Starting phenix.real_space_refine on Sun Jul 5 08:19:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7df3_30660/07_2026/7df3_30660.cif Found real_map, /net/cci-nas-00/data/ceres_data/7df3_30660/07_2026/7df3_30660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7df3_30660/07_2026/7df3_30660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7df3_30660/07_2026/7df3_30660.map" model { file = "/net/cci-nas-00/data/ceres_data/7df3_30660/07_2026/7df3_30660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7df3_30660/07_2026/7df3_30660.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7df3_30660/07_2026/7df3_30660.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7df3_30660/07_2026/7df3_30660.cif" } resolution = 2.7 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= 0.003 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 120 5.16 5 C 16884 2.51 5 N 4341 2.21 5 O 5250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26595 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8501 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 4 Chain: "B" Number of atoms: 8501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8501 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 4 Chain: "C" Number of atoms: 8501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8501 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 4 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 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 chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" 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 chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.22, per 1000 atoms: 0.20 Number of scatterers: 26595 At special positions: 0 Unit cell: (145.86, 147.9, 174.42, 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 120 16.00 O 5250 8.00 N 4341 7.00 C 16884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.04 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 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 331 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 149 " " NAG A1310 " - " ASN A 61 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 331 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 149 " " NAG B1310 " - " ASN B 61 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 331 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 149 " " NAG C1310 " - " ASN C 61 " " NAG D 1 " - " ASN A1134 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 165 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A 17 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B 234 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 122 " " NAG S 1 " - " ASN B 17 " " NAG T 1 " - " ASN C1134 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C 234 " " NAG Y 1 " - " ASN C 165 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 17 " Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6108 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 51 sheets defined 23.3% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.641A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.664A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.570A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 783 " --> pdb=" O GLN A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 836 through 843 removed outlier: 3.713A pdb=" N ASP A 843 " --> pdb=" O ASP A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.503A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.769A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.645A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1031 removed outlier: 3.740A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.640A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.664A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.569A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 Processing helix chain 'B' and resid 836 through 843 removed outlier: 3.713A pdb=" N ASP B 843 " --> pdb=" O ASP B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.502A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.769A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.644A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1031 removed outlier: 3.740A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.640A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.664A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.569A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA C 783 " --> pdb=" O GLN C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 Processing helix chain 'C' and resid 836 through 843 removed outlier: 3.714A pdb=" N ASP C 843 " --> pdb=" O ASP C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.502A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.769A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.645A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1031 removed outlier: 3.740A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 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 48 through 55 removed outlier: 3.679A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.503A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.271A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 157 removed outlier: 3.654A pdb=" N SER A 155 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.260A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.662A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.858A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.831A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.169A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.189A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 807 through 808 removed outlier: 3.917A pdb=" N ARG A 815 " --> pdb=" O ASP A 808 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.679A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.502A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.271A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 154 through 157 removed outlier: 3.654A pdb=" N SER B 155 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.260A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.663A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.858A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.776A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.168A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 807 through 808 removed outlier: 3.917A pdb=" N ARG B 815 " --> pdb=" O ASP B 808 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.678A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.503A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.271A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 154 through 157 removed outlier: 3.654A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.261A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.663A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.858A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.168A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 807 through 808 removed outlier: 3.917A pdb=" N ARG C 815 " --> pdb=" O ASP C 808 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 959 hydrogen bonds defined for protein. 2616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.66 Time building geometry restraints manager: 3.02 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: 8428 1.34 - 1.46: 6524 1.46 - 1.58: 12075 1.58 - 1.70: 3 1.70 - 1.82: 150 Bond restraints: 27180 Sorted by residual: bond pdb=" C1 NAG R 1 " pdb=" C2 NAG R 1 " ideal model delta sigma weight residual 1.532 1.630 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C1 NAG Z 1 " pdb=" C2 NAG Z 1 " ideal model delta sigma weight residual 1.532 1.630 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C1 NAG J 1 " pdb=" C2 NAG J 1 " ideal model delta sigma weight residual 1.532 1.630 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.236 0.098 2.34e-02 1.83e+03 1.75e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.236 0.098 2.34e-02 1.83e+03 1.75e+01 ... (remaining 27175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 36309 2.33 - 4.67: 594 4.67 - 7.00: 57 7.00 - 9.34: 9 9.34 - 11.67: 6 Bond angle restraints: 36975 Sorted by residual: angle pdb=" N ASN C 234 " pdb=" CA ASN C 234 " pdb=" C ASN C 234 " ideal model delta sigma weight residual 109.59 102.06 7.53 1.61e+00 3.86e-01 2.19e+01 angle pdb=" N ASN A 234 " pdb=" CA ASN A 234 " pdb=" C ASN A 234 " ideal model delta sigma weight residual 109.59 102.07 7.52 1.61e+00 3.86e-01 2.18e+01 angle pdb=" N ASN B 234 " pdb=" CA ASN B 234 " pdb=" C ASN B 234 " ideal model delta sigma weight residual 109.59 102.07 7.52 1.61e+00 3.86e-01 2.18e+01 angle pdb=" C6 NAG T 2 " pdb=" C5 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 108.73 120.40 -11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C6 NAG D 2 " pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 108.73 120.40 -11.67 3.00e+00 1.11e-01 1.51e+01 ... (remaining 36970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15147 17.99 - 35.97: 318 35.97 - 53.96: 66 53.96 - 71.94: 27 71.94 - 89.93: 12 Dihedral angle restraints: 15570 sinusoidal: 6072 harmonic: 9498 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 150.40 -57.40 1 1.00e+01 1.00e-02 4.43e+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 93.00 150.40 -57.40 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 150.40 -57.40 1 1.00e+01 1.00e-02 4.43e+01 ... (remaining 15567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 4352 0.208 - 0.415: 40 0.415 - 0.623: 6 0.623 - 0.830: 0 0.830 - 1.038: 6 Chirality restraints: 4404 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.59e+01 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.49e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.42e+01 ... (remaining 4401 not shown) Planarity restraints: 4749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " 0.337 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG A1304 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " -0.503 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " -0.337 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG C1304 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " 0.503 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1304 " 0.337 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG B1304 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B1304 " 0.178 2.00e-02 2.50e+03 pdb=" N2 NAG B1304 " -0.502 2.00e-02 2.50e+03 pdb=" O7 NAG B1304 " 0.072 2.00e-02 2.50e+03 ... (remaining 4746 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 393 2.63 - 3.20: 24649 3.20 - 3.77: 42776 3.77 - 4.33: 60723 4.33 - 4.90: 97866 Nonbonded interactions: 226407 Sorted by model distance: nonbonded pdb=" O3 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.067 3.040 nonbonded pdb=" O3 NAG M 2 " pdb=" O7 NAG M 2 " model vdw 2.067 3.040 nonbonded pdb=" O3 NAG U 2 " pdb=" O7 NAG U 2 " model vdw 2.067 3.040 nonbonded pdb=" O3 NAG B1301 " pdb=" O7 NAG B1301 " model vdw 2.094 3.040 nonbonded pdb=" O3 NAG C1301 " pdb=" O7 NAG C1301 " model vdw 2.094 3.040 ... (remaining 226402 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.550 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 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 : 0.004 0.098 27300 Z= 0.219 Angle : 0.863 45.037 37293 Z= 0.396 Chirality : 0.069 1.038 4404 Planarity : 0.016 0.287 4695 Dihedral : 8.548 89.926 9336 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.47 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: -2.36 (0.12), residues: 3234 helix: -2.80 (0.13), residues: 729 sheet: -0.73 (0.18), residues: 570 loop : -1.30 (0.12), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 466 TYR 0.025 0.002 TYR A 508 PHE 0.023 0.002 PHE B 275 TRP 0.028 0.002 TRP A 64 HIS 0.011 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.22 (27180) covalent geometry : angle 0.69725 / 0.36 (36975) SS BOND : bond 0.00372 / 0.24 ( 42) SS BOND : angle 0.90591 / 0.58 ( 84) hydrogen bonds : bond 0.25871 / 17.08 ( 947) hydrogen bonds : angle 9.82238 / 6.89 ( 2616) link_BETA1-4 : bond 0.00349 / 0.25 ( 24) link_BETA1-4 : angle 2.13018 / 1.34 ( 72) link_NAG-ASN : bond 0.01466 / 0.90 ( 54) link_NAG-ASN : angle 7.62227 / 4.65 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 832 time to evaluate : 1.069 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 309 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6655 (mm-30) REVERT: A 772 VAL cc_start: 0.8657 (t) cc_final: 0.8395 (p) REVERT: A 955 ASN cc_start: 0.7620 (m-40) cc_final: 0.7418 (m-40) REVERT: B 88 ASP cc_start: 0.6566 (m-30) cc_final: 0.6326 (m-30) REVERT: B 111 ASP cc_start: 0.5447 (t0) cc_final: 0.5177 (t0) REVERT: B 271 GLN cc_start: 0.8219 (mt0) cc_final: 0.7985 (mt0) REVERT: B 309 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6350 (mp0) REVERT: B 772 VAL cc_start: 0.8848 (t) cc_final: 0.8594 (p) REVERT: B 1141 LEU cc_start: 0.7917 (tp) cc_final: 0.7696 (mt) REVERT: C 309 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6792 (mp0) REVERT: C 1101 HIS cc_start: 0.7172 (m90) cc_final: 0.6941 (m170) REVERT: C 1141 LEU cc_start: 0.7828 (tp) cc_final: 0.7624 (mt) outliers start: 0 outliers final: 3 residues processed: 832 average time/residue: 0.6048 time to fit residues: 593.2811 Evaluate side-chains 415 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 412 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain C residue 294 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 185 ASN A 196 ASN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 474 GLN A 487 ASN A 580 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 969 ASN A1010 GLN A1119 ASN A1135 ASN B 99 ASN B 115 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 493 GLN B 613 GLN B 641 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 969 ASN B1010 GLN B1119 ASN B1135 ASN C 99 ASN C 115 GLN C 185 ASN ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 675 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN C1083 HIS C1119 ASN C1135 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130464 restraints weight = 33116.188| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.08 r_work: 0.3421 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27300 Z= 0.225 Angle : 0.811 16.927 37293 Z= 0.400 Chirality : 0.053 0.587 4404 Planarity : 0.005 0.056 4695 Dihedral : 5.611 28.070 3507 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.25 % Favored : 96.57 % Rotamer: Outliers : 3.98 % Allowed : 11.30 % Favored : 84.72 % 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 (0.13), residues: 3234 helix: -0.62 (0.17), residues: 738 sheet: -0.48 (0.17), residues: 711 loop : -1.31 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 466 TYR 0.032 0.002 TYR B 200 PHE 0.023 0.003 PHE B 347 TRP 0.025 0.002 TRP C 64 HIS 0.006 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (27180) covalent geometry : angle 0.76987 / 0.39 (36975) SS BOND : bond 0.00514 / 0.36 ( 42) SS BOND : angle 1.85947 / 1.24 ( 84) hydrogen bonds : bond 0.05329 / 3.56 ( 947) hydrogen bonds : angle 6.45696 / 4.56 ( 2616) link_BETA1-4 : bond 0.00660 / 0.39 ( 24) link_BETA1-4 : angle 1.85749 / 1.20 ( 72) link_NAG-ASN : bond 0.00976 / 0.73 ( 54) link_NAG-ASN : angle 3.58228 / 2.32 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 408 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.6598 (t0) cc_final: 0.6340 (t70) REVERT: A 113 LYS cc_start: 0.7839 (mttt) cc_final: 0.6773 (mmpt) REVERT: A 207 HIS cc_start: 0.7139 (t70) cc_final: 0.5312 (m170) REVERT: A 493 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: A 516 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6116 (tm-30) REVERT: A 787 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7945 (mm-40) REVERT: A 957 GLN cc_start: 0.8637 (tt0) cc_final: 0.8414 (tt0) REVERT: A 977 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8750 (tp) REVERT: A 988 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7085 (tp30) REVERT: A 1086 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7713 (ptmt) REVERT: B 88 ASP cc_start: 0.7175 (m-30) cc_final: 0.6880 (m-30) REVERT: B 111 ASP cc_start: 0.6328 (t0) cc_final: 0.6067 (t0) REVERT: B 113 LYS cc_start: 0.7580 (mttt) cc_final: 0.6635 (mmpt) REVERT: B 271 GLN cc_start: 0.8632 (mt0) cc_final: 0.8360 (mt0) REVERT: B 309 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7369 (mp0) REVERT: B 326 ILE cc_start: 0.7914 (mm) cc_final: 0.7387 (pt) REVERT: B 378 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8286 (tptp) REVERT: B 487 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7450 (t0) REVERT: B 646 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7602 (mtp85) REVERT: B 954 GLN cc_start: 0.8275 (mt0) cc_final: 0.7621 (pt0) REVERT: B 988 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7238 (tp30) REVERT: B 1086 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7880 (ptmt) REVERT: C 111 ASP cc_start: 0.6324 (t0) cc_final: 0.6098 (t0) REVERT: C 113 LYS cc_start: 0.7673 (mttt) cc_final: 0.6855 (mmpt) REVERT: C 309 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7370 (mp0) REVERT: C 408 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.6351 (ptt90) REVERT: C 440 ASN cc_start: 0.7834 (p0) cc_final: 0.7577 (m110) REVERT: C 444 LYS cc_start: 0.6766 (pttt) cc_final: 0.6361 (ptpt) REVERT: C 505 TYR cc_start: 0.7910 (t80) cc_final: 0.7347 (m-80) REVERT: C 572 THR cc_start: 0.8682 (p) cc_final: 0.8222 (t) REVERT: C 646 ARG cc_start: 0.7798 (mtp180) cc_final: 0.7341 (ttp-110) REVERT: C 1072 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: C 1086 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7900 (ptmt) outliers start: 113 outliers final: 25 residues processed: 486 average time/residue: 0.6207 time to fit residues: 354.3985 Evaluate side-chains 358 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 323 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1086 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 209 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 280 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN A 245 HIS A 394 ASN A 675 GLN A 872 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 955 ASN A1010 GLN A1119 ASN B 146 HIS B 245 HIS B 314 GLN B 487 ASN B 580 GLN B 675 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 245 HIS C 394 ASN C 580 GLN C 675 GLN C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.150359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124492 restraints weight = 33208.281| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.07 r_work: 0.3345 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 27300 Z= 0.204 Angle : 0.714 13.680 37293 Z= 0.358 Chirality : 0.047 0.474 4404 Planarity : 0.004 0.041 4695 Dihedral : 5.417 28.438 3501 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.36 % Favored : 95.55 % Rotamer: Outliers : 3.70 % Allowed : 13.09 % Favored : 83.21 % 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: -1.13 (0.13), residues: 3234 helix: 0.12 (0.18), residues: 705 sheet: -0.51 (0.17), residues: 687 loop : -1.19 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 765 TYR 0.026 0.002 TYR B 200 PHE 0.025 0.002 PHE B 643 TRP 0.026 0.002 TRP C 64 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (27180) covalent geometry : angle 0.68298 / 0.35 (36975) SS BOND : bond 0.00601 / 0.38 ( 42) SS BOND : angle 1.88309 / 1.19 ( 84) hydrogen bonds : bond 0.04923 / 3.29 ( 947) hydrogen bonds : angle 6.18496 / 4.37 ( 2616) link_BETA1-4 : bond 0.00560 / 0.37 ( 24) link_BETA1-4 : angle 1.80592 / 1.18 ( 72) link_NAG-ASN : bond 0.00588 / 0.44 ( 54) link_NAG-ASN : angle 2.78512 / 1.82 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 343 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.6712 (t0) cc_final: 0.6423 (t70) REVERT: A 113 LYS cc_start: 0.7896 (mttt) cc_final: 0.6596 (mmpt) REVERT: A 207 HIS cc_start: 0.7667 (t70) cc_final: 0.5585 (m170) REVERT: A 370 ASN cc_start: 0.6862 (m-40) cc_final: 0.6640 (m-40) REVERT: A 487 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7485 (t0) REVERT: A 493 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: A 516 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6324 (tm-30) REVERT: A 787 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7881 (mm-40) REVERT: A 921 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7718 (tppt) REVERT: A 935 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6428 (mp10) REVERT: A 957 GLN cc_start: 0.8638 (tt0) cc_final: 0.8413 (tt0) REVERT: A 977 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8689 (tp) REVERT: A 988 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7398 (tp30) REVERT: A 1086 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7795 (ptmt) REVERT: B 111 ASP cc_start: 0.6551 (t0) cc_final: 0.6349 (t0) REVERT: B 113 LYS cc_start: 0.7793 (mttt) cc_final: 0.6897 (mmpt) REVERT: B 271 GLN cc_start: 0.8668 (mt0) cc_final: 0.8449 (mt0) REVERT: B 378 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8280 (tptp) REVERT: B 487 ASN cc_start: 0.8256 (m-40) cc_final: 0.7633 (t0) REVERT: B 516 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6946 (tm-30) REVERT: B 646 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7526 (mtp85) REVERT: B 922 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8552 (tp) REVERT: B 988 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7479 (tp30) REVERT: B 1086 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7841 (ptmt) REVERT: C 113 LYS cc_start: 0.7819 (mttt) cc_final: 0.7001 (mmpt) REVERT: C 326 ILE cc_start: 0.7743 (mm) cc_final: 0.7480 (pt) REVERT: C 408 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.6326 (ptt90) REVERT: C 440 ASN cc_start: 0.7827 (p0) cc_final: 0.7564 (m-40) REVERT: C 444 LYS cc_start: 0.6860 (pttt) cc_final: 0.6431 (ptpt) REVERT: C 505 TYR cc_start: 0.8059 (t80) cc_final: 0.7555 (m-80) REVERT: C 569 ILE cc_start: 0.8277 (tp) cc_final: 0.7946 (pp) REVERT: C 572 THR cc_start: 0.8711 (p) cc_final: 0.8327 (t) REVERT: C 646 ARG cc_start: 0.7853 (mtp180) cc_final: 0.7503 (mtm-85) REVERT: C 935 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6592 (mp10) REVERT: C 1019 ARG cc_start: 0.8453 (ttp-110) cc_final: 0.8107 (ttp-110) REVERT: C 1072 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7884 (pm20) REVERT: C 1086 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7895 (ptmt) REVERT: C 1113 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8089 (mt0) outliers start: 105 outliers final: 40 residues processed: 419 average time/residue: 0.6272 time to fit residues: 309.3774 Evaluate side-chains 349 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 294 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 239 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 211 optimal weight: 0.6980 chunk 259 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 253 optimal weight: 0.9990 chunk 260 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS A 675 GLN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1010 GLN A1119 ASN B 440 ASN B 675 GLN B 901 GLN B 954 GLN B 957 GLN C 314 GLN C 394 ASN C 675 GLN C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.149741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.124035 restraints weight = 32861.840| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.05 r_work: 0.3327 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 27300 Z= 0.182 Angle : 0.677 11.446 37293 Z= 0.341 Chirality : 0.049 0.699 4404 Planarity : 0.004 0.051 4695 Dihedral : 5.304 29.717 3501 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 4.22 % Allowed : 12.67 % Favored : 83.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.13), residues: 3234 helix: 0.41 (0.19), residues: 717 sheet: -0.56 (0.17), residues: 693 loop : -1.07 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 765 TYR 0.025 0.002 TYR B 200 PHE 0.019 0.002 PHE C 906 TRP 0.023 0.002 TRP C 64 HIS 0.005 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (27180) covalent geometry : angle 0.65068 / 0.33 (36975) SS BOND : bond 0.00437 / 0.33 ( 42) SS BOND : angle 1.93092 / 1.23 ( 84) hydrogen bonds : bond 0.04414 / 2.96 ( 947) hydrogen bonds : angle 6.03993 / 4.26 ( 2616) link_BETA1-4 : bond 0.00537 / 0.36 ( 24) link_BETA1-4 : angle 1.77965 / 1.16 ( 72) link_NAG-ASN : bond 0.00508 / 0.41 ( 54) link_NAG-ASN : angle 2.38036 / 1.60 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 340 time to evaluate : 1.032 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 113 LYS cc_start: 0.7980 (mttt) cc_final: 0.7327 (mtmm) REVERT: A 200 TYR cc_start: 0.7637 (OUTLIER) cc_final: 0.7170 (m-80) REVERT: A 207 HIS cc_start: 0.8004 (t70) cc_final: 0.5873 (m170) REVERT: A 370 ASN cc_start: 0.7025 (m-40) cc_final: 0.6710 (m-40) REVERT: A 487 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7707 (t0) REVERT: A 516 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6569 (tm-30) REVERT: A 554 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7576 (mt-10) REVERT: A 787 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7876 (mm-40) REVERT: A 935 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6214 (mp10) REVERT: A 957 GLN cc_start: 0.8654 (tt0) cc_final: 0.8421 (tt0) REVERT: A 977 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8710 (tp) REVERT: A 988 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7462 (tp30) REVERT: A 1086 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7803 (ptmt) REVERT: B 113 LYS cc_start: 0.7781 (mttt) cc_final: 0.6937 (mmpt) REVERT: B 271 GLN cc_start: 0.8672 (mt0) cc_final: 0.8461 (mt0) REVERT: B 378 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8327 (tptp) REVERT: B 427 ASP cc_start: 0.7969 (m-30) cc_final: 0.7759 (m-30) REVERT: B 487 ASN cc_start: 0.8287 (m-40) cc_final: 0.7654 (t0) REVERT: B 572 THR cc_start: 0.8627 (p) cc_final: 0.8246 (t) REVERT: B 646 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7531 (mtp85) REVERT: B 814 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7088 (mttp) REVERT: B 922 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8519 (tp) REVERT: B 988 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7564 (tp30) REVERT: B 1086 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7806 (ptmt) REVERT: B 1113 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8061 (mt0) REVERT: B 1122 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8603 (m) REVERT: C 113 LYS cc_start: 0.7921 (mttt) cc_final: 0.7071 (mmpt) REVERT: C 200 TYR cc_start: 0.7580 (m-80) cc_final: 0.7333 (m-80) REVERT: C 408 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.6287 (ptt90) REVERT: C 444 LYS cc_start: 0.6828 (pttt) cc_final: 0.6424 (ptpt) REVERT: C 505 TYR cc_start: 0.7986 (t80) cc_final: 0.7454 (m-80) REVERT: C 516 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: C 572 THR cc_start: 0.8639 (p) cc_final: 0.8320 (t) REVERT: C 646 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7473 (mtm-85) REVERT: C 1019 ARG cc_start: 0.8455 (ttp-110) cc_final: 0.8080 (ttp-110) REVERT: C 1072 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7974 (pm20) REVERT: C 1086 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7880 (ptmt) REVERT: C 1113 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8125 (mt0) outliers start: 120 outliers final: 46 residues processed: 421 average time/residue: 0.4155 time to fit residues: 206.4215 Evaluate side-chains 365 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 301 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 263 optimal weight: 0.0870 chunk 309 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 295 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 675 GLN A 764 ASN A 872 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 955 ASN A1010 GLN B 30 ASN B 644 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN B 954 GLN B 957 GLN C 440 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 957 GLN C1119 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.149389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.123916 restraints weight = 32677.521| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.04 r_work: 0.3326 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 27300 Z= 0.163 Angle : 0.647 10.055 37293 Z= 0.327 Chirality : 0.048 0.703 4404 Planarity : 0.004 0.065 4695 Dihedral : 5.197 28.474 3501 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.99 % Favored : 95.83 % Rotamer: Outliers : 3.98 % Allowed : 13.62 % Favored : 82.40 % Cbeta Deviations : 0.07 % 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: -0.84 (0.13), residues: 3234 helix: 0.62 (0.19), residues: 717 sheet: -0.67 (0.17), residues: 693 loop : -0.97 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.024 0.002 TYR B 200 PHE 0.025 0.002 PHE B 643 TRP 0.021 0.002 TRP B 64 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (27180) covalent geometry : angle 0.62153 / 0.32 (36975) SS BOND : bond 0.00447 / 0.32 ( 42) SS BOND : angle 1.94918 / 1.22 ( 84) hydrogen bonds : bond 0.04233 / 2.83 ( 947) hydrogen bonds : angle 5.91220 / 4.17 ( 2616) link_BETA1-4 : bond 0.00499 / 0.33 ( 24) link_BETA1-4 : angle 1.78958 / 1.17 ( 72) link_NAG-ASN : bond 0.00315 / 0.23 ( 54) link_NAG-ASN : angle 2.21011 / 1.48 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 328 time to evaluate : 1.038 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 207 HIS cc_start: 0.8028 (t70) cc_final: 0.5863 (m-70) REVERT: A 370 ASN cc_start: 0.7103 (m-40) cc_final: 0.6746 (m-40) REVERT: A 461 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7397 (pp) REVERT: A 554 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: A 787 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7866 (mm-40) REVERT: A 977 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8703 (tp) REVERT: A 988 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7466 (tp30) REVERT: A 1086 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7798 (ptmt) REVERT: B 113 LYS cc_start: 0.7751 (mttt) cc_final: 0.6971 (mmpt) REVERT: B 378 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8341 (tptp) REVERT: B 487 ASN cc_start: 0.8308 (m-40) cc_final: 0.7739 (t0) REVERT: B 572 THR cc_start: 0.8648 (p) cc_final: 0.8323 (t) REVERT: B 646 ARG cc_start: 0.7798 (mtm-85) cc_final: 0.7546 (mtp85) REVERT: B 814 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7074 (mttp) REVERT: B 922 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8516 (tp) REVERT: B 1086 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7896 (ptmt) REVERT: B 1113 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8047 (mt0) REVERT: C 113 LYS cc_start: 0.8033 (mttt) cc_final: 0.7181 (mmpt) REVERT: C 200 TYR cc_start: 0.7810 (m-80) cc_final: 0.7483 (m-80) REVERT: C 408 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.6287 (ptt90) REVERT: C 444 LYS cc_start: 0.6827 (pttt) cc_final: 0.6451 (ptpt) REVERT: C 505 TYR cc_start: 0.7971 (t80) cc_final: 0.7446 (m-80) REVERT: C 516 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6937 (tm-30) REVERT: C 569 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7760 (pp) REVERT: C 572 THR cc_start: 0.8644 (p) cc_final: 0.8361 (t) REVERT: C 646 ARG cc_start: 0.7741 (mtp180) cc_final: 0.7408 (mtm-85) REVERT: C 1019 ARG cc_start: 0.8479 (ttp-110) cc_final: 0.8081 (ttp-110) REVERT: C 1086 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7841 (ptmt) REVERT: C 1113 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8145 (mt0) outliers start: 113 outliers final: 48 residues processed: 408 average time/residue: 0.6090 time to fit residues: 291.7925 Evaluate side-chains 363 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 301 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 255 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 240 optimal weight: 0.0470 chunk 172 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 194 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 274 optimal weight: 0.0970 chunk 297 optimal weight: 0.6980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN A 487 ASN A 644 GLN A 675 GLN A 804 GLN A 872 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 675 GLN B 913 GLN B 954 GLN B 957 GLN B 965 GLN C 487 ASN C 644 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1119 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.149366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.123895 restraints weight = 33165.997| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.06 r_work: 0.3336 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 27300 Z= 0.142 Angle : 0.625 10.270 37293 Z= 0.316 Chirality : 0.046 0.585 4404 Planarity : 0.004 0.058 4695 Dihedral : 5.082 27.016 3501 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.74 % Favored : 96.07 % Rotamer: Outliers : 3.45 % Allowed : 14.50 % Favored : 82.05 % Cbeta Deviations : 0.10 % 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: -0.72 (0.14), residues: 3234 helix: 0.71 (0.19), residues: 723 sheet: -0.47 (0.18), residues: 618 loop : -0.95 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 357 TYR 0.026 0.001 TYR A 200 PHE 0.026 0.001 PHE B 643 TRP 0.020 0.002 TRP B 64 HIS 0.006 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (27180) covalent geometry : angle 0.60085 / 0.31 (36975) SS BOND : bond 0.00403 / 0.30 ( 42) SS BOND : angle 1.98801 / 1.32 ( 84) hydrogen bonds : bond 0.04029 / 2.69 ( 947) hydrogen bonds : angle 5.82323 / 4.11 ( 2616) link_BETA1-4 : bond 0.00508 / 0.34 ( 24) link_BETA1-4 : angle 1.76089 / 1.16 ( 72) link_NAG-ASN : bond 0.00375 / 0.24 ( 54) link_NAG-ASN : angle 2.02718 / 1.38 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 321 time to evaluate : 0.982 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 113 LYS cc_start: 0.8349 (mtmm) cc_final: 0.7235 (mmpt) REVERT: A 200 TYR cc_start: 0.7846 (t80) cc_final: 0.7408 (t80) REVERT: A 207 HIS cc_start: 0.8039 (t70) cc_final: 0.5852 (m-70) REVERT: A 370 ASN cc_start: 0.7109 (m-40) cc_final: 0.6747 (m-40) REVERT: A 487 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.7778 (t0) REVERT: A 505 TYR cc_start: 0.8344 (m-10) cc_final: 0.7470 (t80) REVERT: A 516 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6286 (tm-30) REVERT: A 787 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7859 (mm-40) REVERT: A 977 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8677 (tp) REVERT: A 988 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7477 (tp30) REVERT: A 1086 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7670 (ptmt) REVERT: B 101 ILE cc_start: 0.8054 (mm) cc_final: 0.7692 (mp) REVERT: B 113 LYS cc_start: 0.7768 (mttt) cc_final: 0.6988 (mmpt) REVERT: B 378 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8356 (tptp) REVERT: B 408 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.7023 (ppt90) REVERT: B 487 ASN cc_start: 0.8274 (m-40) cc_final: 0.7677 (t0) REVERT: B 505 TYR cc_start: 0.8054 (t80) cc_final: 0.7849 (t80) REVERT: B 569 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7665 (pp) REVERT: B 572 THR cc_start: 0.8673 (p) cc_final: 0.8337 (t) REVERT: B 646 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7577 (mtp85) REVERT: B 814 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7062 (mttp) REVERT: B 922 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8516 (tp) REVERT: B 973 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8137 (tp) REVERT: B 1113 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8028 (mt0) REVERT: C 113 LYS cc_start: 0.8023 (mttt) cc_final: 0.7181 (mmpt) REVERT: C 153 MET cc_start: 0.6441 (OUTLIER) cc_final: 0.5220 (pmt) REVERT: C 200 TYR cc_start: 0.7971 (m-80) cc_final: 0.7622 (m-80) REVERT: C 408 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.6281 (ptt90) REVERT: C 444 LYS cc_start: 0.6708 (pttt) cc_final: 0.6371 (ptpt) REVERT: C 505 TYR cc_start: 0.7939 (t80) cc_final: 0.7301 (m-80) REVERT: C 569 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7701 (pp) REVERT: C 572 THR cc_start: 0.8637 (p) cc_final: 0.8360 (t) REVERT: C 646 ARG cc_start: 0.7714 (mtp180) cc_final: 0.7388 (mtm-85) REVERT: C 660 TYR cc_start: 0.8777 (m-10) cc_final: 0.8481 (m-80) REVERT: C 1019 ARG cc_start: 0.8411 (ttp-110) cc_final: 0.7996 (ttp-110) REVERT: C 1113 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8172 (mt0) outliers start: 98 outliers final: 43 residues processed: 394 average time/residue: 0.5906 time to fit residues: 273.6239 Evaluate side-chains 355 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 297 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 229 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 675 GLN A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 955 ASN A1071 GLN B 137 ASN B 188 ASN B 675 GLN B 872 GLN B 954 GLN B 957 GLN C 137 ASN C 188 ASN C 487 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN C1119 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.140352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114250 restraints weight = 32941.652| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.06 r_work: 0.3207 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 27300 Z= 0.300 Angle : 0.777 11.564 37293 Z= 0.395 Chirality : 0.050 0.606 4404 Planarity : 0.005 0.068 4695 Dihedral : 5.709 32.555 3501 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.61 % Favored : 95.18 % Rotamer: Outliers : 4.08 % Allowed : 14.57 % Favored : 81.34 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 3234 helix: 0.37 (0.19), residues: 720 sheet: -0.53 (0.19), residues: 591 loop : -1.09 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 273 TYR 0.033 0.003 TYR A 200 PHE 0.029 0.003 PHE A 759 TRP 0.031 0.003 TRP C 64 HIS 0.010 0.003 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.30 (27180) covalent geometry : angle 0.75134 / 0.39 (36975) SS BOND : bond 0.00595 / 0.41 ( 42) SS BOND : angle 2.57877 / 1.66 ( 84) hydrogen bonds : bond 0.04985 / 3.32 ( 947) hydrogen bonds : angle 6.16217 / 4.36 ( 2616) link_BETA1-4 : bond 0.00499 / 0.35 ( 24) link_BETA1-4 : angle 2.00965 / 1.33 ( 72) link_NAG-ASN : bond 0.00511 / 0.32 ( 54) link_NAG-ASN : angle 2.24767 / 1.61 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 322 time to evaluate : 1.151 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 214 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7642 (ptp-170) REVERT: A 505 TYR cc_start: 0.8448 (m-10) cc_final: 0.7579 (t80) REVERT: A 787 GLN cc_start: 0.8438 (mm-40) cc_final: 0.7996 (mm-40) REVERT: A 935 GLN cc_start: 0.7345 (mt0) cc_final: 0.7066 (mt0) REVERT: A 977 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8757 (tp) REVERT: A 988 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7504 (tp30) REVERT: A 1045 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7836 (ptmm) REVERT: A 1086 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7830 (ptmt) REVERT: B 113 LYS cc_start: 0.8098 (mttt) cc_final: 0.7217 (mmpt) REVERT: B 231 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8244 (pp) REVERT: B 408 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.7134 (ptt90) REVERT: B 427 ASP cc_start: 0.8239 (m-30) cc_final: 0.8007 (t0) REVERT: B 487 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7700 (t0) REVERT: B 516 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: B 569 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7715 (OUTLIER) REVERT: B 572 THR cc_start: 0.8657 (p) cc_final: 0.8336 (t) REVERT: B 646 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7549 (mtp85) REVERT: B 814 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7124 (mttp) REVERT: B 1086 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7958 (ptmt) REVERT: B 1113 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8174 (mt0) REVERT: C 111 ASP cc_start: 0.6668 (t0) cc_final: 0.6402 (t0) REVERT: C 408 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.6473 (ptt90) REVERT: C 444 LYS cc_start: 0.7189 (pttt) cc_final: 0.6799 (ptmt) REVERT: C 516 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: C 569 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7974 (pp) REVERT: C 572 THR cc_start: 0.8639 (p) cc_final: 0.8380 (t) REVERT: C 646 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7368 (mtm-85) REVERT: C 1019 ARG cc_start: 0.8533 (ttp-110) cc_final: 0.8316 (ttp-110) REVERT: C 1091 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7678 (mtt-85) REVERT: C 1113 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8266 (mt0) outliers start: 116 outliers final: 46 residues processed: 402 average time/residue: 0.6180 time to fit residues: 291.0137 Evaluate side-chains 345 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 282 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1086 LYS 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 B residue 42 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 230 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 269 optimal weight: 2.9990 chunk 280 optimal weight: 0.6980 chunk 279 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 291 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN A 487 ASN A 675 GLN A 872 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 955 ASN A1119 ASN B 460 ASN B 675 GLN B 872 GLN B 957 GLN C 173 GLN C 460 ASN C 487 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.117502 restraints weight = 32984.819| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.06 r_work: 0.3251 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 27300 Z= 0.188 Angle : 0.734 17.111 37293 Z= 0.369 Chirality : 0.049 0.738 4404 Planarity : 0.004 0.079 4695 Dihedral : 5.533 33.181 3501 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.33 % Favored : 95.49 % Rotamer: Outliers : 3.34 % Allowed : 15.95 % Favored : 80.71 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.13), residues: 3234 helix: 0.54 (0.19), residues: 723 sheet: -0.74 (0.18), residues: 588 loop : -0.98 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 357 TYR 0.017 0.002 TYR C 28 PHE 0.019 0.002 PHE A 643 TRP 0.023 0.002 TRP C 64 HIS 0.007 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (27180) covalent geometry : angle 0.69346 / 0.36 (36975) SS BOND : bond 0.00483 / 0.33 ( 42) SS BOND : angle 3.89776 / 2.57 ( 84) hydrogen bonds : bond 0.04306 / 2.87 ( 947) hydrogen bonds : angle 6.01204 / 4.24 ( 2616) link_BETA1-4 : bond 0.00490 / 0.34 ( 24) link_BETA1-4 : angle 1.90764 / 1.26 ( 72) link_NAG-ASN : bond 0.00461 / 0.30 ( 54) link_NAG-ASN : angle 2.18973 / 1.54 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 301 time to evaluate : 1.065 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 505 TYR cc_start: 0.8361 (m-10) cc_final: 0.7492 (t80) REVERT: A 787 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7979 (mm-40) REVERT: A 935 GLN cc_start: 0.7170 (mt0) cc_final: 0.6918 (mt0) REVERT: A 977 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8655 (tp) REVERT: A 988 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7513 (tp30) REVERT: A 1045 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7775 (ptmm) REVERT: B 113 LYS cc_start: 0.8126 (mttt) cc_final: 0.7246 (mmpt) REVERT: B 118 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8939 (tp) REVERT: B 231 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8017 (pp) REVERT: B 408 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.7058 (ppt90) REVERT: B 427 ASP cc_start: 0.8097 (m-30) cc_final: 0.7826 (t0) REVERT: B 487 ASN cc_start: 0.8176 (m-40) cc_final: 0.7617 (t0) REVERT: B 524 VAL cc_start: 0.8679 (t) cc_final: 0.8373 (t) REVERT: B 569 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7631 (OUTLIER) REVERT: B 572 THR cc_start: 0.8674 (p) cc_final: 0.8335 (t) REVERT: B 646 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.7576 (mtp85) REVERT: B 814 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7053 (mttp) REVERT: B 922 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8696 (tp) REVERT: B 973 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8356 (tp) REVERT: B 1113 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8087 (mt0) REVERT: C 111 ASP cc_start: 0.6639 (t0) cc_final: 0.6379 (t0) REVERT: C 389 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.6934 (p0) REVERT: C 408 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.6355 (ptt90) REVERT: C 444 LYS cc_start: 0.7088 (pttt) cc_final: 0.6660 (ptmt) REVERT: C 461 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8076 (pp) REVERT: C 487 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.7795 (t0) REVERT: C 505 TYR cc_start: 0.8110 (t80) cc_final: 0.7419 (m-80) REVERT: C 516 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7403 (tt0) REVERT: C 569 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7866 (pp) REVERT: C 572 THR cc_start: 0.8611 (p) cc_final: 0.8339 (t) REVERT: C 646 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7318 (ttp-110) REVERT: C 1113 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8177 (mt0) outliers start: 95 outliers final: 44 residues processed: 367 average time/residue: 0.6089 time to fit residues: 262.7234 Evaluate side-chains 343 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 282 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 265 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 181 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN A 487 ASN A 675 GLN A 872 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 955 ASN A1119 ASN B 675 GLN B 872 GLN B 957 GLN C 487 ASN C 613 GLN C 675 GLN C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.143678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118077 restraints weight = 33200.686| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.06 r_work: 0.3254 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 27300 Z= 0.183 Angle : 0.735 15.610 37293 Z= 0.368 Chirality : 0.050 0.843 4404 Planarity : 0.004 0.074 4695 Dihedral : 5.494 34.582 3501 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.39 % Favored : 95.42 % Rotamer: Outliers : 3.06 % Allowed : 16.47 % Favored : 80.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.14), residues: 3234 helix: 0.55 (0.19), residues: 744 sheet: -0.64 (0.18), residues: 588 loop : -1.00 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1091 TYR 0.019 0.002 TYR B 505 PHE 0.029 0.002 PHE C 486 TRP 0.023 0.002 TRP A 64 HIS 0.008 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (27180) covalent geometry : angle 0.69167 / 0.35 (36975) SS BOND : bond 0.00477 / 0.32 ( 42) SS BOND : angle 3.84429 / 2.56 ( 84) hydrogen bonds : bond 0.04242 / 2.84 ( 947) hydrogen bonds : angle 5.98652 / 4.26 ( 2616) link_BETA1-4 : bond 0.00466 / 0.31 ( 24) link_BETA1-4 : angle 1.86413 / 1.22 ( 72) link_NAG-ASN : bond 0.00767 / 0.36 ( 54) link_NAG-ASN : angle 2.42682 / 1.67 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 296 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.5565 (pmt) REVERT: A 505 TYR cc_start: 0.8419 (m-10) cc_final: 0.7566 (t80) REVERT: A 787 GLN cc_start: 0.8419 (mm-40) cc_final: 0.7983 (mm-40) REVERT: A 918 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: A 977 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8623 (tp) REVERT: A 988 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7576 (tp30) REVERT: B 113 LYS cc_start: 0.8184 (mttt) cc_final: 0.7269 (mmpt) REVERT: B 231 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.7999 (pp) REVERT: B 408 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.6931 (ppt90) REVERT: B 427 ASP cc_start: 0.8047 (m-30) cc_final: 0.7798 (t0) REVERT: B 487 ASN cc_start: 0.8174 (m-40) cc_final: 0.7623 (t0) REVERT: B 505 TYR cc_start: 0.8280 (t80) cc_final: 0.8063 (t80) REVERT: B 524 VAL cc_start: 0.8681 (t) cc_final: 0.8391 (t) REVERT: B 569 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7599 (OUTLIER) REVERT: B 572 THR cc_start: 0.8681 (p) cc_final: 0.8353 (t) REVERT: B 646 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7595 (mtp85) REVERT: B 814 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7079 (mttp) REVERT: B 973 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8327 (tp) REVERT: B 1086 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7851 (ptmt) REVERT: B 1113 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8057 (mt0) REVERT: C 111 ASP cc_start: 0.6707 (t0) cc_final: 0.6448 (t0) REVERT: C 408 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.6310 (ptt90) REVERT: C 444 LYS cc_start: 0.7073 (pttt) cc_final: 0.6651 (ptmt) REVERT: C 461 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8022 (pp) REVERT: C 487 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.7872 (t0) REVERT: C 516 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: C 569 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7840 (pp) REVERT: C 572 THR cc_start: 0.8631 (p) cc_final: 0.8369 (t) REVERT: C 646 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7344 (ttp-110) REVERT: C 1113 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8154 (mt0) outliers start: 87 outliers final: 51 residues processed: 357 average time/residue: 0.5945 time to fit residues: 250.0534 Evaluate side-chains 346 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 279 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 278 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 296 optimal weight: 0.0970 chunk 46 optimal weight: 0.9990 chunk 5 optimal weight: 0.0670 chunk 264 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 283 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN A 487 ASN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1119 ASN B 370 ASN B 675 GLN B 690 GLN B 872 GLN B 957 GLN C 487 ASN C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.146314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120973 restraints weight = 33037.942| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.05 r_work: 0.3283 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27300 Z= 0.157 Angle : 0.712 17.417 37293 Z= 0.357 Chirality : 0.049 0.841 4404 Planarity : 0.004 0.077 4695 Dihedral : 5.405 34.441 3501 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.33 % Favored : 95.49 % Rotamer: Outliers : 2.71 % Allowed : 17.00 % Favored : 80.29 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.83 (0.14), residues: 3234 helix: 0.59 (0.19), residues: 741 sheet: -0.63 (0.19), residues: 585 loop : -0.97 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1091 TYR 0.016 0.002 TYR A 660 PHE 0.023 0.002 PHE C 486 TRP 0.023 0.002 TRP B 152 HIS 0.007 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (27180) covalent geometry : angle 0.66793 / 0.34 (36975) SS BOND : bond 0.00451 / 0.28 ( 42) SS BOND : angle 3.85323 / 2.49 ( 84) hydrogen bonds : bond 0.04085 / 2.74 ( 947) hydrogen bonds : angle 5.91523 / 4.18 ( 2616) link_BETA1-4 : bond 0.00462 / 0.32 ( 24) link_BETA1-4 : angle 1.78060 / 1.17 ( 72) link_NAG-ASN : bond 0.00738 / 0.40 ( 54) link_NAG-ASN : angle 2.40803 / 1.65 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 292 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: 0.4603 (OUTLIER) cc_final: 0.4249 (m-70) REVERT: A 505 TYR cc_start: 0.8386 (m-10) cc_final: 0.7519 (t80) REVERT: A 516 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7215 (tt0) REVERT: A 787 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7973 (mm-40) REVERT: A 977 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8657 (tp) REVERT: A 988 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7608 (tp30) REVERT: B 113 LYS cc_start: 0.8190 (mttt) cc_final: 0.7303 (mmpt) REVERT: B 118 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8883 (tp) REVERT: B 231 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8001 (pp) REVERT: B 408 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.6966 (ppt90) REVERT: B 427 ASP cc_start: 0.7940 (m-30) cc_final: 0.7732 (t0) REVERT: B 487 ASN cc_start: 0.8211 (m-40) cc_final: 0.7652 (t0) REVERT: B 505 TYR cc_start: 0.8321 (t80) cc_final: 0.8110 (t80) REVERT: B 524 VAL cc_start: 0.8565 (t) cc_final: 0.8298 (t) REVERT: B 569 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7698 (pp) REVERT: B 572 THR cc_start: 0.8681 (p) cc_final: 0.8363 (t) REVERT: B 814 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6945 (mttp) REVERT: B 973 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8221 (tp) REVERT: B 1086 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7855 (ptmt) REVERT: B 1113 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8045 (mt0) REVERT: C 111 ASP cc_start: 0.6720 (t0) cc_final: 0.6459 (t0) REVERT: C 408 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.6252 (ptt90) REVERT: C 444 LYS cc_start: 0.6937 (pttt) cc_final: 0.6583 (ptmt) REVERT: C 461 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7958 (pp) REVERT: C 487 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7729 (t0) REVERT: C 516 GLU cc_start: 0.7306 (tm-30) cc_final: 0.7067 (tt0) REVERT: C 569 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7797 (pp) REVERT: C 572 THR cc_start: 0.8620 (p) cc_final: 0.8349 (t) REVERT: C 646 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7342 (ttp-110) REVERT: C 1019 ARG cc_start: 0.8390 (ttp-110) cc_final: 0.8187 (ttp-110) REVERT: C 1113 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8129 (mt0) outliers start: 77 outliers final: 44 residues processed: 347 average time/residue: 0.5940 time to fit residues: 242.8117 Evaluate side-chains 340 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 279 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 87 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 90 optimal weight: 0.0870 chunk 77 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 243 optimal weight: 0.8980 chunk 225 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 296 optimal weight: 4.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 487 ASN A 613 GLN A 675 GLN A 872 GLN A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 675 GLN B 872 GLN B 957 GLN C 487 ASN C 658 ASN C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.145639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120381 restraints weight = 32958.231| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.03 r_work: 0.3275 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27300 Z= 0.172 Angle : 0.709 15.872 37293 Z= 0.356 Chirality : 0.048 0.622 4404 Planarity : 0.004 0.074 4695 Dihedral : 5.384 33.586 3501 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.39 % Favored : 95.45 % Rotamer: Outliers : 2.99 % Allowed : 16.97 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3234 helix: 0.66 (0.19), residues: 744 sheet: -0.65 (0.19), residues: 585 loop : -0.96 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1091 TYR 0.021 0.002 TYR C 505 PHE 0.028 0.002 PHE C 486 TRP 0.024 0.002 TRP A 152 HIS 0.007 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (27180) covalent geometry : angle 0.66980 / 0.34 (36975) SS BOND : bond 0.00495 / 0.31 ( 42) SS BOND : angle 3.55781 / 2.37 ( 84) hydrogen bonds : bond 0.04131 / 2.77 ( 947) hydrogen bonds : angle 5.87863 / 4.16 ( 2616) link_BETA1-4 : bond 0.00446 / 0.31 ( 24) link_BETA1-4 : angle 1.76441 / 1.16 ( 72) link_NAG-ASN : bond 0.00604 / 0.34 ( 54) link_NAG-ASN : angle 2.30677 / 1.61 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9545.16 seconds wall clock time: 176 minutes 43.36 seconds (10603.36 seconds total)