Starting phenix.real_space_refine on Fri Feb 6 15:53:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9og4_70451/02_2026/9og4_70451.cif Found real_map, /net/cci-nas-00/data/ceres_data/9og4_70451/02_2026/9og4_70451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9og4_70451/02_2026/9og4_70451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9og4_70451/02_2026/9og4_70451.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9og4_70451/02_2026/9og4_70451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9og4_70451/02_2026/9og4_70451.map" } resolution = 3.56 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= 0.000 sd= 0.020 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 121 5.16 5 C 16262 2.51 5 N 4162 2.21 5 O 5049 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s 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: 25594 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 8217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8217 Classifications: {'peptide': 1053} Link IDs: {'PTRANS': 57, 'TRANS': 995} Chain breaks: 7 Chain: "C" Number of atoms: 7998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7998 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 55, 'TRANS': 969} Chain breaks: 8 Chain: "B" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8434 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 57, 'TRANS': 1021} Chain breaks: 7 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: "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: "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: "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: "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: "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: 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: "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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.66, per 1000 atoms: 0.22 Number of scatterers: 25594 At special positions: 0 Unit cell: (133.952, 146.432, 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 121 16.00 O 5049 8.00 N 4162 7.00 C 16262 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 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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 883 " - pdb=" SG CYS B 705 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=1, symmetry=0 Links applied 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 R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " 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-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A1074 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 331 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 61 " " NAG C1305 " - " ASN C 122 " " NAG C1306 " - " ASN C 164 " " NAG C1307 " - " ASN C 234 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 657 " " NAG D 1 " - " ASN B 343 " " NAG E 1 " - " ASN B 709 " " NAG F 1 " - " ASN B 801 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN A 282 " " NAG I 1 " - " ASN C 343 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN B1074 " " NAG M 1 " - " ASN C1098 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 709 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN A 234 " " NAG S 1 " - " ASN A1134 " " NAG T 1 " - " ASN A 709 " " NAG U 1 " - " ASN A 717 " " NAG V 1 " - " ASN A 801 " " NAG W 1 " - " ASN A1098 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 821.8 milliseconds 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5926 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 50 sheets defined 23.9% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.680A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.641A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.630A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.095A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.527A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 853 through 856 removed outlier: 3.907A pdb=" N ASN A 856 " --> pdb=" O GLN A 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 853 through 856' Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.630A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.720A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.388A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 912 through 918' Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.774A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 967 removed outlier: 4.303A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.655A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.331A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.611A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.729A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.804A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 384 through 390 removed outlier: 4.372A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.267A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 759 through 783 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.295A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.772A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.847A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.916A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.279A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.126A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.873A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.737A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 868 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.607A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.312A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.700A pdb=" N ALA B 930 " --> pdb=" O GLN B 926 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.540A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.966A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.670A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 4.114A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 230 removed outlier: 6.693A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 117 through 118 removed outlier: 3.578A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 188 through 189 removed outlier: 3.676A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.522A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.551A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.643A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 567 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.883A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB6, first strand: chain 'A' and resid 721 through 728 removed outlier: 3.526A pdb=" N PHE A1052 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.374A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'C' and resid 51 through 55 Processing sheet with id=AC2, first strand: chain 'C' and resid 63 through 64 Processing sheet with id=AC3, first strand: chain 'C' and resid 168 through 171 removed outlier: 3.804A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.834A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 195 through 197 Processing sheet with id=AC6, first strand: chain 'C' and resid 278 through 279 removed outlier: 3.928A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.533A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.764A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.543A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.197A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.861A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AD5, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AD6, first strand: chain 'C' and resid 718 through 722 removed outlier: 3.595A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.463A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.836A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 229 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 50 through 55 removed outlier: 7.448A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AE4, first strand: chain 'B' and resid 116 through 120 Processing sheet with id=AE5, first strand: chain 'B' and resid 143 through 144 removed outlier: 3.669A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AE7, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AE8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.563A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 451 through 454 removed outlier: 4.026A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.510A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.528A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B1052 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.528A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.650A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.010A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) 828 hydrogen bonds defined for protein. 2244 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: 4.98 Time building geometry restraints manager: 2.96 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: 8037 1.34 - 1.46: 6528 1.46 - 1.59: 11446 1.59 - 1.71: 0 1.71 - 1.83: 149 Bond restraints: 26160 Sorted by residual: bond pdb=" N ILE A 119 " pdb=" CA ILE A 119 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 8.97e+00 bond pdb=" N ILE C 624 " pdb=" CA ILE C 624 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.91e+00 bond pdb=" N LEU B 176 " pdb=" CA LEU B 176 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.15e+00 bond pdb=" N VAL A 826 " pdb=" CA VAL A 826 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.29e-02 6.01e+03 7.96e+00 bond pdb=" N ALA C 623 " pdb=" CA ALA C 623 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.20e-02 6.94e+03 6.74e+00 ... (remaining 26155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 34868 1.77 - 3.55: 627 3.55 - 5.32: 84 5.32 - 7.10: 20 7.10 - 8.87: 7 Bond angle restraints: 35606 Sorted by residual: angle pdb=" C ARG B 214 " pdb=" CA ARG B 214 " pdb=" CB ARG B 214 " ideal model delta sigma weight residual 115.79 110.44 5.35 1.19e+00 7.06e-01 2.02e+01 angle pdb=" N LEU B 223 " pdb=" CA LEU B 223 " pdb=" CB LEU B 223 " ideal model delta sigma weight residual 110.97 104.42 6.55 1.56e+00 4.11e-01 1.77e+01 angle pdb=" N ILE B 805 " pdb=" CA ILE B 805 " pdb=" C ILE B 805 " ideal model delta sigma weight residual 113.53 109.68 3.85 9.80e-01 1.04e+00 1.54e+01 angle pdb=" N LEU A 828 " pdb=" CA LEU A 828 " pdb=" C LEU A 828 " ideal model delta sigma weight residual 113.18 108.19 4.99 1.33e+00 5.65e-01 1.41e+01 angle pdb=" CA VAL C 622 " pdb=" C VAL C 622 " pdb=" O VAL C 622 " ideal model delta sigma weight residual 121.97 118.33 3.64 9.80e-01 1.04e+00 1.38e+01 ... (remaining 35601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 14022 18.00 - 36.00: 1794 36.00 - 54.00: 573 54.00 - 72.00: 92 72.00 - 90.00: 39 Dihedral angle restraints: 16520 sinusoidal: 7326 harmonic: 9194 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 7.55 85.45 1 1.00e+01 1.00e-02 8.84e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 163.37 -70.37 1 1.00e+01 1.00e-02 6.38e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 28.77 64.23 1 1.00e+01 1.00e-02 5.43e+01 ... (remaining 16517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3863 0.082 - 0.163: 362 0.163 - 0.245: 9 0.245 - 0.326: 12 0.326 - 0.408: 3 Chirality restraints: 4249 Sorted by residual: chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 4246 not shown) Planarity restraints: 4564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 560 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO C 561 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 222 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C ALA B 222 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA B 222 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 223 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 825 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C LYS A 825 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS A 825 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 826 " -0.013 2.00e-02 2.50e+03 ... (remaining 4561 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.95: 12726 2.95 - 3.44: 25049 3.44 - 3.93: 41185 3.93 - 4.41: 45837 4.41 - 4.90: 75942 Nonbonded interactions: 200739 Sorted by model distance: nonbonded pdb=" N THR B 632 " pdb=" OG1 THR B 632 " model vdw 2.469 2.496 nonbonded pdb=" C4 NAG R 2 " pdb=" O5 BMA R 3 " model vdw 2.471 2.776 nonbonded pdb=" C4 NAG F 2 " pdb=" O5 BMA F 3 " model vdw 2.482 2.776 nonbonded pdb=" O ALA C 623 " pdb=" N HIS C 625 " model vdw 2.490 3.120 nonbonded pdb=" O ASP A 614 " pdb=" OD1 ASP A 614 " model vdw 2.514 3.040 ... (remaining 200734 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 26 through 175 or resid 188 through 242 or resid 262 throu \ gh 443 or resid 450 through 621 or resid 636 through 828 or resid 851 through 13 \ 04)) selection = (chain 'B' and (resid 26 through 66 or resid 79 through 143 or resid 153 through \ 175 or resid 188 through 242 or resid 262 through 443 or resid 450 through 631 \ or resid 636 through 828 or resid 851 through 1304)) selection = (chain 'C' and (resid 26 through 175 or resid 188 through 242 or resid 262 throu \ gh 443 or resid 450 through 621 or resid 636 through 1304)) } 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 'T' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'R' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 21.530 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 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 0.042 26272 Z= 0.144 Angle : 0.630 12.836 35897 Z= 0.313 Chirality : 0.047 0.408 4249 Planarity : 0.004 0.065 4522 Dihedral : 17.312 89.995 10468 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.37 % Favored : 90.18 % Rotamer: Outliers : 5.60 % Allowed : 31.38 % Favored : 63.02 % 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: -1.86 (0.15), residues: 3107 helix: 1.63 (0.21), residues: 635 sheet: -1.65 (0.22), residues: 535 loop : -2.24 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 403 TYR 0.020 0.001 TYR A1138 PHE 0.030 0.001 PHE B 175 TRP 0.028 0.001 TRP A 436 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00286 (26160) covalent geometry : angle 0.59167 (35606) SS BOND : bond 0.00243 ( 42) SS BOND : angle 1.01460 ( 84) hydrogen bonds : bond 0.17700 ( 812) hydrogen bonds : angle 8.37418 ( 2244) Misc. bond : bond 0.00004 ( 1) link_BETA1-4 : bond 0.00472 ( 27) link_BETA1-4 : angle 1.71130 ( 81) link_NAG-ASN : bond 0.00732 ( 42) link_NAG-ASN : angle 3.41936 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 227 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.6155 (p90) REVERT: A 134 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: A 153 MET cc_start: 0.6109 (ttt) cc_final: 0.4572 (ppp) REVERT: A 351 TYR cc_start: 0.8100 (p90) cc_final: 0.7630 (p90) REVERT: A 353 TRP cc_start: 0.7569 (p-90) cc_final: 0.7011 (p-90) REVERT: A 359 SER cc_start: 0.8136 (p) cc_final: 0.7639 (t) REVERT: A 409 GLN cc_start: 0.6918 (mm110) cc_final: 0.6652 (mm-40) REVERT: A 430 THR cc_start: 0.7945 (OUTLIER) cc_final: 0.7657 (m) REVERT: A 816 SER cc_start: 0.9130 (t) cc_final: 0.8671 (p) REVERT: A 984 LEU cc_start: 0.8827 (mt) cc_final: 0.8625 (mp) REVERT: A 1001 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8588 (mp) REVERT: C 84 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.6944 (mt) REVERT: C 92 PHE cc_start: 0.8341 (t80) cc_final: 0.8066 (t80) REVERT: C 121 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8090 (p0) REVERT: C 242 LEU cc_start: 0.8190 (tt) cc_final: 0.7794 (mp) REVERT: C 351 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.6828 (p90) REVERT: C 392 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8168 (p90) REVERT: C 400 PHE cc_start: 0.7866 (p90) cc_final: 0.7421 (p90) REVERT: C 436 TRP cc_start: 0.7898 (p-90) cc_final: 0.7520 (p-90) REVERT: C 1000 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.7316 (mtt-85) REVERT: C 1019 ARG cc_start: 0.8547 (tmm-80) cc_final: 0.8010 (tpt170) REVERT: C 1029 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.7868 (tpp) REVERT: C 1041 ASP cc_start: 0.7718 (t0) cc_final: 0.7493 (t0) REVERT: B 33 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7808 (p) REVERT: B 66 HIS cc_start: 0.6078 (t-90) cc_final: 0.5208 (p-80) REVERT: B 92 PHE cc_start: 0.8010 (t80) cc_final: 0.7319 (t80) REVERT: B 166 CYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5348 (p) REVERT: B 351 TYR cc_start: 0.8205 (t80) cc_final: 0.7674 (t80) REVERT: B 399 SER cc_start: 0.8607 (p) cc_final: 0.8179 (t) REVERT: B 498 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.5827 (mp10) REVERT: B 567 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7280 (tpp-160) REVERT: B 886 TRP cc_start: 0.8555 (OUTLIER) cc_final: 0.8213 (p90) REVERT: B 900 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8281 (mtp) outliers start: 155 outliers final: 113 residues processed: 357 average time/residue: 0.1379 time to fit residues: 82.4250 Evaluate side-chains 349 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 220 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1000 ARG Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 ASN A 901 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 913 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.142970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.089760 restraints weight = 47305.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.092968 restraints weight = 23195.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095028 restraints weight = 15346.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096177 restraints weight = 12088.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.096961 restraints weight = 10607.846| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.0647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26272 Z= 0.214 Angle : 0.657 12.964 35897 Z= 0.317 Chirality : 0.047 0.401 4249 Planarity : 0.004 0.066 4522 Dihedral : 8.774 83.260 5018 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.62 % Favored : 88.99 % Rotamer: Outliers : 8.88 % Allowed : 27.99 % Favored : 63.13 % 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: -1.84 (0.15), residues: 3107 helix: 1.72 (0.21), residues: 644 sheet: -1.57 (0.21), residues: 557 loop : -2.31 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 273 TYR 0.022 0.001 TYR C1067 PHE 0.025 0.002 PHE B 175 TRP 0.013 0.001 TRP A 104 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00505 (26160) covalent geometry : angle 0.61876 (35606) SS BOND : bond 0.00377 ( 42) SS BOND : angle 1.12175 ( 84) hydrogen bonds : bond 0.05089 ( 812) hydrogen bonds : angle 6.27710 ( 2244) Misc. bond : bond 0.00034 ( 1) link_BETA1-4 : bond 0.00470 ( 27) link_BETA1-4 : angle 1.79348 ( 81) link_NAG-ASN : bond 0.00669 ( 42) link_NAG-ASN : angle 3.47210 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 230 time to evaluate : 0.856 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 134 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: A 153 MET cc_start: 0.6025 (ttt) cc_final: 0.4436 (pmm) REVERT: A 329 PHE cc_start: 0.5259 (OUTLIER) cc_final: 0.3186 (m-10) REVERT: A 351 TYR cc_start: 0.8031 (p90) cc_final: 0.7629 (p90) REVERT: A 353 TRP cc_start: 0.7585 (p-90) cc_final: 0.6937 (p-90) REVERT: A 359 SER cc_start: 0.8117 (p) cc_final: 0.7671 (t) REVERT: A 402 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7509 (tp) REVERT: A 409 GLN cc_start: 0.6984 (mm110) cc_final: 0.6703 (mm-40) REVERT: A 430 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7765 (m) REVERT: A 452 LEU cc_start: 0.5051 (OUTLIER) cc_final: 0.4127 (mp) REVERT: A 816 SER cc_start: 0.9175 (t) cc_final: 0.8748 (p) REVERT: A 979 ASP cc_start: 0.8295 (t0) cc_final: 0.7823 (t0) REVERT: C 84 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.6964 (mt) REVERT: C 92 PHE cc_start: 0.8477 (t80) cc_final: 0.8178 (t80) REVERT: C 121 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.8050 (p0) REVERT: C 242 LEU cc_start: 0.8168 (tt) cc_final: 0.7744 (mp) REVERT: C 351 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.6937 (p90) REVERT: C 392 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8021 (p90) REVERT: C 394 ASN cc_start: 0.8158 (m-40) cc_final: 0.7731 (t0) REVERT: C 400 PHE cc_start: 0.7934 (p90) cc_final: 0.7562 (p90) REVERT: C 436 TRP cc_start: 0.7836 (p-90) cc_final: 0.7502 (p-90) REVERT: C 515 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8727 (m-80) REVERT: C 625 HIS cc_start: 0.3715 (OUTLIER) cc_final: 0.3345 (t-170) REVERT: C 935 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: C 947 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7905 (mtpt) REVERT: C 1019 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7970 (tpt-90) REVERT: C 1041 ASP cc_start: 0.7747 (t0) cc_final: 0.7538 (t0) REVERT: C 1072 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8448 (pm20) REVERT: B 33 THR cc_start: 0.8090 (p) cc_final: 0.7825 (p) REVERT: B 92 PHE cc_start: 0.8069 (t80) cc_final: 0.7319 (t80) REVERT: B 351 TYR cc_start: 0.8168 (t80) cc_final: 0.7574 (t80) REVERT: B 399 SER cc_start: 0.8709 (p) cc_final: 0.8404 (t) REVERT: B 498 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.5772 (mp10) REVERT: B 914 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8590 (t0) outliers start: 246 outliers final: 156 residues processed: 449 average time/residue: 0.1423 time to fit residues: 107.4770 Evaluate side-chains 394 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 221 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 828 LEU 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 874 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 31 optimal weight: 10.0000 chunk 295 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 206 optimal weight: 5.9990 chunk 291 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 278 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN C 30 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN B 66 HIS ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.141631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.088631 restraints weight = 47277.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.092547 restraints weight = 24921.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.092920 restraints weight = 15626.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.093711 restraints weight = 13716.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.093776 restraints weight = 12344.688| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 26272 Z= 0.262 Angle : 0.692 13.109 35897 Z= 0.335 Chirality : 0.048 0.407 4249 Planarity : 0.004 0.067 4522 Dihedral : 8.290 82.288 4926 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.10 % Favored : 88.54 % Rotamer: Outliers : 9.43 % Allowed : 27.95 % Favored : 62.62 % 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: -1.93 (0.15), residues: 3107 helix: 1.57 (0.21), residues: 645 sheet: -1.62 (0.22), residues: 546 loop : -2.34 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.023 0.001 TYR C1067 PHE 0.019 0.002 PHE A 374 TRP 0.016 0.001 TRP B 436 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00622 (26160) covalent geometry : angle 0.65310 (35606) SS BOND : bond 0.00390 ( 42) SS BOND : angle 1.29182 ( 84) hydrogen bonds : bond 0.05208 ( 812) hydrogen bonds : angle 6.05558 ( 2244) Misc. bond : bond 0.00076 ( 1) link_BETA1-4 : bond 0.00478 ( 27) link_BETA1-4 : angle 1.84566 ( 81) link_NAG-ASN : bond 0.00675 ( 42) link_NAG-ASN : angle 3.53021 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 261 poor density : 232 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5928 (ttt) cc_final: 0.4444 (pmm) REVERT: A 329 PHE cc_start: 0.5355 (OUTLIER) cc_final: 0.3321 (m-10) REVERT: A 346 ARG cc_start: 0.6444 (OUTLIER) cc_final: 0.6241 (pmt-80) REVERT: A 351 TYR cc_start: 0.8042 (p90) cc_final: 0.7625 (p90) REVERT: A 353 TRP cc_start: 0.7591 (p-90) cc_final: 0.6860 (p-90) REVERT: A 359 SER cc_start: 0.8183 (p) cc_final: 0.7608 (t) REVERT: A 402 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7449 (tp) REVERT: A 409 GLN cc_start: 0.6891 (mm110) cc_final: 0.6650 (mm-40) REVERT: A 430 THR cc_start: 0.7984 (OUTLIER) cc_final: 0.7666 (m) REVERT: A 452 LEU cc_start: 0.5159 (OUTLIER) cc_final: 0.4199 (mp) REVERT: A 670 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8811 (mm) REVERT: A 816 SER cc_start: 0.9220 (t) cc_final: 0.8745 (p) REVERT: A 979 ASP cc_start: 0.8338 (t0) cc_final: 0.7900 (t0) REVERT: A 1001 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8610 (mp) REVERT: C 84 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.6884 (mt) REVERT: C 92 PHE cc_start: 0.8422 (t80) cc_final: 0.8087 (t80) REVERT: C 121 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8071 (p0) REVERT: C 351 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.6992 (p90) REVERT: C 392 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8054 (p90) REVERT: C 394 ASN cc_start: 0.8080 (m-40) cc_final: 0.7617 (t0) REVERT: C 400 PHE cc_start: 0.8089 (p90) cc_final: 0.7564 (p90) REVERT: C 436 TRP cc_start: 0.7606 (p-90) cc_final: 0.7160 (p-90) REVERT: C 515 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8806 (m-80) REVERT: C 935 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: C 947 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7995 (mtpt) REVERT: C 1019 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8079 (tpt-90) REVERT: C 1072 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8449 (pm20) REVERT: B 33 THR cc_start: 0.8122 (p) cc_final: 0.7840 (p) REVERT: B 92 PHE cc_start: 0.8014 (t80) cc_final: 0.7352 (t80) REVERT: B 177 MET cc_start: 0.6629 (OUTLIER) cc_final: 0.5751 (ppp) REVERT: B 317 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8083 (m-40) REVERT: B 378 LYS cc_start: 0.8872 (tppt) cc_final: 0.8473 (mmmm) REVERT: B 399 SER cc_start: 0.8766 (p) cc_final: 0.8465 (t) REVERT: B 498 GLN cc_start: 0.6779 (OUTLIER) cc_final: 0.5844 (mp10) REVERT: B 567 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7176 (tpp-160) outliers start: 261 outliers final: 188 residues processed: 464 average time/residue: 0.1414 time to fit residues: 110.6156 Evaluate side-chains 424 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 216 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 828 LEU 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 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 883 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 13 optimal weight: 7.9990 chunk 300 optimal weight: 0.9990 chunk 213 optimal weight: 6.9990 chunk 303 optimal weight: 0.8980 chunk 223 optimal weight: 9.9990 chunk 58 optimal weight: 0.0370 chunk 295 optimal weight: 3.9990 chunk 290 optimal weight: 0.6980 chunk 74 optimal weight: 0.0980 chunk 97 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN B 69 HIS ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 506 GLN B 544 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.145871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.092486 restraints weight = 46681.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.095905 restraints weight = 22755.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.098035 restraints weight = 14830.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.099271 restraints weight = 11637.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.100043 restraints weight = 10168.831| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26272 Z= 0.109 Angle : 0.613 12.927 35897 Z= 0.293 Chirality : 0.046 0.402 4249 Planarity : 0.004 0.063 4522 Dihedral : 7.806 82.380 4917 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.24 % Favored : 90.41 % Rotamer: Outliers : 6.25 % Allowed : 30.91 % Favored : 62.84 % 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: -1.66 (0.15), residues: 3107 helix: 1.98 (0.21), residues: 656 sheet: -1.40 (0.22), residues: 550 loop : -2.27 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.019 0.001 TYR B1067 PHE 0.026 0.001 PHE B 175 TRP 0.018 0.001 TRP A 436 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00235 (26160) covalent geometry : angle 0.57365 (35606) SS BOND : bond 0.00223 ( 42) SS BOND : angle 0.97634 ( 84) hydrogen bonds : bond 0.04042 ( 812) hydrogen bonds : angle 5.56373 ( 2244) Misc. bond : bond 0.00016 ( 1) link_BETA1-4 : bond 0.00497 ( 27) link_BETA1-4 : angle 1.69422 ( 81) link_NAG-ASN : bond 0.00724 ( 42) link_NAG-ASN : angle 3.42699 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 244 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7159 (tm-30) REVERT: A 153 MET cc_start: 0.6029 (ttt) cc_final: 0.4567 (ppp) REVERT: A 351 TYR cc_start: 0.8077 (p90) cc_final: 0.7668 (p90) REVERT: A 353 TRP cc_start: 0.7499 (p-90) cc_final: 0.7074 (p-90) REVERT: A 359 SER cc_start: 0.8203 (p) cc_final: 0.7659 (t) REVERT: A 402 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7253 (tp) REVERT: A 409 GLN cc_start: 0.6949 (mm110) cc_final: 0.6630 (mm-40) REVERT: A 430 THR cc_start: 0.7980 (OUTLIER) cc_final: 0.7695 (m) REVERT: A 452 LEU cc_start: 0.4883 (OUTLIER) cc_final: 0.3848 (mp) REVERT: A 816 SER cc_start: 0.9110 (t) cc_final: 0.8697 (p) REVERT: A 1001 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8585 (mp) REVERT: C 84 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.6968 (mt) REVERT: C 92 PHE cc_start: 0.8364 (t80) cc_final: 0.8076 (t80) REVERT: C 121 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8122 (p0) REVERT: C 191 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8330 (mt-10) REVERT: C 242 LEU cc_start: 0.8171 (tt) cc_final: 0.7702 (mp) REVERT: C 351 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.6995 (p90) REVERT: C 392 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.7960 (p90) REVERT: C 394 ASN cc_start: 0.8001 (m-40) cc_final: 0.7592 (t0) REVERT: C 436 TRP cc_start: 0.7754 (p-90) cc_final: 0.7327 (p-90) REVERT: C 515 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8707 (m-80) REVERT: C 733 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7348 (mtpt) REVERT: C 935 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: C 947 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7666 (mtpt) REVERT: C 1019 ARG cc_start: 0.8554 (tmm-80) cc_final: 0.7982 (tpt170) REVERT: C 1041 ASP cc_start: 0.7679 (t0) cc_final: 0.7414 (t0) REVERT: C 1072 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8428 (pm20) REVERT: B 33 THR cc_start: 0.8029 (p) cc_final: 0.7743 (p) REVERT: B 92 PHE cc_start: 0.8180 (t80) cc_final: 0.7370 (t80) REVERT: B 171 VAL cc_start: 0.7640 (OUTLIER) cc_final: 0.7384 (t) REVERT: B 177 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.5751 (ppp) REVERT: B 317 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.7985 (m-40) REVERT: B 351 TYR cc_start: 0.8207 (t80) cc_final: 0.7634 (t80) REVERT: B 378 LYS cc_start: 0.8840 (tppt) cc_final: 0.8519 (mmmm) REVERT: B 380 TYR cc_start: 0.7866 (m-10) cc_final: 0.7649 (m-10) REVERT: B 399 SER cc_start: 0.8577 (p) cc_final: 0.8257 (t) REVERT: B 417 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6861 (tttm) REVERT: B 498 GLN cc_start: 0.6573 (mm110) cc_final: 0.5767 (mp10) REVERT: B 567 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7334 (tpp-160) REVERT: B 886 TRP cc_start: 0.8581 (OUTLIER) cc_final: 0.8189 (p90) REVERT: B 900 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8272 (mtp) REVERT: B 913 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7958 (mp10) REVERT: B 914 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8312 (t0) outliers start: 173 outliers final: 106 residues processed: 392 average time/residue: 0.1436 time to fit residues: 94.0346 Evaluate side-chains 352 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 223 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1126 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 178 optimal weight: 0.0060 chunk 257 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 206 optimal weight: 0.0570 chunk 255 optimal weight: 2.9990 chunk 115 optimal weight: 0.0870 chunk 198 optimal weight: 0.5980 chunk 263 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.146851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.093767 restraints weight = 46656.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.097227 restraints weight = 22595.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.099400 restraints weight = 14739.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.100670 restraints weight = 11549.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.101268 restraints weight = 10079.040| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26272 Z= 0.102 Angle : 0.599 12.927 35897 Z= 0.284 Chirality : 0.046 0.400 4249 Planarity : 0.004 0.064 4522 Dihedral : 7.432 80.184 4902 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.11 % Favored : 90.57 % Rotamer: Outliers : 6.36 % Allowed : 30.55 % Favored : 63.09 % 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: -1.50 (0.15), residues: 3107 helix: 2.14 (0.21), residues: 659 sheet: -1.28 (0.22), residues: 533 loop : -2.20 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 346 TYR 0.019 0.001 TYR A1138 PHE 0.022 0.001 PHE A 157 TRP 0.018 0.001 TRP A 436 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00219 (26160) covalent geometry : angle 0.55954 (35606) SS BOND : bond 0.00254 ( 42) SS BOND : angle 0.93689 ( 84) hydrogen bonds : bond 0.03756 ( 812) hydrogen bonds : angle 5.36070 ( 2244) Misc. bond : bond 0.00002 ( 1) link_BETA1-4 : bond 0.00488 ( 27) link_BETA1-4 : angle 1.70840 ( 81) link_NAG-ASN : bond 0.00715 ( 42) link_NAG-ASN : angle 3.36570 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 241 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: A 153 MET cc_start: 0.5974 (ttt) cc_final: 0.4502 (ppp) REVERT: A 351 TYR cc_start: 0.8058 (p90) cc_final: 0.7641 (p90) REVERT: A 353 TRP cc_start: 0.7521 (p-90) cc_final: 0.7189 (p-90) REVERT: A 359 SER cc_start: 0.8184 (p) cc_final: 0.7736 (t) REVERT: A 402 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7202 (tp) REVERT: A 409 GLN cc_start: 0.6857 (mm110) cc_final: 0.6542 (mm-40) REVERT: A 430 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7671 (m) REVERT: A 452 LEU cc_start: 0.4831 (OUTLIER) cc_final: 0.3779 (mp) REVERT: A 816 SER cc_start: 0.9073 (t) cc_final: 0.8683 (p) REVERT: A 1001 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8561 (mp) REVERT: C 84 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.6949 (mt) REVERT: C 92 PHE cc_start: 0.8344 (t80) cc_final: 0.8063 (t80) REVERT: C 121 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8106 (p0) REVERT: C 191 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8283 (mt-10) REVERT: C 242 LEU cc_start: 0.8088 (tt) cc_final: 0.7627 (mp) REVERT: C 351 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.6957 (p90) REVERT: C 392 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.7935 (p90) REVERT: C 394 ASN cc_start: 0.8029 (m-40) cc_final: 0.7635 (t0) REVERT: C 400 PHE cc_start: 0.7912 (p90) cc_final: 0.7490 (p90) REVERT: C 436 TRP cc_start: 0.7776 (p-90) cc_final: 0.7318 (p-90) REVERT: C 515 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8683 (m-80) REVERT: C 651 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8609 (pt) REVERT: C 733 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7328 (mtpt) REVERT: C 787 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: C 935 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: C 947 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7675 (mtpt) REVERT: C 1019 ARG cc_start: 0.8532 (tmm-80) cc_final: 0.7880 (tpt-90) REVERT: C 1040 VAL cc_start: 0.9102 (t) cc_final: 0.8842 (p) REVERT: C 1041 ASP cc_start: 0.7657 (t0) cc_final: 0.7359 (t0) REVERT: B 33 THR cc_start: 0.8025 (p) cc_final: 0.7737 (p) REVERT: B 92 PHE cc_start: 0.8211 (t80) cc_final: 0.7316 (t80) REVERT: B 166 CYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5418 (p) REVERT: B 177 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.5878 (ppp) REVERT: B 317 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.7979 (m-40) REVERT: B 351 TYR cc_start: 0.8203 (t80) cc_final: 0.7645 (t80) REVERT: B 378 LYS cc_start: 0.8861 (tppt) cc_final: 0.8604 (mmmm) REVERT: B 399 SER cc_start: 0.8583 (p) cc_final: 0.8233 (t) REVERT: B 417 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6797 (tttp) REVERT: B 567 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7406 (tpp-160) REVERT: B 886 TRP cc_start: 0.8506 (OUTLIER) cc_final: 0.8208 (p90) REVERT: B 900 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8248 (mtp) outliers start: 176 outliers final: 118 residues processed: 390 average time/residue: 0.1496 time to fit residues: 98.2604 Evaluate side-chains 373 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 233 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 174 optimal weight: 9.9990 chunk 279 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 313 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 146 optimal weight: 0.9980 chunk 297 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 901 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 580 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.146480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.093218 restraints weight = 46966.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.096610 restraints weight = 22758.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.098774 restraints weight = 14907.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.100019 restraints weight = 11669.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.100788 restraints weight = 10198.138| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26272 Z= 0.112 Angle : 0.599 13.291 35897 Z= 0.283 Chirality : 0.046 0.395 4249 Planarity : 0.004 0.060 4522 Dihedral : 7.300 78.211 4897 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.04 % Favored : 90.63 % Rotamer: Outliers : 6.46 % Allowed : 30.26 % Favored : 63.27 % 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: -1.46 (0.15), residues: 3107 helix: 2.17 (0.21), residues: 658 sheet: -1.24 (0.22), residues: 533 loop : -2.17 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 346 TYR 0.017 0.001 TYR B1067 PHE 0.027 0.001 PHE C 168 TRP 0.018 0.001 TRP A 436 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00251 (26160) covalent geometry : angle 0.55912 (35606) SS BOND : bond 0.00236 ( 42) SS BOND : angle 0.97462 ( 84) hydrogen bonds : bond 0.03791 ( 812) hydrogen bonds : angle 5.23754 ( 2244) Misc. bond : bond 0.00012 ( 1) link_BETA1-4 : bond 0.00470 ( 27) link_BETA1-4 : angle 1.71850 ( 81) link_NAG-ASN : bond 0.00690 ( 42) link_NAG-ASN : angle 3.35448 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 240 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.6188 (p90) REVERT: A 134 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: A 153 MET cc_start: 0.6054 (ttt) cc_final: 0.4614 (pmm) REVERT: A 351 TYR cc_start: 0.8078 (p90) cc_final: 0.7626 (p90) REVERT: A 353 TRP cc_start: 0.7517 (p-90) cc_final: 0.7201 (p-90) REVERT: A 359 SER cc_start: 0.8273 (p) cc_final: 0.7761 (t) REVERT: A 402 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7161 (tp) REVERT: A 409 GLN cc_start: 0.6857 (mm110) cc_final: 0.6529 (mm-40) REVERT: A 430 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7658 (m) REVERT: A 452 LEU cc_start: 0.4777 (OUTLIER) cc_final: 0.3748 (mp) REVERT: A 816 SER cc_start: 0.9087 (t) cc_final: 0.8674 (p) REVERT: A 1001 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8533 (mp) REVERT: C 84 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.6927 (mt) REVERT: C 92 PHE cc_start: 0.8295 (t80) cc_final: 0.8024 (t80) REVERT: C 121 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8081 (p0) REVERT: C 191 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8240 (mt-10) REVERT: C 242 LEU cc_start: 0.8104 (tt) cc_final: 0.7615 (mp) REVERT: C 351 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.6765 (p90) REVERT: C 392 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8063 (p90) REVERT: C 394 ASN cc_start: 0.8018 (m-40) cc_final: 0.7603 (t0) REVERT: C 400 PHE cc_start: 0.7946 (p90) cc_final: 0.7515 (p90) REVERT: C 436 TRP cc_start: 0.7743 (p-90) cc_final: 0.7211 (p-90) REVERT: C 515 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8704 (m-80) REVERT: C 651 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8605 (pt) REVERT: C 733 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7263 (mtpt) REVERT: C 759 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.7381 (m-10) REVERT: C 787 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8059 (mt0) REVERT: C 935 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: C 947 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7711 (mtpt) REVERT: C 1019 ARG cc_start: 0.8534 (tmm-80) cc_final: 0.7965 (tpt170) REVERT: C 1040 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8838 (p) REVERT: C 1041 ASP cc_start: 0.7702 (t0) cc_final: 0.7425 (t0) REVERT: B 33 THR cc_start: 0.8026 (p) cc_final: 0.7737 (p) REVERT: B 66 HIS cc_start: 0.5924 (t-90) cc_final: 0.5249 (p-80) REVERT: B 92 PHE cc_start: 0.8186 (t80) cc_final: 0.7302 (t80) REVERT: B 166 CYS cc_start: 0.5991 (OUTLIER) cc_final: 0.5477 (p) REVERT: B 177 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6038 (ppp) REVERT: B 351 TYR cc_start: 0.8230 (t80) cc_final: 0.7672 (t80) REVERT: B 378 LYS cc_start: 0.8841 (tppt) cc_final: 0.8547 (mmmm) REVERT: B 399 SER cc_start: 0.8597 (p) cc_final: 0.8208 (t) REVERT: B 417 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6785 (tttp) REVERT: B 498 GLN cc_start: 0.6616 (mm110) cc_final: 0.5839 (mp10) REVERT: B 567 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7384 (tpp-160) REVERT: B 886 TRP cc_start: 0.8523 (OUTLIER) cc_final: 0.8214 (p90) REVERT: B 900 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8282 (mtp) REVERT: B 914 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8278 (t0) outliers start: 179 outliers final: 129 residues processed: 395 average time/residue: 0.1498 time to fit residues: 99.3509 Evaluate side-chains 382 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 228 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 289 optimal weight: 4.9990 chunk 59 optimal weight: 0.0170 chunk 313 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 100 optimal weight: 0.6980 chunk 176 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 250 optimal weight: 20.0000 chunk 265 optimal weight: 9.9990 chunk 253 optimal weight: 2.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.145685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.092304 restraints weight = 46578.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.095664 restraints weight = 22740.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.097780 restraints weight = 14952.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.099046 restraints weight = 11763.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.099626 restraints weight = 10295.159| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26272 Z= 0.135 Angle : 0.610 13.570 35897 Z= 0.288 Chirality : 0.046 0.394 4249 Planarity : 0.004 0.060 4522 Dihedral : 7.247 76.699 4895 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.43 % Favored : 90.25 % Rotamer: Outliers : 6.72 % Allowed : 29.90 % Favored : 63.38 % 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: -1.48 (0.15), residues: 3107 helix: 2.15 (0.21), residues: 656 sheet: -1.28 (0.22), residues: 538 loop : -2.17 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.019 0.001 TYR A1138 PHE 0.032 0.001 PHE B 192 TRP 0.019 0.001 TRP A 436 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00314 (26160) covalent geometry : angle 0.57126 (35606) SS BOND : bond 0.00306 ( 42) SS BOND : angle 1.02599 ( 84) hydrogen bonds : bond 0.03924 ( 812) hydrogen bonds : angle 5.20878 ( 2244) Misc. bond : bond 0.00026 ( 1) link_BETA1-4 : bond 0.00474 ( 27) link_BETA1-4 : angle 1.74493 ( 81) link_NAG-ASN : bond 0.00686 ( 42) link_NAG-ASN : angle 3.34647 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 234 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.6174 (p90) REVERT: A 134 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7683 (pp30) REVERT: A 153 MET cc_start: 0.6053 (ttt) cc_final: 0.4619 (pmm) REVERT: A 351 TYR cc_start: 0.8027 (p90) cc_final: 0.7613 (p90) REVERT: A 353 TRP cc_start: 0.7490 (p-90) cc_final: 0.7265 (p-90) REVERT: A 359 SER cc_start: 0.8302 (p) cc_final: 0.7787 (t) REVERT: A 402 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7186 (tp) REVERT: A 409 GLN cc_start: 0.6879 (mm110) cc_final: 0.6547 (mm-40) REVERT: A 430 THR cc_start: 0.7953 (OUTLIER) cc_final: 0.7680 (m) REVERT: A 452 LEU cc_start: 0.4970 (OUTLIER) cc_final: 0.3915 (mp) REVERT: A 816 SER cc_start: 0.9117 (t) cc_final: 0.8699 (p) REVERT: A 1001 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8556 (mp) REVERT: C 84 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.6946 (mt) REVERT: C 92 PHE cc_start: 0.8332 (t80) cc_final: 0.8061 (t80) REVERT: C 121 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8095 (p0) REVERT: C 191 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8292 (mt-10) REVERT: C 242 LEU cc_start: 0.8111 (tt) cc_final: 0.7604 (mp) REVERT: C 351 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.6781 (p90) REVERT: C 392 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8054 (p90) REVERT: C 394 ASN cc_start: 0.8004 (m-40) cc_final: 0.7603 (t0) REVERT: C 400 PHE cc_start: 0.7957 (p90) cc_final: 0.7573 (p90) REVERT: C 436 TRP cc_start: 0.7748 (p-90) cc_final: 0.7228 (p-90) REVERT: C 515 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8713 (m-80) REVERT: C 651 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8630 (pt) REVERT: C 733 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7280 (mtpt) REVERT: C 759 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7461 (m-10) REVERT: C 787 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8062 (mt0) REVERT: C 935 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: C 947 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7755 (mtpt) REVERT: C 1019 ARG cc_start: 0.8561 (tmm-80) cc_final: 0.8025 (tpt170) REVERT: C 1041 ASP cc_start: 0.7717 (t0) cc_final: 0.7444 (t0) REVERT: B 33 THR cc_start: 0.8051 (p) cc_final: 0.7765 (p) REVERT: B 66 HIS cc_start: 0.5943 (t-90) cc_final: 0.5257 (p-80) REVERT: B 92 PHE cc_start: 0.8180 (t80) cc_final: 0.7404 (t80) REVERT: B 177 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6012 (ppp) REVERT: B 351 TYR cc_start: 0.8213 (t80) cc_final: 0.7658 (t80) REVERT: B 378 LYS cc_start: 0.8848 (tppt) cc_final: 0.8557 (mmmm) REVERT: B 399 SER cc_start: 0.8591 (p) cc_final: 0.8284 (t) REVERT: B 417 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6761 (tttm) REVERT: B 498 GLN cc_start: 0.6620 (mm110) cc_final: 0.5836 (mp10) REVERT: B 567 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7414 (tpp-160) REVERT: B 886 TRP cc_start: 0.8530 (OUTLIER) cc_final: 0.8261 (p90) REVERT: B 900 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8310 (mtp) REVERT: B 914 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8343 (t0) outliers start: 186 outliers final: 138 residues processed: 391 average time/residue: 0.1500 time to fit residues: 98.2158 Evaluate side-chains 396 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 235 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 105 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 246 optimal weight: 0.0770 chunk 90 optimal weight: 0.6980 chunk 12 optimal weight: 20.0000 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.144416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.090766 restraints weight = 46680.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.094071 restraints weight = 22996.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.096143 restraints weight = 15193.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.097387 restraints weight = 11969.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.097961 restraints weight = 10502.466| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26272 Z= 0.162 Angle : 0.628 13.258 35897 Z= 0.298 Chirality : 0.046 0.389 4249 Planarity : 0.004 0.061 4522 Dihedral : 7.231 74.250 4892 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.95 % Favored : 89.73 % Rotamer: Outliers : 6.97 % Allowed : 29.97 % Favored : 63.06 % 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: -1.54 (0.15), residues: 3107 helix: 2.03 (0.21), residues: 657 sheet: -1.34 (0.22), residues: 536 loop : -2.18 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 34 TYR 0.033 0.001 TYR B 380 PHE 0.033 0.001 PHE B 175 TRP 0.023 0.001 TRP A 436 HIS 0.002 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00380 (26160) covalent geometry : angle 0.58943 (35606) SS BOND : bond 0.00295 ( 42) SS BOND : angle 1.09222 ( 84) hydrogen bonds : bond 0.04237 ( 812) hydrogen bonds : angle 5.24969 ( 2244) Misc. bond : bond 0.00044 ( 1) link_BETA1-4 : bond 0.00488 ( 27) link_BETA1-4 : angle 1.79557 ( 81) link_NAG-ASN : bond 0.00658 ( 42) link_NAG-ASN : angle 3.35313 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 235 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8551 (pp) REVERT: A 134 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7505 (pp30) REVERT: A 153 MET cc_start: 0.6076 (ttt) cc_final: 0.4664 (pmm) REVERT: A 351 TYR cc_start: 0.8009 (p90) cc_final: 0.7586 (p90) REVERT: A 353 TRP cc_start: 0.7482 (p-90) cc_final: 0.7072 (p-90) REVERT: A 359 SER cc_start: 0.8310 (p) cc_final: 0.7779 (t) REVERT: A 402 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7260 (tp) REVERT: A 409 GLN cc_start: 0.6878 (mm110) cc_final: 0.6565 (mm-40) REVERT: A 430 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7684 (m) REVERT: A 452 LEU cc_start: 0.5052 (OUTLIER) cc_final: 0.4021 (mp) REVERT: A 816 SER cc_start: 0.9160 (t) cc_final: 0.8724 (p) REVERT: A 979 ASP cc_start: 0.8309 (t0) cc_final: 0.7841 (t0) REVERT: A 1001 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8546 (mp) REVERT: C 84 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.6895 (mt) REVERT: C 92 PHE cc_start: 0.8343 (t80) cc_final: 0.8134 (t80) REVERT: C 121 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8101 (p0) REVERT: C 242 LEU cc_start: 0.8054 (tt) cc_final: 0.7549 (mp) REVERT: C 351 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.6873 (p90) REVERT: C 392 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8016 (p90) REVERT: C 394 ASN cc_start: 0.8014 (m-40) cc_final: 0.7634 (t0) REVERT: C 436 TRP cc_start: 0.7722 (p-90) cc_final: 0.7186 (p-90) REVERT: C 515 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8648 (m-80) REVERT: C 651 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8595 (pt) REVERT: C 733 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7341 (mtpt) REVERT: C 759 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7623 (m-10) REVERT: C 935 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: C 947 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7826 (mtpt) REVERT: C 1019 ARG cc_start: 0.8577 (tmm-80) cc_final: 0.8047 (tpt170) REVERT: C 1041 ASP cc_start: 0.7702 (t0) cc_final: 0.7484 (t0) REVERT: B 66 HIS cc_start: 0.5959 (t-90) cc_final: 0.5222 (p-80) REVERT: B 92 PHE cc_start: 0.8202 (t80) cc_final: 0.7487 (t80) REVERT: B 177 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.5974 (ppp) REVERT: B 351 TYR cc_start: 0.8230 (t80) cc_final: 0.7697 (t80) REVERT: B 378 LYS cc_start: 0.8834 (tppt) cc_final: 0.8614 (mmmm) REVERT: B 399 SER cc_start: 0.8608 (p) cc_final: 0.8310 (t) REVERT: B 417 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6574 (tttm) REVERT: B 498 GLN cc_start: 0.6677 (mm110) cc_final: 0.5861 (mp10) REVERT: B 567 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7357 (tpp-160) REVERT: B 886 TRP cc_start: 0.8600 (OUTLIER) cc_final: 0.8215 (p90) REVERT: B 914 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8401 (t0) outliers start: 193 outliers final: 151 residues processed: 399 average time/residue: 0.1367 time to fit residues: 91.7551 Evaluate side-chains 401 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 230 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 142 optimal weight: 8.9990 chunk 237 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 292 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 300 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.143251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.090279 restraints weight = 46952.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.094064 restraints weight = 24064.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.095233 restraints weight = 14575.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095743 restraints weight = 12146.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.095917 restraints weight = 12007.432| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 26272 Z= 0.199 Angle : 0.654 13.138 35897 Z= 0.312 Chirality : 0.047 0.392 4249 Planarity : 0.004 0.061 4522 Dihedral : 7.380 71.500 4889 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.43 % Favored : 89.25 % Rotamer: Outliers : 6.61 % Allowed : 30.26 % Favored : 63.13 % 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: -1.61 (0.15), residues: 3107 helix: 1.93 (0.21), residues: 650 sheet: -1.42 (0.22), residues: 536 loop : -2.17 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.027 0.001 TYR B 380 PHE 0.030 0.002 PHE A 157 TRP 0.022 0.001 TRP A 436 HIS 0.002 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00471 (26160) covalent geometry : angle 0.61521 (35606) SS BOND : bond 0.00322 ( 42) SS BOND : angle 1.33888 ( 84) hydrogen bonds : bond 0.04558 ( 812) hydrogen bonds : angle 5.33164 ( 2244) Misc. bond : bond 0.00061 ( 1) link_BETA1-4 : bond 0.00491 ( 27) link_BETA1-4 : angle 1.85290 ( 81) link_NAG-ASN : bond 0.00655 ( 42) link_NAG-ASN : angle 3.39513 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 229 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7547 (pp30) REVERT: A 153 MET cc_start: 0.6076 (ttt) cc_final: 0.4623 (pmm) REVERT: A 351 TYR cc_start: 0.8059 (p90) cc_final: 0.7604 (p90) REVERT: A 353 TRP cc_start: 0.7497 (p-90) cc_final: 0.7005 (p-90) REVERT: A 359 SER cc_start: 0.8280 (p) cc_final: 0.7633 (t) REVERT: A 409 GLN cc_start: 0.6814 (mm110) cc_final: 0.6541 (mm-40) REVERT: A 430 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7687 (m) REVERT: A 753 LEU cc_start: 0.8950 (tt) cc_final: 0.8622 (tt) REVERT: A 816 SER cc_start: 0.9181 (t) cc_final: 0.8724 (p) REVERT: A 979 ASP cc_start: 0.8334 (t0) cc_final: 0.7876 (t0) REVERT: C 84 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.6859 (mt) REVERT: C 92 PHE cc_start: 0.8299 (t80) cc_final: 0.8064 (t80) REVERT: C 121 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8177 (p0) REVERT: C 242 LEU cc_start: 0.8117 (tt) cc_final: 0.7574 (mp) REVERT: C 351 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.6925 (p90) REVERT: C 392 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8091 (p90) REVERT: C 394 ASN cc_start: 0.8035 (m-40) cc_final: 0.7617 (t0) REVERT: C 400 PHE cc_start: 0.7772 (p90) cc_final: 0.7354 (p90) REVERT: C 436 TRP cc_start: 0.7651 (p-90) cc_final: 0.7170 (p-90) REVERT: C 465 GLU cc_start: 0.8686 (tt0) cc_final: 0.8275 (mt-10) REVERT: C 515 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8702 (m-80) REVERT: C 733 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7336 (mtpt) REVERT: C 759 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7541 (m-10) REVERT: C 935 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: C 947 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7857 (mtpt) REVERT: C 1019 ARG cc_start: 0.8581 (tmm-80) cc_final: 0.8045 (tpt170) REVERT: B 33 THR cc_start: 0.8067 (p) cc_final: 0.7780 (p) REVERT: B 66 HIS cc_start: 0.5926 (t-90) cc_final: 0.5188 (p-80) REVERT: B 92 PHE cc_start: 0.8161 (t80) cc_final: 0.7436 (t80) REVERT: B 177 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.5847 (ppp) REVERT: B 378 LYS cc_start: 0.8832 (tppt) cc_final: 0.8615 (mmmm) REVERT: B 399 SER cc_start: 0.8624 (p) cc_final: 0.8304 (t) REVERT: B 417 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6621 (tttm) REVERT: B 498 GLN cc_start: 0.6754 (mm110) cc_final: 0.5851 (mp10) REVERT: B 567 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7174 (tpp-160) REVERT: B 914 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8452 (t0) outliers start: 183 outliers final: 152 residues processed: 385 average time/residue: 0.1397 time to fit residues: 90.4197 Evaluate side-chains 392 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 226 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 135 optimal weight: 0.3980 chunk 222 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 183 optimal weight: 0.0770 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.146123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.092916 restraints weight = 46683.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.096321 restraints weight = 22734.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.098463 restraints weight = 14869.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.099743 restraints weight = 11661.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.100469 restraints weight = 10185.066| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26272 Z= 0.111 Angle : 0.622 13.550 35897 Z= 0.295 Chirality : 0.046 0.390 4249 Planarity : 0.004 0.060 4522 Dihedral : 7.046 68.866 4885 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.01 % Favored : 90.67 % Rotamer: Outliers : 5.53 % Allowed : 31.31 % Favored : 63.16 % 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: -1.48 (0.15), residues: 3107 helix: 2.15 (0.21), residues: 656 sheet: -1.28 (0.22), residues: 536 loop : -2.17 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 34 TYR 0.023 0.001 TYR B 380 PHE 0.036 0.001 PHE A 157 TRP 0.027 0.001 TRP A 436 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00244 (26160) covalent geometry : angle 0.58320 (35606) SS BOND : bond 0.00239 ( 42) SS BOND : angle 1.07691 ( 84) hydrogen bonds : bond 0.03880 ( 812) hydrogen bonds : angle 5.13295 ( 2244) Misc. bond : bond 0.00018 ( 1) link_BETA1-4 : bond 0.00501 ( 27) link_BETA1-4 : angle 1.80966 ( 81) link_NAG-ASN : bond 0.00705 ( 42) link_NAG-ASN : angle 3.33059 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 243 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.7767 (tm-30) cc_final: 0.7550 (pp30) REVERT: A 153 MET cc_start: 0.6044 (ttt) cc_final: 0.4625 (pmm) REVERT: A 351 TYR cc_start: 0.7976 (p90) cc_final: 0.7547 (p90) REVERT: A 353 TRP cc_start: 0.7452 (p-90) cc_final: 0.7114 (p-90) REVERT: A 359 SER cc_start: 0.8239 (p) cc_final: 0.7766 (t) REVERT: A 402 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7233 (tp) REVERT: A 409 GLN cc_start: 0.6901 (mm110) cc_final: 0.6585 (mm-40) REVERT: A 430 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7782 (m) REVERT: A 816 SER cc_start: 0.9094 (t) cc_final: 0.8706 (p) REVERT: A 984 LEU cc_start: 0.8856 (mt) cc_final: 0.8545 (mp) REVERT: A 1001 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8580 (mp) REVERT: C 84 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.6978 (mt) REVERT: C 92 PHE cc_start: 0.8354 (t80) cc_final: 0.8125 (t80) REVERT: C 191 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8261 (mt-10) REVERT: C 242 LEU cc_start: 0.7963 (tt) cc_final: 0.7519 (mp) REVERT: C 351 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.7072 (p90) REVERT: C 380 TYR cc_start: 0.7634 (m-10) cc_final: 0.7417 (m-10) REVERT: C 392 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.8026 (p90) REVERT: C 394 ASN cc_start: 0.7904 (m-40) cc_final: 0.7543 (t0) REVERT: C 400 PHE cc_start: 0.7602 (p90) cc_final: 0.7349 (p90) REVERT: C 436 TRP cc_start: 0.7773 (p-90) cc_final: 0.7286 (p-90) REVERT: C 465 GLU cc_start: 0.8494 (tt0) cc_final: 0.8256 (mt-10) REVERT: C 651 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8574 (pt) REVERT: C 733 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7283 (mtpt) REVERT: C 759 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7423 (m-10) REVERT: C 935 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: C 947 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7696 (mtpt) REVERT: C 1019 ARG cc_start: 0.8536 (tmm-80) cc_final: 0.8072 (tpt170) REVERT: B 33 THR cc_start: 0.8002 (p) cc_final: 0.7720 (p) REVERT: B 66 HIS cc_start: 0.5955 (t-90) cc_final: 0.5256 (p-80) REVERT: B 92 PHE cc_start: 0.8231 (t80) cc_final: 0.7447 (t80) REVERT: B 166 CYS cc_start: 0.6001 (OUTLIER) cc_final: 0.5448 (p) REVERT: B 177 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6003 (ppp) REVERT: B 317 ASN cc_start: 0.8313 (OUTLIER) cc_final: 0.7994 (m-40) REVERT: B 378 LYS cc_start: 0.8827 (tppt) cc_final: 0.8617 (mmmm) REVERT: B 399 SER cc_start: 0.8509 (p) cc_final: 0.8199 (t) REVERT: B 417 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6574 (tttp) REVERT: B 567 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7446 (tpp-160) REVERT: B 886 TRP cc_start: 0.8516 (OUTLIER) cc_final: 0.8234 (p90) REVERT: B 900 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8272 (mtp) outliers start: 153 outliers final: 126 residues processed: 374 average time/residue: 0.1407 time to fit residues: 88.4745 Evaluate side-chains 378 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 234 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 222 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 187 optimal weight: 0.0030 chunk 26 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.144068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.090574 restraints weight = 46487.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.093878 restraints weight = 22911.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.095974 restraints weight = 15113.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.097177 restraints weight = 11902.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.097743 restraints weight = 10455.008| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26272 Z= 0.181 Angle : 0.648 13.602 35897 Z= 0.309 Chirality : 0.047 0.388 4249 Planarity : 0.004 0.061 4522 Dihedral : 7.082 64.913 4880 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.27 % Favored : 89.41 % Rotamer: Outliers : 5.56 % Allowed : 31.31 % Favored : 63.13 % 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: -1.54 (0.15), residues: 3107 helix: 1.98 (0.21), residues: 656 sheet: -1.35 (0.22), residues: 536 loop : -2.14 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 34 TYR 0.024 0.001 TYR B 380 PHE 0.032 0.001 PHE B 192 TRP 0.024 0.001 TRP A 436 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00428 (26160) covalent geometry : angle 0.60983 (35606) SS BOND : bond 0.00331 ( 42) SS BOND : angle 1.21602 ( 84) hydrogen bonds : bond 0.04293 ( 812) hydrogen bonds : angle 5.19575 ( 2244) Misc. bond : bond 0.00022 ( 1) link_BETA1-4 : bond 0.00526 ( 27) link_BETA1-4 : angle 1.87865 ( 81) link_NAG-ASN : bond 0.00632 ( 42) link_NAG-ASN : angle 3.35338 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5067.30 seconds wall clock time: 88 minutes 12.35 seconds (5292.35 seconds total)