Starting phenix.real_space_refine on Fri Feb 6 15:51:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9og6_70454/02_2026/9og6_70454.cif Found real_map, /net/cci-nas-00/data/ceres_data/9og6_70454/02_2026/9og6_70454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9og6_70454/02_2026/9og6_70454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9og6_70454/02_2026/9og6_70454.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9og6_70454/02_2026/9og6_70454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9og6_70454/02_2026/9og6_70454.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.041 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 118 5.16 5 C 16303 2.51 5 N 4169 2.21 5 O 5055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25645 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 8496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8496 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 57, 'TRANS': 1030} Chain breaks: 6 Chain: "C" Number of atoms: 7962 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1018, 7948 Classifications: {'peptide': 1018} Link IDs: {'PTRANS': 56, 'TRANS': 961} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1018, 7948 Classifications: {'peptide': 1018} Link IDs: {'PTRANS': 56, 'TRANS': 961} Chain breaks: 7 bond proxies already assigned to first conformer: 8115 Chain: "B" Number of atoms: 8239 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1053, 8230 Classifications: {'peptide': 1053} Link IDs: {'PTRANS': 58, 'TRANS': 994} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1053, 8230 Classifications: {'peptide': 1053} Link IDs: {'PTRANS': 58, 'TRANS': 994} Chain breaks: 7 bond proxies already assigned to first conformer: 8410 Chain: "a" 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: 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: "D" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 9.00, per 1000 atoms: 0.35 Number of scatterers: 25645 At special positions: 0 Unit cell: (138.944, 143.936, 176.384, 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 118 16.00 O 5055 8.00 N 4169 7.00 C 16303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 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=2.04 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 705 " - pdb=" SG CYS C 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS B 705 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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 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 705 " - pdb=" SG CYS B 883 " 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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 BETA1-3 " NAG S 2 " - " BMA S 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " 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 U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG a 1 " - " NAG a 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 125 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 164 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 17 " " NAG C1301 " - " ASN C 137 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C1074 " " NAG D 1 " - " ASN A 343 " " NAG E 1 " - " ASN A 709 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN C 282 " " NAG I 1 " - " ASN B 343 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 709 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 234 " " NAG S 1 " - " ASN C1134 " " NAG T 1 " - " ASN C 709 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG a 1 " - " ASN B 234 " " NAG c 1 " - " ASN C 343 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.7 seconds 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5934 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 47 sheets defined 25.3% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.817A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.892A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.624A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.522A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.571A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 831 through 838 removed outlier: 4.104A pdb=" N LYS A 835 " --> pdb=" O GLY A 832 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN A 836 " --> pdb=" O PHE A 833 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 838 " --> pdb=" O LYS A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 890' Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.621A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.204A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.515A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 991 through 1032 removed outlier: 3.605A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.670A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.733A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.917A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.125A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.945A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.551A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.726A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 890' Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.725A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.082A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.836A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.705A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.744A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.170A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.171A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.508A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.252A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.834A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.585A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 443' Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.598A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.502A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.632A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.560A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.640A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 890' Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.035A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.903A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.713A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.630A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.816A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.045A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.755A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 156 removed outlier: 3.559A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.914A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.696A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 584 through 586 removed outlier: 3.602A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.974A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.772A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AB8, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.764A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 90 through 91 removed outlier: 4.290A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.863A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AC3, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AC4, first strand: chain 'C' and resid 325 through 326 removed outlier: 5.404A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AC6, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.570A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 701 through 703 Processing sheet with id=AD2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.479A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.479A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.525A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.801A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AD9, first strand: chain 'B' and resid 116 through 118 Processing sheet with id=AE1, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.576A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.736A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.540A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.728A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.192A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 711 through 722 removed outlier: 6.387A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.602A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'B' and resid 1120 through 1122 902 hydrogen bonds defined for protein. 2435 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.90 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8056 1.34 - 1.47: 6679 1.47 - 1.59: 11341 1.59 - 1.72: 0 1.72 - 1.84: 145 Bond restraints: 26221 Sorted by residual: bond pdb=" N LEU A 212 " pdb=" CA LEU A 212 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.20e+00 bond pdb=" N VAL A 620 " pdb=" CA VAL A 620 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.23e-02 6.61e+03 5.94e+00 bond pdb=" N GLU C 281 " pdb=" CA GLU C 281 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.35e-02 5.49e+03 4.49e+00 bond pdb=" N GLU A 619 " pdb=" CA GLU A 619 " ideal model delta sigma weight residual 1.460 1.484 -0.024 1.22e-02 6.72e+03 3.87e+00 bond pdb=" N ASN C 282 " pdb=" CA ASN C 282 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.32e-02 5.74e+03 3.65e+00 ... (remaining 26216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 35551 3.37 - 6.74: 127 6.74 - 10.11: 18 10.11 - 13.47: 1 13.47 - 16.84: 1 Bond angle restraints: 35698 Sorted by residual: angle pdb=" N THR A 618 " pdb=" CA THR A 618 " pdb=" C THR A 618 " ideal model delta sigma weight residual 113.28 96.44 16.84 1.22e+00 6.72e-01 1.91e+02 angle pdb=" C ASN C 282 " pdb=" CA ASN C 282 " pdb=" CB ASN C 282 " ideal model delta sigma weight residual 110.09 100.75 9.34 1.67e+00 3.59e-01 3.13e+01 angle pdb=" C PHE B 32 " pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " ideal model delta sigma weight residual 116.34 110.44 5.90 1.40e+00 5.10e-01 1.78e+01 angle pdb=" C GLU A 619 " pdb=" CA GLU A 619 " pdb=" CB GLU A 619 " ideal model delta sigma weight residual 111.03 104.00 7.03 1.87e+00 2.86e-01 1.41e+01 angle pdb=" CB ILE A 197 " pdb=" CG1 ILE A 197 " pdb=" CD1 ILE A 197 " ideal model delta sigma weight residual 113.80 121.24 -7.44 2.10e+00 2.27e-01 1.25e+01 ... (remaining 35693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.10: 14569 21.10 - 42.20: 1577 42.20 - 63.30: 346 63.30 - 84.40: 51 84.40 - 105.50: 19 Dihedral angle restraints: 16562 sinusoidal: 7348 harmonic: 9214 Sorted by residual: dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual -86.00 -172.33 86.33 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 172.32 -79.32 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS A 883 " pdb=" SG CYS A 883 " pdb=" SG CYS B 705 " pdb=" CB CYS B 705 " ideal model delta sinusoidal sigma weight residual -86.00 -164.37 78.37 1 1.00e+01 1.00e-02 7.66e+01 ... (remaining 16559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 4247 0.338 - 0.677: 4 0.677 - 1.015: 0 1.015 - 1.354: 0 1.354 - 1.692: 1 Chirality restraints: 4252 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.71 -1.69 2.00e-01 2.50e+01 7.16e+01 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.63e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.79e+00 ... (remaining 4249 not shown) Planarity restraints: 4579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.344 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" C7 NAG H 1 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.051 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.334 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG H 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.175 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.498 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 282 " 0.022 2.00e-02 2.50e+03 2.36e-02 6.96e+00 pdb=" CG ASN C 282 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN C 282 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN C 282 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.029 2.00e-02 2.50e+03 ... (remaining 4576 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 7895 2.83 - 3.34: 22544 3.34 - 3.86: 41935 3.86 - 4.38: 49473 4.38 - 4.90: 86283 Nonbonded interactions: 208130 Sorted by model distance: nonbonded pdb=" N THR A 618 " pdb=" N GLU A 619 " model vdw 2.307 2.560 nonbonded pdb=" C4 NAG H 1 " pdb=" O5 NAG H 2 " model vdw 2.485 2.776 nonbonded pdb=" O5 NAG H 2 " pdb=" O6 NAG H 2 " model vdw 2.486 2.432 nonbonded pdb=" C4 NAG D 1 " pdb=" O5 NAG D 2 " model vdw 2.498 2.776 nonbonded pdb=" C4 NAG F 2 " pdb=" O5 BMA F 3 " model vdw 2.509 2.776 ... (remaining 208125 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 25 through 66 or resid 79 through 143 or resid 155 through \ 175 or resid 187 through 243 or resid 263 through 443 or resid 450 through 621 \ or resid 640 through 827 or resid 852 through 954 or resid 956 through 1137 or r \ esid 1139 through 1303)) selection = (chain 'B' and (resid 25 through 66 or resid 79 through 175 or resid 187 through \ 243 or resid 263 through 443 or resid 450 through 621 or resid 640 through 827 \ or resid 852 through 954 or resid 956 through 1137 or resid 1139 through 1303)) selection = (chain 'C' and (resid 25 through 143 or resid 155 through 443 or resid 450 throu \ gh 954 or resid 956 through 1137 or resid 1139 through 1303)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' 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 'T' selection = chain 'a' selection = chain 'c' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' } 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=0.37 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.230 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 0.047 26332 Z= 0.147 Angle : 0.680 16.842 35989 Z= 0.336 Chirality : 0.056 1.692 4252 Planarity : 0.007 0.296 4538 Dihedral : 17.368 105.499 10502 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.83 % Favored : 90.91 % Rotamer: Outliers : 3.97 % Allowed : 27.52 % Favored : 68.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.15), residues: 3116 helix: 1.56 (0.21), residues: 640 sheet: -0.59 (0.21), residues: 560 loop : -1.99 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.017 0.001 TYR A1067 PHE 0.015 0.001 PHE A 898 TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00319 (26221) covalent geometry : angle 0.62196 (35698) SS BOND : bond 0.00374 ( 42) SS BOND : angle 0.95897 ( 84) hydrogen bonds : bond 0.12319 ( 890) hydrogen bonds : angle 7.01843 ( 2435) link_BETA1-3 : bond 0.00332 ( 1) link_BETA1-3 : angle 1.87654 ( 3) link_BETA1-4 : bond 0.01019 ( 27) link_BETA1-4 : angle 1.90362 ( 81) link_NAG-ASN : bond 0.00761 ( 41) link_NAG-ASN : angle 4.46912 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 208 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1796 (ppp) cc_final: 0.0050 (tmm) REVERT: A 190 ARG cc_start: 0.7096 (mmt180) cc_final: 0.6026 (mmm160) REVERT: A 202 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6309 (mptt) REVERT: A 206 LYS cc_start: 0.4625 (OUTLIER) cc_final: 0.2549 (tptp) REVERT: A 271 GLN cc_start: 0.7226 (tt0) cc_final: 0.6742 (mt0) REVERT: A 282 ASN cc_start: 0.7318 (m-40) cc_final: 0.7022 (t0) REVERT: A 386 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7644 (mtpt) REVERT: A 414 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6310 (mp10) REVERT: A 439 ASN cc_start: 0.4913 (OUTLIER) cc_final: 0.4502 (p0) REVERT: A 554 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6613 (pt0) REVERT: A 564 GLN cc_start: 0.5589 (pp30) cc_final: 0.5284 (pp30) REVERT: A 636 TYR cc_start: 0.2992 (OUTLIER) cc_final: 0.0752 (p90) REVERT: A 790 LYS cc_start: 0.8402 (mttm) cc_final: 0.7950 (mmmt) REVERT: A 833 PHE cc_start: 0.5952 (OUTLIER) cc_final: 0.3964 (m-80) REVERT: A 837 TYR cc_start: 0.5014 (OUTLIER) cc_final: 0.4246 (m-10) REVERT: A 841 LEU cc_start: 0.4836 (OUTLIER) cc_final: 0.4505 (pp) REVERT: A 916 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8285 (tt) REVERT: C 175 PHE cc_start: 0.2637 (OUTLIER) cc_final: 0.0251 (m-80) REVERT: C 321 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7705 (mp10) REVERT: C 357 ARG cc_start: 0.8134 (ttp80) cc_final: 0.7656 (ttp80) REVERT: C 493 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: C 854 LYS cc_start: 0.6842 (mmtt) cc_final: 0.6103 (ptmt) REVERT: B 780 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7998 (mt-10) REVERT: B 1092 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7056 (pp20) outliers start: 109 outliers final: 90 residues processed: 304 average time/residue: 0.1654 time to fit residues: 82.5281 Evaluate side-chains 307 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 203 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 907 ASN C 388 ASN C 901 GLN C 907 ASN B 99 ASN B1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.219750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.170919 restraints weight = 37391.973| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 4.77 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26332 Z= 0.152 Angle : 0.634 15.632 35989 Z= 0.300 Chirality : 0.049 0.556 4252 Planarity : 0.004 0.048 4538 Dihedral : 9.991 105.734 5006 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.99 % Favored : 90.75 % Rotamer: Outliers : 4.69 % Allowed : 26.76 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.15), residues: 3116 helix: 1.69 (0.21), residues: 644 sheet: -0.72 (0.20), residues: 579 loop : -2.04 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 78 TYR 0.018 0.001 TYR B1067 PHE 0.016 0.001 PHE A 898 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00364 (26221) covalent geometry : angle 0.58206 (35698) SS BOND : bond 0.00506 ( 42) SS BOND : angle 0.94944 ( 84) hydrogen bonds : bond 0.04214 ( 890) hydrogen bonds : angle 5.70310 ( 2435) link_BETA1-3 : bond 0.00405 ( 1) link_BETA1-3 : angle 1.79927 ( 3) link_BETA1-4 : bond 0.00518 ( 27) link_BETA1-4 : angle 1.71570 ( 81) link_NAG-ASN : bond 0.00684 ( 41) link_NAG-ASN : angle 4.06219 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 208 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1683 (ppp) cc_final: -0.0249 (tmm) REVERT: A 190 ARG cc_start: 0.7166 (mmt180) cc_final: 0.6553 (mmm160) REVERT: A 206 LYS cc_start: 0.5598 (OUTLIER) cc_final: 0.3711 (tptp) REVERT: A 439 ASN cc_start: 0.4991 (OUTLIER) cc_final: 0.4718 (p0) REVERT: A 564 GLN cc_start: 0.5646 (pp30) cc_final: 0.5416 (pp30) REVERT: A 636 TYR cc_start: 0.3151 (OUTLIER) cc_final: 0.1240 (p90) REVERT: A 815 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7770 (mtp180) REVERT: A 916 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8125 (tt) REVERT: C 175 PHE cc_start: 0.3214 (OUTLIER) cc_final: 0.0623 (m-80) REVERT: C 321 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7768 (mp10) REVERT: C 357 ARG cc_start: 0.7588 (ttp80) cc_final: 0.7314 (ttp80) REVERT: C 493 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: C 675 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6700 (mp10) REVERT: C 854 LYS cc_start: 0.6920 (mmtt) cc_final: 0.6274 (ptmt) REVERT: B 780 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7427 (mt-10) REVERT: B 1092 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6792 (pp20) outliers start: 129 outliers final: 89 residues processed: 324 average time/residue: 0.1636 time to fit residues: 87.3929 Evaluate side-chains 299 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 200 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 98 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 206 optimal weight: 0.0970 chunk 117 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 285 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 189 optimal weight: 0.6980 chunk 221 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 901 GLN C 907 ASN B 99 ASN B1010 GLN B1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.187106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.143937 restraints weight = 52770.861| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.68 r_work: 0.3415 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26332 Z= 0.131 Angle : 0.614 13.945 35989 Z= 0.291 Chirality : 0.048 0.483 4252 Planarity : 0.004 0.046 4538 Dihedral : 9.837 106.683 4939 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.61 % Favored : 91.13 % Rotamer: Outliers : 5.55 % Allowed : 26.00 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.15), residues: 3116 helix: 1.83 (0.22), residues: 645 sheet: -0.58 (0.21), residues: 539 loop : -1.96 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.018 0.001 TYR B1067 PHE 0.016 0.001 PHE C 106 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00310 (26221) covalent geometry : angle 0.56903 (35698) SS BOND : bond 0.00396 ( 42) SS BOND : angle 0.80113 ( 84) hydrogen bonds : bond 0.03795 ( 890) hydrogen bonds : angle 5.43819 ( 2435) link_BETA1-3 : bond 0.00388 ( 1) link_BETA1-3 : angle 1.73016 ( 3) link_BETA1-4 : bond 0.00468 ( 27) link_BETA1-4 : angle 1.70492 ( 81) link_NAG-ASN : bond 0.00685 ( 41) link_NAG-ASN : angle 3.73949 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 218 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.1294 (OUTLIER) cc_final: 0.0887 (tp) REVERT: A 153 MET cc_start: 0.1317 (ppp) cc_final: -0.0337 (tmm) REVERT: A 190 ARG cc_start: 0.7203 (mmt180) cc_final: 0.6638 (mmm160) REVERT: A 206 LYS cc_start: 0.5866 (OUTLIER) cc_final: 0.3648 (tptp) REVERT: A 386 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8234 (mtpt) REVERT: A 414 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6550 (mp10) REVERT: A 439 ASN cc_start: 0.4982 (OUTLIER) cc_final: 0.4679 (p0) REVERT: A 636 TYR cc_start: 0.3371 (OUTLIER) cc_final: 0.0976 (p90) REVERT: A 815 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7973 (mtp180) REVERT: A 833 PHE cc_start: 0.6412 (OUTLIER) cc_final: 0.4283 (m-80) REVERT: A 841 LEU cc_start: 0.5657 (OUTLIER) cc_final: 0.5225 (pp) REVERT: C 175 PHE cc_start: 0.3520 (OUTLIER) cc_final: 0.0674 (m-80) REVERT: C 321 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: C 357 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7933 (ttp80) REVERT: C 493 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: C 675 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.6873 (mp10) REVERT: C 854 LYS cc_start: 0.7167 (mmtt) cc_final: 0.6499 (ptmt) REVERT: B 780 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8074 (mt-10) REVERT: B 1092 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7259 (pp20) outliers start: 153 outliers final: 103 residues processed: 354 average time/residue: 0.1649 time to fit residues: 95.7925 Evaluate side-chains 320 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 203 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 235 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 196 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 157 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN C 901 GLN C 907 ASN B 99 ASN B1010 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.218218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.161857 restraints weight = 31078.504| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 6.51 r_work: 0.2753 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.0664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 26332 Z= 0.208 Angle : 0.672 14.176 35989 Z= 0.319 Chirality : 0.050 0.464 4252 Planarity : 0.004 0.047 4538 Dihedral : 9.506 106.584 4929 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.22 % Favored : 90.52 % Rotamer: Outliers : 5.99 % Allowed : 25.46 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.15), residues: 3116 helix: 1.51 (0.21), residues: 655 sheet: -0.74 (0.21), residues: 567 loop : -2.03 (0.13), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 328 TYR 0.019 0.001 TYR B1067 PHE 0.018 0.002 PHE C 898 TRP 0.011 0.001 TRP B 436 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00513 (26221) covalent geometry : angle 0.62626 (35698) SS BOND : bond 0.00627 ( 42) SS BOND : angle 1.23715 ( 84) hydrogen bonds : bond 0.04390 ( 890) hydrogen bonds : angle 5.49897 ( 2435) link_BETA1-3 : bond 0.00402 ( 1) link_BETA1-3 : angle 1.62982 ( 3) link_BETA1-4 : bond 0.00479 ( 27) link_BETA1-4 : angle 1.74460 ( 81) link_NAG-ASN : bond 0.00646 ( 41) link_NAG-ASN : angle 3.88115 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 204 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.0321 (OUTLIER) cc_final: -0.0061 (tp) REVERT: A 153 MET cc_start: 0.1750 (ppp) cc_final: 0.0178 (tmm) REVERT: A 190 ARG cc_start: 0.6433 (mmt180) cc_final: 0.5500 (mmm160) REVERT: A 206 LYS cc_start: 0.3897 (OUTLIER) cc_final: 0.1992 (tptp) REVERT: A 386 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7192 (mtpt) REVERT: A 414 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6150 (mp10) REVERT: A 564 GLN cc_start: 0.5644 (pp30) cc_final: 0.5261 (pp30) REVERT: A 636 TYR cc_start: 0.2792 (OUTLIER) cc_final: 0.0759 (p90) REVERT: A 815 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7640 (mtp180) REVERT: A 833 PHE cc_start: 0.5772 (OUTLIER) cc_final: 0.3954 (m-80) REVERT: A 916 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8431 (tt) REVERT: C 175 PHE cc_start: 0.2045 (OUTLIER) cc_final: 0.0036 (m-80) REVERT: C 321 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7642 (mp10) REVERT: C 357 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7852 (ttp80) REVERT: C 493 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6430 (tm-30) REVERT: C 675 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.6470 (mp10) REVERT: C 854 LYS cc_start: 0.6843 (mmtt) cc_final: 0.5787 (ptmt) REVERT: B 633 TRP cc_start: 0.8920 (OUTLIER) cc_final: 0.8622 (m100) REVERT: B 740 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8593 (ttp) REVERT: B 780 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8315 (mt-10) REVERT: B 811 LYS cc_start: 0.6605 (mttm) cc_final: 0.5887 (mtmp) REVERT: B 815 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7348 (mtp180) REVERT: B 1092 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7193 (pp20) outliers start: 165 outliers final: 122 residues processed: 348 average time/residue: 0.1583 time to fit residues: 89.3914 Evaluate side-chains 337 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 199 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 28 optimal weight: 4.9990 chunk 310 optimal weight: 0.5980 chunk 193 optimal weight: 0.6980 chunk 45 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 chunk 246 optimal weight: 9.9990 chunk 151 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 chunk 286 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 710 ASN A 853 GLN A 907 ASN C 388 ASN C 907 ASN B 99 ASN B 935 GLN B1010 GLN ** B1101 HIS ** 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 = 0.4475 r_free = 0.4475 target = 0.225365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.169306 restraints weight = 32213.806| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 5.48 r_work: 0.2952 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.0690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26332 Z= 0.156 Angle : 0.630 14.160 35989 Z= 0.300 Chirality : 0.048 0.455 4252 Planarity : 0.004 0.044 4538 Dihedral : 9.404 106.397 4925 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.87 % Favored : 90.88 % Rotamer: Outliers : 5.55 % Allowed : 26.00 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.15), residues: 3116 helix: 1.71 (0.21), residues: 643 sheet: -0.70 (0.21), residues: 558 loop : -1.98 (0.13), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.018 0.001 TYR B1067 PHE 0.017 0.001 PHE C 898 TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00377 (26221) covalent geometry : angle 0.58389 (35698) SS BOND : bond 0.00545 ( 42) SS BOND : angle 1.25404 ( 84) hydrogen bonds : bond 0.04009 ( 890) hydrogen bonds : angle 5.40383 ( 2435) link_BETA1-3 : bond 0.00439 ( 1) link_BETA1-3 : angle 1.61290 ( 3) link_BETA1-4 : bond 0.00498 ( 27) link_BETA1-4 : angle 1.71460 ( 81) link_NAG-ASN : bond 0.00646 ( 41) link_NAG-ASN : angle 3.77096 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 209 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.0365 (OUTLIER) cc_final: -0.0048 (tp) REVERT: A 153 MET cc_start: 0.1726 (ppp) cc_final: 0.0145 (tmm) REVERT: A 190 ARG cc_start: 0.6511 (mmt180) cc_final: 0.5600 (mmm160) REVERT: A 206 LYS cc_start: 0.4255 (OUTLIER) cc_final: 0.2165 (tptp) REVERT: A 386 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7517 (mtpt) REVERT: A 414 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6169 (mp10) REVERT: A 636 TYR cc_start: 0.2888 (OUTLIER) cc_final: 0.0609 (p90) REVERT: A 815 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.7862 (mtp180) REVERT: A 833 PHE cc_start: 0.6094 (OUTLIER) cc_final: 0.4055 (m-80) REVERT: A 916 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8505 (tt) REVERT: C 154 GLU cc_start: 0.4348 (OUTLIER) cc_final: 0.3618 (tp30) REVERT: C 175 PHE cc_start: 0.2069 (OUTLIER) cc_final: 0.0055 (m-80) REVERT: C 321 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: C 357 ARG cc_start: 0.8433 (ttp80) cc_final: 0.7991 (ttp80) REVERT: C 493 GLN cc_start: 0.7242 (OUTLIER) cc_final: 0.6536 (tm-30) REVERT: C 675 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6586 (mp10) REVERT: C 854 LYS cc_start: 0.7022 (mmtt) cc_final: 0.6047 (ptmt) REVERT: B 633 TRP cc_start: 0.9078 (OUTLIER) cc_final: 0.8806 (m100) REVERT: B 740 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8748 (ttp) REVERT: B 780 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8297 (mt-10) REVERT: B 815 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7708 (mtp180) REVERT: B 935 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: B 1092 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7299 (pp20) outliers start: 153 outliers final: 116 residues processed: 345 average time/residue: 0.1530 time to fit residues: 85.5745 Evaluate side-chains 337 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 203 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 795 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 291 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 230 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 287 optimal weight: 0.9990 chunk 257 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 GLN A 907 ASN C 388 ASN C 901 GLN C 907 ASN B 99 ASN B1010 GLN ** B1101 HIS ** 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 = 0.4419 r_free = 0.4419 target = 0.217363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.159181 restraints weight = 49997.630| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 7.47 r_work: 0.2723 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 26332 Z= 0.231 Angle : 0.671 14.386 35989 Z= 0.321 Chirality : 0.050 0.450 4252 Planarity : 0.004 0.045 4538 Dihedral : 9.477 107.533 4923 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.60 % Favored : 90.17 % Rotamer: Outliers : 5.95 % Allowed : 25.86 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.15), residues: 3116 helix: 1.43 (0.21), residues: 649 sheet: -0.81 (0.21), residues: 568 loop : -2.01 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.019 0.001 TYR B1067 PHE 0.019 0.002 PHE C1121 TRP 0.012 0.001 TRP B 436 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00573 (26221) covalent geometry : angle 0.62658 (35698) SS BOND : bond 0.00675 ( 42) SS BOND : angle 1.29745 ( 84) hydrogen bonds : bond 0.04540 ( 890) hydrogen bonds : angle 5.48694 ( 2435) link_BETA1-3 : bond 0.00426 ( 1) link_BETA1-3 : angle 1.52334 ( 3) link_BETA1-4 : bond 0.00502 ( 27) link_BETA1-4 : angle 1.76000 ( 81) link_NAG-ASN : bond 0.00638 ( 41) link_NAG-ASN : angle 3.83588 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 201 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.0332 (OUTLIER) cc_final: -0.0089 (tp) REVERT: A 153 MET cc_start: 0.1695 (ppp) cc_final: 0.0169 (tmm) REVERT: A 190 ARG cc_start: 0.6383 (mmt180) cc_final: 0.5464 (mmm160) REVERT: A 206 LYS cc_start: 0.3993 (OUTLIER) cc_final: 0.2021 (tptp) REVERT: A 414 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6139 (mp10) REVERT: A 462 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7115 (mmtt) REVERT: A 564 GLN cc_start: 0.5665 (pp30) cc_final: 0.5300 (pp30) REVERT: A 636 TYR cc_start: 0.2750 (OUTLIER) cc_final: 0.0778 (p90) REVERT: A 815 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7658 (mtp180) REVERT: A 833 PHE cc_start: 0.5941 (OUTLIER) cc_final: 0.4247 (m-80) REVERT: A 848 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6883 (t0) REVERT: A 916 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8445 (tt) REVERT: C 154 GLU cc_start: 0.4385 (OUTLIER) cc_final: 0.3510 (tm-30) REVERT: C 175 PHE cc_start: 0.2023 (OUTLIER) cc_final: 0.0127 (m-80) REVERT: C 321 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7646 (mp10) REVERT: C 357 ARG cc_start: 0.8386 (ttp80) cc_final: 0.7894 (ttp80) REVERT: C 493 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.6388 (tm-30) REVERT: C 675 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6446 (mp10) REVERT: C 854 LYS cc_start: 0.6944 (mmtt) cc_final: 0.5956 (ptmt) REVERT: B 133 PHE cc_start: 0.8897 (m-80) cc_final: 0.8696 (m-80) REVERT: B 633 TRP cc_start: 0.8921 (OUTLIER) cc_final: 0.8651 (m100) REVERT: B 740 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8526 (ttp) REVERT: B 780 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8340 (mt-10) REVERT: B 811 LYS cc_start: 0.6523 (mttm) cc_final: 0.5946 (mtmp) REVERT: B 815 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7330 (mtp180) REVERT: B 1092 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7207 (pp20) outliers start: 164 outliers final: 127 residues processed: 343 average time/residue: 0.1584 time to fit residues: 88.4063 Evaluate side-chains 347 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 202 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 795 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 213 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 176 optimal weight: 0.0470 chunk 113 optimal weight: 9.9990 chunk 206 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 218 GLN A 907 ASN C 388 ASN C 907 ASN B 99 ASN B1010 GLN B1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.220883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.168630 restraints weight = 36772.495| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 5.53 r_work: 0.2836 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26332 Z= 0.114 Angle : 0.610 14.041 35989 Z= 0.289 Chirality : 0.047 0.444 4252 Planarity : 0.004 0.044 4538 Dihedral : 9.195 106.189 4922 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.42 % Favored : 91.36 % Rotamer: Outliers : 4.94 % Allowed : 26.83 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.15), residues: 3116 helix: 1.95 (0.21), residues: 639 sheet: -0.59 (0.21), residues: 539 loop : -1.89 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.018 0.001 TYR C1067 PHE 0.016 0.001 PHE A 898 TRP 0.012 0.001 TRP C 886 HIS 0.004 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00262 (26221) covalent geometry : angle 0.56578 (35698) SS BOND : bond 0.00342 ( 42) SS BOND : angle 0.98329 ( 84) hydrogen bonds : bond 0.03589 ( 890) hydrogen bonds : angle 5.24882 ( 2435) link_BETA1-3 : bond 0.00438 ( 1) link_BETA1-3 : angle 1.57886 ( 3) link_BETA1-4 : bond 0.00484 ( 27) link_BETA1-4 : angle 1.69966 ( 81) link_NAG-ASN : bond 0.00660 ( 41) link_NAG-ASN : angle 3.63036 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 213 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.0315 (OUTLIER) cc_final: -0.0080 (tp) REVERT: A 153 MET cc_start: 0.1634 (ppp) cc_final: 0.0722 (ptm) REVERT: A 190 ARG cc_start: 0.6413 (mmt180) cc_final: 0.5509 (mmm160) REVERT: A 206 LYS cc_start: 0.4195 (OUTLIER) cc_final: 0.2147 (tptp) REVERT: A 271 GLN cc_start: 0.7015 (tt0) cc_final: 0.6388 (tp-100) REVERT: A 414 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6153 (mp10) REVERT: A 462 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7210 (mmtt) REVERT: A 471 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5690 (pp20) REVERT: A 564 GLN cc_start: 0.5688 (pp30) cc_final: 0.5330 (pp30) REVERT: A 636 TYR cc_start: 0.2775 (OUTLIER) cc_final: 0.0603 (p90) REVERT: A 815 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7643 (mtp180) REVERT: A 833 PHE cc_start: 0.5791 (OUTLIER) cc_final: 0.4077 (m-80) REVERT: A 848 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6917 (t0) REVERT: A 916 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8364 (tt) REVERT: C 154 GLU cc_start: 0.4317 (OUTLIER) cc_final: 0.3597 (tp30) REVERT: C 175 PHE cc_start: 0.2040 (OUTLIER) cc_final: 0.0075 (m-80) REVERT: C 321 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: C 357 ARG cc_start: 0.8320 (ttp80) cc_final: 0.7864 (ttp80) REVERT: C 493 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6502 (tm-30) REVERT: C 675 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6490 (mp10) REVERT: C 745 ASP cc_start: 0.6771 (t0) cc_final: 0.6494 (p0) REVERT: C 854 LYS cc_start: 0.6910 (mmtt) cc_final: 0.5965 (ptmt) REVERT: B 441 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.5895 (tp) REVERT: B 780 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8273 (mt-10) REVERT: B 811 LYS cc_start: 0.6565 (mttm) cc_final: 0.6147 (mttp) REVERT: B 815 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7465 (mtp180) REVERT: B 1092 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7195 (pp20) outliers start: 136 outliers final: 99 residues processed: 335 average time/residue: 0.1533 time to fit residues: 83.6094 Evaluate side-chains 322 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 205 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 239 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 289 optimal weight: 0.5980 chunk 114 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN C 907 ASN B 99 ASN B 394 ASN B1010 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.218227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.167672 restraints weight = 41986.393| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 4.96 r_work: 0.3057 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 26332 Z= 0.201 Angle : 0.658 14.223 35989 Z= 0.314 Chirality : 0.050 0.435 4252 Planarity : 0.004 0.045 4538 Dihedral : 9.272 107.080 4922 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.41 % Favored : 90.40 % Rotamer: Outliers : 5.70 % Allowed : 26.14 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 3116 helix: 1.62 (0.21), residues: 649 sheet: -0.71 (0.21), residues: 560 loop : -1.95 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.018 0.001 TYR B1067 PHE 0.020 0.002 PHE C 92 TRP 0.011 0.001 TRP B 436 HIS 0.005 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00497 (26221) covalent geometry : angle 0.61486 (35698) SS BOND : bond 0.00579 ( 42) SS BOND : angle 1.40873 ( 84) hydrogen bonds : bond 0.04297 ( 890) hydrogen bonds : angle 5.37001 ( 2435) link_BETA1-3 : bond 0.00480 ( 1) link_BETA1-3 : angle 1.50551 ( 3) link_BETA1-4 : bond 0.00500 ( 27) link_BETA1-4 : angle 1.73570 ( 81) link_NAG-ASN : bond 0.00628 ( 41) link_NAG-ASN : angle 3.70691 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 206 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.0467 (OUTLIER) cc_final: 0.0025 (tp) REVERT: A 153 MET cc_start: 0.1669 (ppp) cc_final: 0.0663 (ptm) REVERT: A 190 ARG cc_start: 0.6783 (mmt180) cc_final: 0.5809 (mmm160) REVERT: A 206 LYS cc_start: 0.5048 (OUTLIER) cc_final: 0.2609 (tptp) REVERT: A 271 GLN cc_start: 0.7332 (tt0) cc_final: 0.6713 (tp-100) REVERT: A 414 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6323 (mp10) REVERT: A 462 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7355 (mmtt) REVERT: A 471 GLU cc_start: 0.6305 (OUTLIER) cc_final: 0.5914 (pp20) REVERT: A 564 GLN cc_start: 0.6041 (pp30) cc_final: 0.5649 (pp30) REVERT: A 636 TYR cc_start: 0.3173 (OUTLIER) cc_final: 0.0912 (p90) REVERT: A 725 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8467 (tt0) REVERT: A 815 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7962 (mtp180) REVERT: A 833 PHE cc_start: 0.6384 (OUTLIER) cc_final: 0.4405 (m-80) REVERT: A 848 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.7091 (t0) REVERT: A 916 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8556 (tt) REVERT: C 154 GLU cc_start: 0.4477 (OUTLIER) cc_final: 0.3446 (tm-30) REVERT: C 175 PHE cc_start: 0.2562 (OUTLIER) cc_final: 0.0257 (m-80) REVERT: C 321 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: C 357 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8073 (ttp80) REVERT: C 493 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6827 (tm-30) REVERT: C 745 ASP cc_start: 0.7038 (t0) cc_final: 0.6783 (p0) REVERT: C 854 LYS cc_start: 0.7205 (mmtt) cc_final: 0.6332 (ptmt) REVERT: B 441 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6095 (tp) REVERT: B 740 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8772 (ttp) REVERT: B 780 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8290 (mt-10) REVERT: B 815 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7787 (mtp180) REVERT: B 1092 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7286 (pp20) outliers start: 157 outliers final: 123 residues processed: 346 average time/residue: 0.1655 time to fit residues: 93.0719 Evaluate side-chains 345 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 203 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 75 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 294 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 212 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 173 optimal weight: 0.0980 chunk 204 optimal weight: 0.7980 chunk 220 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN C 388 ASN C 901 GLN C 907 ASN B 99 ASN B1010 GLN B1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.220915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.170139 restraints weight = 43602.837| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 5.23 r_work: 0.3093 rms_B_bonded: 5.17 restraints_weight: 2.0000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26332 Z= 0.122 Angle : 0.610 13.977 35989 Z= 0.289 Chirality : 0.047 0.409 4252 Planarity : 0.004 0.044 4538 Dihedral : 9.013 106.076 4920 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.16 % Favored : 91.62 % Rotamer: Outliers : 5.41 % Allowed : 26.43 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.15), residues: 3116 helix: 1.98 (0.21), residues: 640 sheet: -0.49 (0.21), residues: 583 loop : -1.88 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.017 0.001 TYR C1067 PHE 0.022 0.001 PHE B 133 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00290 (26221) covalent geometry : angle 0.56781 (35698) SS BOND : bond 0.00353 ( 42) SS BOND : angle 1.08289 ( 84) hydrogen bonds : bond 0.03552 ( 890) hydrogen bonds : angle 5.18891 ( 2435) link_BETA1-3 : bond 0.00531 ( 1) link_BETA1-3 : angle 1.57325 ( 3) link_BETA1-4 : bond 0.00502 ( 27) link_BETA1-4 : angle 1.69657 ( 81) link_NAG-ASN : bond 0.00645 ( 41) link_NAG-ASN : angle 3.53156 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 206 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.0571 (OUTLIER) cc_final: 0.0082 (tp) REVERT: A 153 MET cc_start: 0.1564 (ppp) cc_final: 0.0569 (ptm) REVERT: A 190 ARG cc_start: 0.6934 (mmt180) cc_final: 0.5999 (mmm160) REVERT: A 206 LYS cc_start: 0.5400 (OUTLIER) cc_final: 0.2923 (tptp) REVERT: A 271 GLN cc_start: 0.7464 (tt0) cc_final: 0.6861 (tp-100) REVERT: A 414 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6296 (mp10) REVERT: A 462 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7471 (mmtt) REVERT: A 471 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6011 (pp20) REVERT: A 636 TYR cc_start: 0.3070 (OUTLIER) cc_final: 0.0829 (p90) REVERT: A 815 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7909 (mtp180) REVERT: A 833 PHE cc_start: 0.6336 (OUTLIER) cc_final: 0.4353 (m-80) REVERT: A 916 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8400 (tt) REVERT: C 154 GLU cc_start: 0.4480 (OUTLIER) cc_final: 0.3757 (tp30) REVERT: C 175 PHE cc_start: 0.2639 (OUTLIER) cc_final: 0.0245 (m-80) REVERT: C 287 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7673 (m-30) REVERT: C 321 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7949 (mp10) REVERT: C 357 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8077 (ttp80) REVERT: C 493 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.6753 (tm-30) REVERT: C 675 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.6782 (mp10) REVERT: C 854 LYS cc_start: 0.7117 (mmtt) cc_final: 0.6321 (ptmt) REVERT: B 441 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6222 (tp) REVERT: B 780 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8328 (mt-10) REVERT: B 811 LYS cc_start: 0.6939 (mttm) cc_final: 0.6588 (mttp) REVERT: B 815 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7778 (mtp180) REVERT: B 1092 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7380 (pp20) outliers start: 149 outliers final: 121 residues processed: 336 average time/residue: 0.1696 time to fit residues: 92.5049 Evaluate side-chains 341 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 202 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 263 optimal weight: 0.1980 chunk 215 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 188 optimal weight: 5.9990 chunk 304 optimal weight: 0.7980 chunk 277 optimal weight: 4.9990 chunk 271 optimal weight: 0.3980 chunk 158 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 GLN A 907 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN B 99 ASN B 935 GLN B1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.188120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.141738 restraints weight = 36101.377| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.36 r_work: 0.3490 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26332 Z= 0.113 Angle : 0.608 13.899 35989 Z= 0.288 Chirality : 0.047 0.410 4252 Planarity : 0.004 0.045 4538 Dihedral : 8.876 105.474 4920 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.38 % Favored : 91.39 % Rotamer: Outliers : 4.87 % Allowed : 27.08 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.15), residues: 3116 helix: 2.10 (0.21), residues: 640 sheet: -0.43 (0.20), residues: 583 loop : -1.84 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.017 0.001 TYR B1067 PHE 0.025 0.001 PHE B 133 TRP 0.009 0.001 TRP B 436 HIS 0.002 0.000 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00263 (26221) covalent geometry : angle 0.56650 (35698) SS BOND : bond 0.00335 ( 42) SS BOND : angle 1.00659 ( 84) hydrogen bonds : bond 0.03448 ( 890) hydrogen bonds : angle 5.13495 ( 2435) link_BETA1-3 : bond 0.00471 ( 1) link_BETA1-3 : angle 1.55382 ( 3) link_BETA1-4 : bond 0.00506 ( 27) link_BETA1-4 : angle 1.68716 ( 81) link_NAG-ASN : bond 0.00644 ( 41) link_NAG-ASN : angle 3.49823 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 204 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.1188 (OUTLIER) cc_final: 0.0677 (tp) REVERT: A 153 MET cc_start: 0.1104 (ppp) cc_final: 0.0214 (ptm) REVERT: A 190 ARG cc_start: 0.7113 (mmt180) cc_final: 0.6580 (mmm160) REVERT: A 206 LYS cc_start: 0.6051 (OUTLIER) cc_final: 0.3804 (tptp) REVERT: A 271 GLN cc_start: 0.7507 (tt0) cc_final: 0.7171 (tp-100) REVERT: A 414 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6439 (mp10) REVERT: A 462 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7800 (mmtt) REVERT: A 636 TYR cc_start: 0.3304 (OUTLIER) cc_final: 0.0985 (p90) REVERT: A 815 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7734 (mtp180) REVERT: A 833 PHE cc_start: 0.6254 (OUTLIER) cc_final: 0.4283 (m-80) REVERT: A 916 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8155 (tt) REVERT: C 154 GLU cc_start: 0.4363 (OUTLIER) cc_final: 0.3869 (tp30) REVERT: C 175 PHE cc_start: 0.3439 (OUTLIER) cc_final: 0.0641 (m-80) REVERT: C 321 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: C 357 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7899 (ttp80) REVERT: C 493 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: C 675 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6746 (mp10) REVERT: C 854 LYS cc_start: 0.7002 (mmtt) cc_final: 0.6539 (ptmt) REVERT: B 441 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6513 (tp) REVERT: B 780 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7966 (mt-10) REVERT: B 809 PRO cc_start: 0.7022 (Cg_endo) cc_final: 0.6459 (Cg_exo) REVERT: B 815 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7713 (mtp180) REVERT: B 1092 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7077 (pp20) outliers start: 134 outliers final: 106 residues processed: 325 average time/residue: 0.1740 time to fit residues: 91.2529 Evaluate side-chains 325 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 203 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 100 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 289 optimal weight: 0.1980 chunk 210 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 GLN A 907 ASN C 907 ASN B 99 ASN B 935 GLN B1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.220200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.171881 restraints weight = 38467.000| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 4.62 r_work: 0.3098 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26332 Z= 0.149 Angle : 0.626 13.982 35989 Z= 0.297 Chirality : 0.048 0.428 4252 Planarity : 0.004 0.044 4538 Dihedral : 8.815 105.755 4917 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.54 % Favored : 91.26 % Rotamer: Outliers : 4.98 % Allowed : 26.94 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.15), residues: 3116 helix: 1.97 (0.21), residues: 640 sheet: -0.55 (0.21), residues: 575 loop : -1.86 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.018 0.001 TYR B1067 PHE 0.023 0.001 PHE B 133 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00362 (26221) covalent geometry : angle 0.58504 (35698) SS BOND : bond 0.00453 ( 42) SS BOND : angle 1.08185 ( 84) hydrogen bonds : bond 0.03784 ( 890) hydrogen bonds : angle 5.19018 ( 2435) link_BETA1-3 : bond 0.00456 ( 1) link_BETA1-3 : angle 1.51719 ( 3) link_BETA1-4 : bond 0.00511 ( 27) link_BETA1-4 : angle 1.70499 ( 81) link_NAG-ASN : bond 0.00632 ( 41) link_NAG-ASN : angle 3.53811 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7255.27 seconds wall clock time: 124 minutes 56.69 seconds (7496.69 seconds total)