate : 3.024 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: symmetry clash REVERT: C 29 THR cc_start: 0.8001 (t) cc_final: 0.6682 (p) REVERT: C 42 VAL cc_start: 0.8369 (p) cc_final: 0.8009 (m) REVERT: C 99 ASN cc_start: 0.7870 (t0) cc_final: 0.7543 (t0) REVERT: C 170 TYR cc_start: 0.8324 (t80) cc_final: 0.8083 (t80) REVERT: C 267 VAL cc_start: 0.8372 (t) cc_final: 0.8052 (p) REVERT: C 276 LEU cc_start: 0.8722 (tt) cc_final: 0.8474 (tp) REVERT: C 284 THR cc_start: 0.8602 (m) cc_final: 0.8197 (t) REVERT: C 289 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8541 (m) REVERT: C 305 SER cc_start: 0.8910 (t) cc_final: 0.8558 (p) REVERT: C 309 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7243 (mm-30) REVERT: C 353 TRP cc_start: 0.8082 (p-90) cc_final: 0.7831 (p-90) REVERT: C 362 VAL cc_start: 0.8130 (t) cc_final: 0.7896 (m) REVERT: C 378 LYS cc_start: 0.8043 (mttt) cc_final: 0.7662 (mttt) REVERT: C 398 ASP cc_start: 0.7482 (p0) cc_final: 0.7054 (p0) REVERT: C 400 PHE cc_start: 0.7452 (p90) cc_final: 0.7006 (p90) REVERT: C 424 LYS cc_start: 0.7377 (tttt) cc_final: 0.6664 (ttpp) REVERT: C 464 PHE cc_start: 0.8358 (m-10) cc_final: 0.8133 (m-10) REVERT: C 495 TYR cc_start: 0.7160 (m-80) cc_final: 0.6362 (m-80) REVERT: C 588 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8191 (p) REVERT: C 703 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7560 (m110) REVERT: C 704 SER cc_start: 0.8503 (m) cc_final: 0.7944 (t) REVERT: C 747 THR cc_start: 0.8093 (m) cc_final: 0.7680 (p) REVERT: C 773 GLU cc_start: 0.7521 (tt0) cc_final: 0.7186 (tt0) REVERT: C 774 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7614 (mp-120) REVERT: C 803 SER cc_start: 0.8749 (t) cc_final: 0.8542 (p) REVERT: C 804 GLN cc_start: 0.8212 (mt0) cc_final: 0.7900 (mt0) REVERT: C 868 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7316 (tp30) REVERT: C 886 TRP cc_start: 0.8247 (OUTLIER) cc_final: 0.7846 (p90) REVERT: C 949 GLN cc_start: 0.8282 (tp40) cc_final: 0.7780 (tp40) REVERT: C 994 ASP cc_start: 0.7993 (t70) cc_final: 0.7625 (t0) REVERT: C 1017 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7965 (tp30) REVERT: C 1107 ARG cc_start: 0.7871 (mtt180) cc_final: 0.6587 (mtt90) REVERT: C 1119 ASN cc_start: 0.8332 (m-40) cc_final: 0.7888 (m110) REVERT: C 1139 ASP cc_start: 0.8317 (t0) cc_final: 0.7922 (t70) REVERT: B 79 PHE cc_start: 0.7516 (t80) cc_final: 0.7262 (t80) REVERT: B 90 VAL cc_start: 0.8513 (p) cc_final: 0.8106 (m) REVERT: B 195 LYS cc_start: 0.7918 (mtmt) cc_final: 0.7680 (ptpp) REVERT: B 206 LYS cc_start: 0.8443 (tptm) cc_final: 0.8131 (tptp) REVERT: B 294 ASP cc_start: 0.8157 (p0) cc_final: 0.7831 (p0) REVERT: B 296 LEU cc_start: 0.8363 (tp) cc_final: 0.8125 (tp) REVERT: B 360 ASN cc_start: 0.8018 (m110) cc_final: 0.7787 (m110) REVERT: B 394 ASN cc_start: 0.8353 (p0) cc_final: 0.8003 (p0) REVERT: B 532 ASN cc_start: 0.8273 (t0) cc_final: 0.7993 (t0) REVERT: B 562 PHE cc_start: 0.6548 (p90) cc_final: 0.6217 (p90) REVERT: B 576 VAL cc_start: 0.8818 (p) cc_final: 0.8484 (t) REVERT: B 599 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8087 (p) REVERT: B 673 SER cc_start: 0.8915 (t) cc_final: 0.8411 (m) REVERT: B 764 ASN cc_start: 0.8366 (m110) cc_final: 0.7997 (m-40) REVERT: B 790 LYS cc_start: 0.8465 (ptmt) cc_final: 0.8223 (ptmt) REVERT: B 820 ASP cc_start: 0.7569 (t0) cc_final: 0.7260 (t0) REVERT: B 904 TYR cc_start: 0.7583 (m-10) cc_final: 0.7066 (m-10) REVERT: B 929 SER cc_start: 0.8428 (t) cc_final: 0.8099 (p) REVERT: B 950 ASP cc_start: 0.7813 (t0) cc_final: 0.7075 (t0) REVERT: B 954 GLN cc_start: 0.7991 (mt0) cc_final: 0.7393 (mt0) REVERT: B 964 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8192 (mtmm) REVERT: B 982 SER cc_start: 0.8415 (m) cc_final: 0.8175 (p) REVERT: B 1003 SER cc_start: 0.8397 (m) cc_final: 0.8112 (t) REVERT: B 1073 LYS cc_start: 0.8518 (mtmt) cc_final: 0.8266 (mtmm) REVERT: B 1117 THR cc_start: 0.8299 (m) cc_final: 0.7945 (t) REVERT: A 41 LYS cc_start: 0.7840 (mttt) cc_final: 0.7517 (mttm) REVERT: A 120 VAL cc_start: 0.7956 (t) cc_final: 0.7633 (m) REVERT: A 191 GLU cc_start: 0.7445 (mp0) cc_final: 0.7002 (mt-10) REVERT: A 239 GLN cc_start: 0.8193 (tt0) cc_final: 0.7897 (tt0) REVERT: A 535 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8583 (mttm) REVERT: A 544 ASN cc_start: 0.7848 (t0) cc_final: 0.7623 (t0) REVERT: A 546 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6945 (pt) REVERT: A 549 THR cc_start: 0.7853 (m) cc_final: 0.7543 (p) REVERT: A 557 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7905 (mttt) REVERT: A 558 LYS cc_start: 0.8507 (mmtm) cc_final: 0.8043 (mmmt) REVERT: A 580 GLN cc_start: 0.7109 (mm-40) cc_final: 0.6860 (mp-120) REVERT: A 605 SER cc_start: 0.8712 (t) cc_final: 0.8394 (m) REVERT: A 697 MET cc_start: 0.8553 (ptm) cc_final: 0.8337 (ptm) REVERT: A 719 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8267 (p) REVERT: A 725 GLU cc_start: 0.7781 (tp30) cc_final: 0.7359 (tt0) REVERT: A 758 SER cc_start: 0.8276 (m) cc_final: 0.7806 (p) REVERT: A 790 LYS cc_start: 0.8276 (ttmm) cc_final: 0.8023 (mtmm) REVERT: A 825 LYS cc_start: 0.8381 (mmmt) cc_final: 0.7972 (mmmm) REVERT: A 866 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8215 (t) REVERT: A 878 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8183 (mt) REVERT: A 900 MET cc_start: 0.8354 (mtp) cc_final: 0.7826 (mtp) REVERT: A 921 LYS cc_start: 0.8175 (mmtp) cc_final: 0.7918 (mmtp) REVERT: A 933 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8142 (mttp) REVERT: A 950 ASP cc_start: 0.7504 (t0) cc_final: 0.7113 (t0) REVERT: A 963 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8541 (p) REVERT: A 1019 ARG cc_start: 0.7728 (ttm110) cc_final: 0.7346 (ttp80) REVERT: A 1045 LYS cc_start: 0.8377 (mttt) cc_final: 0.8111 (mttt) REVERT: A 1073 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8227 (mtpp) REVERT: D 42 GLN cc_start: 0.8113 (tp40) cc_final: 0.7317 (tp40) REVERT: D 74 LYS cc_start: 0.8536 (tppp) cc_final: 0.8036 (tppp) REVERT: D 309 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8612 (mmtt) REVERT: D 312 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8265 (mm-30) REVERT: D 314 PHE cc_start: 0.8862 (t80) cc_final: 0.8487 (m-10) REVERT: D 315 PHE cc_start: 0.7538 (m-10) cc_final: 0.7199 (m-10) REVERT: D 340 GLN cc_start: 0.2066 (tm-30) cc_final: 0.1607 (tm-30) REVERT: D 360 MET cc_start: 0.3013 (tmm) cc_final: 0.2705 (tmm) REVERT: D 383 MET cc_start: 0.7151 (mpp) cc_final: 0.6683 (mpp) REVERT: D 454 TYR cc_start: 0.5824 (t80) cc_final: 0.5358 (t80) REVERT: D 479 GLU cc_start: 0.8026 (pt0) cc_final: 0.7654 (pp20) REVERT: D 481 LYS cc_start: 0.1557 (OUTLIER) cc_final: 0.0963 (ptmm) REVERT: D 487 VAL cc_start: 0.6133 (p) cc_final: 0.5785 (t) REVERT: D 497 TYR cc_start: 0.6729 (m-80) cc_final: 0.6366 (m-80) REVERT: D 521 TYR cc_start: 0.5398 (m-10) cc_final: 0.4952 (m-80) REVERT: D 555 PHE cc_start: 0.6176 (m-10) cc_final: 0.5700 (m-80) REVERT: D 557 MET cc_start: 0.7288 (tmm) cc_final: 0.6888 (tmm) REVERT: D 570 LEU cc_start: 0.1834 (OUTLIER) cc_final: -0.0475 (mm) outliers start: 109 outliers final: 80 residues processed: 710 average time/residue: 0.4301 time to fit residues: 484.7672 Evaluate side-chains 711 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 615 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER 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 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 553 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR 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 981 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain B residue 127 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 391 CYS 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 519 HIS 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 547 THR Chi-restraints excluded: chain B residue 599 THR 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 981 LEU Chi-restraints excluded: chain B residue 990 GLU 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 118 LEU Chi-restraints excluded: chain A residue 127 VAL 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 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU 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 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 370 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 481 LYS 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 95 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 209 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 287 optimal weight: 0.0770 chunk 74 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 156 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 B 777 ASN B1119 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.185343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.137973 restraints weight = 50770.369| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.81 r_work: 0.3512 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31780 Z= 0.134 Angle : 0.625 12.063 43372 Z= 0.307 Chirality : 0.046 0.520 5026 Planarity : 0.004 0.070 5477 Dihedral : 5.371 79.802 5600 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.12 % Allowed : 16.56 % Favored : 80.32 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3761 helix: 1.85 (0.17), residues: 1016 sheet: -0.11 (0.19), residues: 666 loop : -1.32 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 152 HIS 0.005 0.001 HIS D 373 PHE 0.022 0.001 PHE B 201 TYR 0.063 0.001 TYR D 183 ARG 0.012 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 50) link_NAG-ASN : angle 2.22312 ( 150) link_BETA1-4 : bond 0.00316 ( 21) link_BETA1-4 : angle 1.09120 ( 63) hydrogen bonds : bond 0.03585 ( 1172) hydrogen bonds : angle 5.01339 ( 3312) SS BOND : bond 0.00367 ( 45) SS BOND : angle 2.26070 ( 90) covalent geometry : bond 0.00306 (31664) covalent geometry : angle 0.60320 (43069) ********************** 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 722 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 618 time to evaluate : 3.183 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: symmetry clash REVERT: C 29 THR cc_start: 0.7853 (t) cc_final: 0.6477 (p) REVERT: C 42 VAL cc_start: 0.8366 (p) cc_final: 0.8005 (m) REVERT: C 99 ASN cc_start: 0.7843 (t0) cc_final: 0.7522 (t0) REVERT: C 170 TYR cc_start: 0.8317 (t80) cc_final: 0.8066 (t80) REVERT: C 239 GLN cc_start: 0.8128 (tt0) cc_final: 0.7557 (mt0) REVERT: C 267 VAL cc_start: 0.8326 (t) cc_final: 0.8001 (p) REVERT: C 276 LEU cc_start: 0.8719 (tt) cc_final: 0.8479 (tp) REVERT: C 284 THR cc_start: 0.8588 (m) cc_final: 0.8185 (t) REVERT: C 289 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8483 (m) REVERT: C 305 SER cc_start: 0.8935 (t) cc_final: 0.8556 (p) REVERT: C 353 TRP cc_start: 0.8075 (p-90) cc_final: 0.7821 (p-90) REVERT: C 356 LYS cc_start: 0.8684 (ptpt) cc_final: 0.8449 (pttt) REVERT: C 362 VAL cc_start: 0.8109 (t) cc_final: 0.7892 (m) REVERT: C 378 LYS cc_start: 0.7971 (mttt) cc_final: 0.7582 (mttt) REVERT: C 396 TYR cc_start: 0.8312 (m-80) cc_final: 0.8043 (m-80) REVERT: C 398 ASP cc_start: 0.7502 (p0) cc_final: 0.7079 (p0) REVERT: C 400 PHE cc_start: 0.7493 (p90) cc_final: 0.7019 (p90) REVERT: C 424 LYS cc_start: 0.7360 (tttt) cc_final: 0.6643 (ttpp) REVERT: C 464 PHE cc_start: 0.8334 (m-10) cc_final: 0.8076 (m-10) REVERT: C 495 TYR cc_start: 0.7146 (m-80) cc_final: 0.6352 (m-80) REVERT: C 588 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8159 (p) REVERT: C 703 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7583 (m110) REVERT: C 704 SER cc_start: 0.8371 (m) cc_final: 0.7805 (t) REVERT: C 747 THR cc_start: 0.8068 (m) cc_final: 0.7668 (p) REVERT: C 773 GLU cc_start: 0.7510 (tt0) cc_final: 0.7178 (tt0) REVERT: C 774 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7561 (mp-120) REVERT: C 803 SER cc_start: 0.8754 (t) cc_final: 0.8520 (p) REVERT: C 804 GLN cc_start: 0.8278 (mt0) cc_final: 0.8024 (mt0) REVERT: C 868 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7308 (tp30) REVERT: C 886 TRP cc_start: 0.8244 (OUTLIER) cc_final: 0.7838 (p90) REVERT: C 949 GLN cc_start: 0.8268 (tp40) cc_final: 0.7752 (tp40) REVERT: C 994 ASP cc_start: 0.7957 (t70) cc_final: 0.7578 (t0) REVERT: C 1017 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7969 (tp30) REVERT: C 1073 LYS cc_start: 0.7796 (mmmm) cc_final: 0.7566 (mmmm) REVERT: C 1119 ASN cc_start: 0.8308 (m-40) cc_final: 0.7844 (m110) REVERT: B 79 PHE cc_start: 0.7481 (t80) cc_final: 0.7249 (t80) REVERT: B 90 VAL cc_start: 0.8497 (p) cc_final: 0.8090 (m) REVERT: B 195 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7681 (ptpp) REVERT: B 206 LYS cc_start: 0.8455 (tptm) cc_final: 0.8125 (tptp) REVERT: B 294 ASP cc_start: 0.8145 (p0) cc_final: 0.7802 (p0) REVERT: B 296 LEU cc_start: 0.8335 (tp) cc_final: 0.8087 (tp) REVERT: B 360 ASN cc_start: 0.8019 (m110) cc_final: 0.7783 (m110) REVERT: B 394 ASN cc_start: 0.8341 (p0) cc_final: 0.8005 (p0) REVERT: B 532 ASN cc_start: 0.8296 (t0) cc_final: 0.8013 (t0) REVERT: B 537 LYS cc_start: 0.8511 (ttpp) cc_final: 0.8261 (tttp) REVERT: B 562 PHE cc_start: 0.6548 (p90) cc_final: 0.6237 (p90) REVERT: B 576 VAL cc_start: 0.8788 (p) cc_final: 0.8468 (t) REVERT: B 599 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8095 (p) REVERT: B 673 SER cc_start: 0.8899 (t) cc_final: 0.8391 (m) REVERT: B 764 ASN cc_start: 0.8340 (m110) cc_final: 0.7999 (m-40) REVERT: B 779 GLN cc_start: 0.8026 (tt0) cc_final: 0.7746 (tp40) REVERT: B 790 LYS cc_start: 0.8469 (ptmt) cc_final: 0.8221 (ptmt) REVERT: B 820 ASP cc_start: 0.7569 (t0) cc_final: 0.7173 (t0) REVERT: B 900 MET cc_start: 0.8114 (mmm) cc_final: 0.7811 (mtp) REVERT: B 929 SER cc_start: 0.8392 (t) cc_final: 0.8046 (p) REVERT: B 950 ASP cc_start: 0.7795 (t0) cc_final: 0.7051 (t0) REVERT: B 954 GLN cc_start: 0.7996 (mt0) cc_final: 0.7393 (mt0) REVERT: B 964 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8219 (mtmm) REVERT: B 982 SER cc_start: 0.8460 (m) cc_final: 0.8199 (p) REVERT: B 1003 SER cc_start: 0.8397 (m) cc_final: 0.8113 (t) REVERT: B 1073 LYS cc_start: 0.8528 (mtmt) cc_final: 0.8278 (mtmm) REVERT: B 1117 THR cc_start: 0.8300 (m) cc_final: 0.7933 (t) REVERT: A 21 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7643 (ptm-80) REVERT: A 41 LYS cc_start: 0.7860 (mttt) cc_final: 0.7489 (mttm) REVERT: A 120 VAL cc_start: 0.7938 (t) cc_final: 0.7634 (m) REVERT: A 191 GLU cc_start: 0.7436 (mp0) cc_final: 0.6991 (mt-10) REVERT: A 239 GLN cc_start: 0.8171 (tt0) cc_final: 0.7903 (tt0) REVERT: A 535 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8582 (mttm) REVERT: A 544 ASN cc_start: 0.7867 (t0) cc_final: 0.7622 (t0) REVERT: A 546 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6940 (pt) REVERT: A 549 THR cc_start: 0.7823 (m) cc_final: 0.7507 (p) REVERT: A 557 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7921 (mttt) REVERT: A 558 LYS cc_start: 0.8530 (mmtm) cc_final: 0.8043 (mmmt) REVERT: A 580 GLN cc_start: 0.7041 (mm-40) cc_final: 0.6539 (mp-120) REVERT: A 605 SER cc_start: 0.8718 (t) cc_final: 0.8401 (m) REVERT: A 719 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8272 (p) REVERT: A 725 GLU cc_start: 0.7817 (tp30) cc_final: 0.7370 (tt0) REVERT: A 758 SER cc_start: 0.8229 (m) cc_final: 0.7736 (p) REVERT: A 790 LYS cc_start: 0.8291 (ttmm) cc_final: 0.8061 (mtmm) REVERT: A 825 LYS cc_start: 0.8355 (mmmt) cc_final: 0.7944 (mmmm) REVERT: A 866 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8182 (t) REVERT: A 878 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8147 (mt) REVERT: A 900 MET cc_start: 0.8329 (mtp) cc_final: 0.7804 (mtp) REVERT: A 921 LYS cc_start: 0.8155 (mmtp) cc_final: 0.7897 (mmtp) REVERT: A 933 LYS cc_start: 0.8377 (mtmm) cc_final: 0.8133 (mttp) REVERT: A 950 ASP cc_start: 0.7524 (t0) cc_final: 0.7122 (t0) REVERT: A 963 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8539 (p) REVERT: A 1019 ARG cc_start: 0.7718 (ttm110) cc_final: 0.7335 (ttp80) REVERT: A 1045 LYS cc_start: 0.8366 (mttt) cc_final: 0.8092 (mttt) REVERT: A 1073 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8223 (mtpp) REVERT: D 42 GLN cc_start: 0.8147 (tp40) cc_final: 0.7360 (tp40) REVERT: D 74 LYS cc_start: 0.8549 (tppp) cc_final: 0.8053 (tppp) REVERT: D 309 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8619 (mmtt) REVERT: D 312 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8376 (mm-30) REVERT: D 314 PHE cc_start: 0.8875 (t80) cc_final: 0.8463 (m-10) REVERT: D 315 PHE cc_start: 0.7567 (m-10) cc_final: 0.7182 (m-10) REVERT: D 340 GLN cc_start: 0.1963 (tm-30) cc_final: 0.1486 (tm-30) REVERT: D 360 MET cc_start: 0.2874 (tmm) cc_final: 0.2568 (tmm) REVERT: D 383 MET cc_start: 0.7160 (mpp) cc_final: 0.6711 (mpp) REVERT: D 454 TYR cc_start: 0.5854 (t80) cc_final: 0.5420 (t80) REVERT: D 479 GLU cc_start: 0.8040 (pt0) cc_final: 0.7695 (pp20) REVERT: D 481 LYS cc_start: 0.1866 (OUTLIER) cc_final: 0.1314 (ptmm) REVERT: D 487 VAL cc_start: 0.6122 (p) cc_final: 0.5735 (t) REVERT: D 497 TYR cc_start: 0.6764 (m-80) cc_final: 0.6434 (m-80) REVERT: D 521 TYR cc_start: 0.5302 (m-10) cc_final: 0.4985 (m-80) REVERT: D 555 PHE cc_start: 0.6505 (m-10) cc_final: 0.6018 (m-80) REVERT: D 557 MET cc_start: 0.7266 (tmm) cc_final: 0.6860 (tmm) REVERT: D 570 LEU cc_start: 0.1924 (OUTLIER) cc_final: -0.0622 (tp) outliers start: 104 outliers final: 77 residues processed: 697 average time/residue: 0.4252 time to fit residues: 469.2403 Evaluate side-chains 708 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 614 time to evaluate : 3.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 289 VAL 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 465 GLU 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 553 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR 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 981 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET 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 346 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR 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 599 THR Chi-restraints excluded: chain B residue 754 LEU 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 966 LEU Chi-restraints excluded: chain B residue 981 LEU 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 118 LEU Chi-restraints excluded: chain A residue 127 VAL 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 590 CYS 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 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 370 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 481 LYS 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 75 optimal weight: 0.0070 chunk 223 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 308 optimal weight: 1.9990 chunk 164 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 303 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- 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 B 777 ASN B 824 ASN B1119 ASN A 69 HIS A 146 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** 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** 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 = 0.184491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137211 restraints weight = 50553.332| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.75 r_work: 0.3505 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3922 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= 0.165 Angle : 0.636 10.993 43372 Z= 0.313 Chirality : 0.046 0.458 5026 Planarity : 0.004 0.093 5477 Dihedral : 5.344 79.734 5600 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.06 % Allowed : 16.53 % Favored : 80.41 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3761 helix: 1.84 (0.17), residues: 1018 sheet: -0.15 (0.19), residues: 671 loop : -1.30 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 152 HIS 0.005 0.001 HIS D 373 PHE 0.021 0.002 PHE D 369 TYR 0.022 0.001 TYR D 183 ARG 0.010 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 50) link_NAG-ASN : angle 2.11906 ( 150) link_BETA1-4 : bond 0.00295 ( 21) link_BETA1-4 : angle 1.12809 ( 63) hydrogen bonds : bond 0.03778 ( 1172) hydrogen bonds : angle 5.04437 ( 3312) SS BOND : bond 0.00374 ( 45) SS BOND : angle 2.27910 ( 90) covalent geometry : bond 0.00374 (31664) covalent geometry : angle 0.61588 (43069) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20217.02 seconds wall clock time: 349 minutes 12.15 seconds (20952.15 seconds total)