Starting phenix.real_space_refine on Sun Jul 5 04:24:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sxv_25507/07_2026/7sxv_25507.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxv_25507/07_2026/7sxv_25507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7sxv_25507/07_2026/7sxv_25507.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sxv_25507/07_2026/7sxv_25507.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sxv_25507/07_2026/7sxv_25507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxv_25507/07_2026/7sxv_25507.map" model { file = "/net/cci-nas-00/data/ceres_data/7sxv_25507/07_2026/7sxv_25507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxv_25507/07_2026/7sxv_25507.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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 111 5.16 5 C 16071 2.51 5 N 4128 2.21 5 O 4935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 25245 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.72, per 1000 atoms: 0.23 Number of scatterers: 25245 At special positions: 0 Unit cell: (141, 145, 198, 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 111 16.00 O 4935 8.00 N 4128 7.00 C 16071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 985.4 milliseconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 51 sheets defined 24.6% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.063A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.654A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.465A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.114A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 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: 3.659A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.900A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.016A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.587A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.936A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.685A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.912A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.644A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.981A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 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: 3.619A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.514A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.580A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.867A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.535A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) 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 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.937A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.565A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.823A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.694A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.903A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.579A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.913A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 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: 3.692A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.951A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.606A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.301A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.561A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.237A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.855A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.844A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 163 removed outlier: 5.233A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.264A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 10.197A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.824A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.074A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.109A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.569A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.030A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.854A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.633A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.633A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.217A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.698A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (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 27 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.333A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.033A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.342A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.494A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.995A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.784A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.931A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.555A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.274A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.615A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.907A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.532A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.014A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.748A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.567A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.567A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.294A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (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 27 through 30 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.249A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.095A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.818A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.781A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.879A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.770A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.166A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.080A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.841A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.711A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.510A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.211A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.552A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.552A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.198A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 1075 hydrogen bonds defined for protein. 2958 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: 6.35 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7599 1.34 - 1.46: 6290 1.46 - 1.58: 11788 1.58 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 25815 Sorted by residual: bond pdb=" C LEU C 560 " pdb=" N PRO C 561 " ideal model delta sigma weight residual 1.334 1.386 -0.052 1.51e-02 4.39e+03 1.16e+01 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.13e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.89e+00 ... (remaining 25810 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 34031 2.01 - 4.02: 997 4.02 - 6.03: 79 6.03 - 8.04: 27 8.04 - 10.05: 8 Bond angle restraints: 35142 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.40 -5.70 1.22e+00 6.72e-01 2.18e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.29 -5.59 1.22e+00 6.72e-01 2.10e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.98 -5.28 1.22e+00 6.72e-01 1.87e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 122.19 -8.09 2.00e+00 2.50e-01 1.64e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.61 -4.68 1.20e+00 6.94e-01 1.52e+01 ... (remaining 35137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13756 17.99 - 35.98: 960 35.98 - 53.97: 115 53.97 - 71.97: 50 71.97 - 89.96: 29 Dihedral angle restraints: 14910 sinusoidal: 5829 harmonic: 9081 Sorted by residual: dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA PHE C 515 " pdb=" C PHE C 515 " pdb=" N GLU C 516 " pdb=" CA GLU C 516 " ideal model delta harmonic sigma weight residual 180.00 157.32 22.68 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 14907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3344 0.067 - 0.133: 743 0.133 - 0.200: 62 0.200 - 0.267: 5 0.267 - 0.333: 4 Chirality restraints: 4158 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 4155 not shown) Planarity restraints: 4518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.016 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C MET C 902 " 0.057 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 135 " 0.016 2.00e-02 2.50e+03 2.42e-02 1.03e+01 pdb=" CG PHE B 135 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B 135 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE B 135 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 135 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE B 135 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE B 135 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 920 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.09e+00 pdb=" C GLN C 920 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN C 920 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS C 921 " -0.018 2.00e-02 2.50e+03 ... (remaining 4515 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6876 2.81 - 3.33: 20880 3.33 - 3.86: 42755 3.86 - 4.38: 48858 4.38 - 4.90: 84223 Nonbonded interactions: 203592 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.315 3.040 nonbonded pdb=" OE1 GLN B 115 " pdb=" OG1 THR B 167 " model vdw 2.318 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.318 3.040 nonbonded pdb=" O ASP B 80 " pdb=" OH TYR B 265 " model vdw 2.329 3.040 ... (remaining 203587 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: 0.02 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' } 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: 5.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.650 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 : 0.005 0.068 25917 Z= 0.226 Angle : 0.804 15.057 35406 Z= 0.416 Chirality : 0.053 0.333 4158 Planarity : 0.007 0.067 4476 Dihedral : 13.037 89.958 8940 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.13), residues: 3072 helix: 0.18 (0.18), residues: 648 sheet: 0.19 (0.19), residues: 682 loop : -0.92 (0.13), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 357 TYR 0.023 0.002 TYR C1067 PHE 0.048 0.002 PHE B 135 TRP 0.018 0.002 TRP A 886 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.23 (25815) covalent geometry : angle 0.77623 / 0.41 (35142) SS BOND : bond 0.00250 / 0.17 ( 42) SS BOND : angle 1.40080 / 0.92 ( 84) hydrogen bonds : bond 0.16971 / 11.09 ( 1025) hydrogen bonds : angle 7.99738 / 5.73 ( 2958) link_BETA1-4 : bond 0.00724 / 0.47 ( 18) link_BETA1-4 : angle 1.29723 / 0.89 ( 54) link_NAG-ASN : bond 0.00896 / 0.45 ( 42) link_NAG-ASN : angle 3.37016 / 2.85 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.756 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 99 ASN cc_start: 0.7566 (m-40) cc_final: 0.7136 (p0) REVERT: A 304 LYS cc_start: 0.9230 (mmmm) cc_final: 0.8989 (mmmm) REVERT: A 869 MET cc_start: 0.8443 (mtm) cc_final: 0.8170 (mtp) REVERT: A 950 ASP cc_start: 0.8096 (t0) cc_final: 0.7787 (t0) REVERT: A 954 GLN cc_start: 0.8536 (mt0) cc_final: 0.8074 (mt0) REVERT: B 353 TRP cc_start: 0.7328 (p-90) cc_final: 0.7066 (p-90) REVERT: B 386 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8335 (mmtp) REVERT: B 565 PHE cc_start: 0.8151 (p90) cc_final: 0.6791 (m-80) REVERT: B 858 LEU cc_start: 0.8785 (mt) cc_final: 0.8395 (pt) REVERT: B 985 ASP cc_start: 0.7368 (p0) cc_final: 0.6823 (p0) REVERT: C 41 LYS cc_start: 0.7011 (mmtp) cc_final: 0.6259 (tttt) REVERT: C 85 PRO cc_start: 0.8353 (Cg_exo) cc_final: 0.8032 (Cg_endo) REVERT: C 140 PHE cc_start: 0.7664 (p90) cc_final: 0.6972 (OUTLIER) REVERT: C 175 PHE cc_start: 0.6216 (m-10) cc_final: 0.5723 (m-80) REVERT: C 269 TYR cc_start: 0.7067 (m-80) cc_final: 0.6749 (m-80) REVERT: C 298 GLU cc_start: 0.8408 (tt0) cc_final: 0.8180 (mt-10) REVERT: C 353 TRP cc_start: 0.6271 (p-90) cc_final: 0.5717 (p-90) REVERT: C 532 ASN cc_start: 0.8747 (t0) cc_final: 0.8419 (t0) REVERT: C 582 LEU cc_start: 0.9167 (mp) cc_final: 0.8915 (pp) REVERT: C 902 MET cc_start: 0.8626 (tpt) cc_final: 0.8365 (tpt) outliers start: 0 outliers final: 2 residues processed: 280 average time/residue: 0.6441 time to fit residues: 208.9112 Evaluate side-chains 139 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN A 957 GLN A1002 GLN B 66 HIS B 121 ASN B 370 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1002 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 762 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.125267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.079573 restraints weight = 69835.613| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.98 r_work: 0.3143 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25917 Z= 0.229 Angle : 0.642 12.492 35406 Z= 0.324 Chirality : 0.046 0.244 4158 Planarity : 0.005 0.144 4476 Dihedral : 4.668 28.884 3347 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.28 % Allowed : 6.59 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3072 helix: 1.44 (0.20), residues: 683 sheet: 0.19 (0.19), residues: 702 loop : -0.73 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG C 567 TYR 0.024 0.002 TYR C 200 PHE 0.021 0.002 PHE B 135 TRP 0.013 0.002 TRP C 436 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 (25815) covalent geometry : angle 0.62178 / 0.32 (35142) SS BOND : bond 0.00191 / 0.12 ( 42) SS BOND : angle 0.83798 / 0.58 ( 84) hydrogen bonds : bond 0.04665 / 2.97 ( 1025) hydrogen bonds : angle 6.17785 / 4.41 ( 2958) link_BETA1-4 : bond 0.00308 / 0.18 ( 18) link_BETA1-4 : angle 1.05697 / 0.75 ( 54) link_NAG-ASN : bond 0.00628 / 0.36 ( 42) link_NAG-ASN : angle 2.65338 / 2.19 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8815 (tm-30) REVERT: A 88 ASP cc_start: 0.8724 (m-30) cc_final: 0.8201 (p0) REVERT: A 99 ASN cc_start: 0.7832 (m-40) cc_final: 0.7161 (p0) REVERT: A 188 ASN cc_start: 0.7098 (m-40) cc_final: 0.6334 (p0) REVERT: A 304 LYS cc_start: 0.9340 (mmmm) cc_final: 0.8983 (mmmm) REVERT: A 950 ASP cc_start: 0.9082 (t0) cc_final: 0.8804 (t0) REVERT: A 954 GLN cc_start: 0.9141 (mt0) cc_final: 0.8756 (mt0) REVERT: A 985 ASP cc_start: 0.8532 (m-30) cc_final: 0.8059 (m-30) REVERT: A 1010 GLN cc_start: 0.8999 (mp10) cc_final: 0.8586 (mp10) REVERT: B 52 GLN cc_start: 0.8882 (tp40) cc_final: 0.8680 (tp-100) REVERT: B 353 TRP cc_start: 0.6697 (p-90) cc_final: 0.6476 (p90) REVERT: B 386 LYS cc_start: 0.8581 (mmtt) cc_final: 0.7826 (mmtp) REVERT: C 53 ASP cc_start: 0.7032 (t0) cc_final: 0.6811 (t0) REVERT: C 140 PHE cc_start: 0.7818 (p90) cc_final: 0.7130 (OUTLIER) REVERT: C 532 ASN cc_start: 0.9108 (t0) cc_final: 0.8761 (t0) REVERT: C 582 LEU cc_start: 0.9290 (mp) cc_final: 0.9026 (pp) REVERT: C 902 MET cc_start: 0.9339 (tpt) cc_final: 0.9079 (tpt) REVERT: C 957 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8227 (tm-30) REVERT: C 964 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8987 (mppt) REVERT: C 1002 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8473 (tm-30) REVERT: C 1010 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8845 (mp10) outliers start: 35 outliers final: 9 residues processed: 168 average time/residue: 0.6101 time to fit residues: 120.2223 Evaluate side-chains 133 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 305 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 111 optimal weight: 0.3980 chunk 216 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 957 GLN A1002 GLN B 66 HIS B 901 GLN B 957 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.123722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.079895 restraints weight = 70035.124| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.69 r_work: 0.3137 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 25917 Z= 0.209 Angle : 0.601 12.710 35406 Z= 0.302 Chirality : 0.046 0.260 4158 Planarity : 0.004 0.088 4476 Dihedral : 4.508 29.944 3347 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.65 % Allowed : 7.50 % Favored : 90.85 % 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: 0.07 (0.15), residues: 3072 helix: 1.70 (0.20), residues: 702 sheet: 0.03 (0.18), residues: 714 loop : -0.66 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 567 TYR 0.022 0.001 TYR A1067 PHE 0.024 0.001 PHE B 238 TRP 0.028 0.002 TRP A 104 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (25815) covalent geometry : angle 0.58211 / 0.30 (35142) SS BOND : bond 0.00146 / 0.09 ( 42) SS BOND : angle 0.75086 / 0.51 ( 84) hydrogen bonds : bond 0.04568 / 2.91 ( 1025) hydrogen bonds : angle 5.86889 / 4.18 ( 2958) link_BETA1-4 : bond 0.00243 / 0.16 ( 18) link_BETA1-4 : angle 0.94219 / 0.67 ( 54) link_NAG-ASN : bond 0.00595 / 0.33 ( 42) link_NAG-ASN : angle 2.49994 / 2.14 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 133 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8811 (tm-30) REVERT: A 88 ASP cc_start: 0.8774 (m-30) cc_final: 0.8138 (p0) REVERT: A 188 ASN cc_start: 0.7197 (m-40) cc_final: 0.6414 (p0) REVERT: A 304 LYS cc_start: 0.9311 (mmmm) cc_final: 0.9006 (mmmm) REVERT: A 950 ASP cc_start: 0.9039 (t0) cc_final: 0.8747 (t0) REVERT: A 954 GLN cc_start: 0.9103 (mt0) cc_final: 0.8662 (mt0) REVERT: A 1144 GLU cc_start: 0.7601 (mm-30) cc_final: 0.6952 (tm-30) REVERT: B 309 GLU cc_start: 0.8555 (mp0) cc_final: 0.8152 (pm20) REVERT: B 434 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6325 (pp) REVERT: B 1001 LEU cc_start: 0.9680 (OUTLIER) cc_final: 0.9453 (tm) REVERT: B 1002 GLN cc_start: 0.8956 (tp40) cc_final: 0.8264 (tp-100) REVERT: B 1138 TYR cc_start: 0.8541 (t80) cc_final: 0.8320 (t80) REVERT: B 1142 GLN cc_start: 0.8103 (tp40) cc_final: 0.7869 (tm-30) REVERT: C 140 PHE cc_start: 0.7795 (p90) cc_final: 0.7121 (p90) REVERT: C 532 ASN cc_start: 0.9209 (t0) cc_final: 0.8961 (t0) REVERT: C 582 LEU cc_start: 0.9258 (mp) cc_final: 0.8968 (pp) REVERT: C 762 GLN cc_start: 0.9004 (mt0) cc_final: 0.8646 (mt0) REVERT: C 957 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8050 (tm-30) REVERT: C 1002 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8445 (tm-30) REVERT: C 1010 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8823 (mp10) REVERT: C 1145 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7488 (pt) outliers start: 45 outliers final: 11 residues processed: 162 average time/residue: 0.5455 time to fit residues: 105.4900 Evaluate side-chains 125 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 214 optimal weight: 0.9990 chunk 47 optimal weight: 30.0000 chunk 53 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 243 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 270 optimal weight: 0.8980 chunk 192 optimal weight: 0.6980 chunk 147 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 487 ASN A 907 ASN A 957 GLN A1002 GLN B 66 HIS B 957 GLN B1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.124932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.081792 restraints weight = 69815.764| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.61 r_work: 0.3144 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25917 Z= 0.143 Angle : 0.549 10.420 35406 Z= 0.275 Chirality : 0.044 0.251 4158 Planarity : 0.004 0.036 4476 Dihedral : 4.285 31.667 3347 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.57 % Allowed : 8.49 % Favored : 89.94 % 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: 0.19 (0.15), residues: 3072 helix: 1.86 (0.20), residues: 700 sheet: 0.06 (0.19), residues: 701 loop : -0.58 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.021 0.001 TYR A1067 PHE 0.020 0.001 PHE B 392 TRP 0.024 0.001 TRP A 104 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (25815) covalent geometry : angle 0.53104 / 0.27 (35142) SS BOND : bond 0.00158 / 0.11 ( 42) SS BOND : angle 0.72010 / 0.49 ( 84) hydrogen bonds : bond 0.04107 / 2.61 ( 1025) hydrogen bonds : angle 5.63100 / 4.00 ( 2958) link_BETA1-4 : bond 0.00301 / 0.20 ( 18) link_BETA1-4 : angle 0.84177 / 0.59 ( 54) link_NAG-ASN : bond 0.00542 / 0.29 ( 42) link_NAG-ASN : angle 2.34683 / 2.02 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9166 (tm-30) cc_final: 0.8823 (tm-30) REVERT: A 79 PHE cc_start: 0.5842 (t80) cc_final: 0.5315 (t80) REVERT: A 88 ASP cc_start: 0.8759 (m-30) cc_final: 0.8188 (p0) REVERT: A 188 ASN cc_start: 0.7094 (m110) cc_final: 0.6393 (p0) REVERT: A 304 LYS cc_start: 0.9302 (mmmm) cc_final: 0.9009 (mmmm) REVERT: A 950 ASP cc_start: 0.8995 (t0) cc_final: 0.8726 (t0) REVERT: A 954 GLN cc_start: 0.9111 (mt0) cc_final: 0.8679 (mt0) REVERT: A 1010 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8454 (mp10) REVERT: A 1144 GLU cc_start: 0.7569 (mm-30) cc_final: 0.6829 (tm-30) REVERT: B 52 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8791 (tp-100) REVERT: B 309 GLU cc_start: 0.8637 (mp0) cc_final: 0.8180 (pm20) REVERT: B 434 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6524 (pp) REVERT: B 661 GLU cc_start: 0.8791 (tt0) cc_final: 0.8512 (pp20) REVERT: B 773 GLU cc_start: 0.8932 (tt0) cc_final: 0.8618 (tt0) REVERT: B 1001 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9410 (tm) REVERT: B 1002 GLN cc_start: 0.8965 (tp40) cc_final: 0.8261 (tp-100) REVERT: B 1010 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8499 (pp30) REVERT: B 1144 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7470 (tm-30) REVERT: C 45 SER cc_start: 0.7989 (OUTLIER) cc_final: 0.7722 (t) REVERT: C 140 PHE cc_start: 0.7813 (p90) cc_final: 0.7179 (p90) REVERT: C 189 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8517 (mt) REVERT: C 237 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7240 (ttp-110) REVERT: C 532 ASN cc_start: 0.9169 (t0) cc_final: 0.8929 (t0) REVERT: C 569 ILE cc_start: 0.6315 (mm) cc_final: 0.6113 (mp) REVERT: C 582 LEU cc_start: 0.9262 (mp) cc_final: 0.8973 (pp) REVERT: C 762 GLN cc_start: 0.9015 (mt0) cc_final: 0.8647 (mt0) REVERT: C 957 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8051 (tm-30) REVERT: C 1002 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8441 (tm-30) REVERT: C 1010 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8716 (mp10) REVERT: C 1145 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7715 (pt) outliers start: 43 outliers final: 13 residues processed: 159 average time/residue: 0.5780 time to fit residues: 108.1802 Evaluate side-chains 135 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 295 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 279 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 246 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 141 optimal weight: 0.0370 chunk 254 optimal weight: 10.0000 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 957 GLN A1002 GLN B 66 HIS B 957 GLN C 87 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.124946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.080148 restraints weight = 68764.754| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.91 r_work: 0.3152 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 25917 Z= 0.113 Angle : 0.531 10.398 35406 Z= 0.266 Chirality : 0.044 0.251 4158 Planarity : 0.003 0.039 4476 Dihedral : 4.163 32.193 3347 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.54 % Allowed : 9.11 % Favored : 89.35 % 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: 0.29 (0.15), residues: 3072 helix: 1.90 (0.20), residues: 712 sheet: 0.13 (0.19), residues: 676 loop : -0.51 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.019 0.001 TYR A1067 PHE 0.020 0.001 PHE B 392 TRP 0.023 0.001 TRP A 104 HIS 0.003 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (25815) covalent geometry : angle 0.51342 / 0.26 (35142) SS BOND : bond 0.00252 / 0.20 ( 42) SS BOND : angle 0.63889 / 0.44 ( 84) hydrogen bonds : bond 0.03888 / 2.48 ( 1025) hydrogen bonds : angle 5.47537 / 3.89 ( 2958) link_BETA1-4 : bond 0.00322 / 0.21 ( 18) link_BETA1-4 : angle 0.83571 / 0.58 ( 54) link_NAG-ASN : bond 0.00523 / 0.27 ( 42) link_NAG-ASN : angle 2.27399 / 1.98 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9183 (tm-30) cc_final: 0.8726 (tm-30) REVERT: A 79 PHE cc_start: 0.5982 (t80) cc_final: 0.5680 (t80) REVERT: A 88 ASP cc_start: 0.8774 (m-30) cc_final: 0.8139 (p0) REVERT: A 188 ASN cc_start: 0.7094 (m110) cc_final: 0.6426 (p0) REVERT: A 304 LYS cc_start: 0.9287 (mmmm) cc_final: 0.8980 (mmmm) REVERT: A 950 ASP cc_start: 0.8991 (t0) cc_final: 0.8739 (t0) REVERT: A 954 GLN cc_start: 0.9111 (mt0) cc_final: 0.8666 (mt0) REVERT: A 1141 LEU cc_start: 0.7790 (tt) cc_final: 0.6745 (tm) REVERT: A 1144 GLU cc_start: 0.7579 (mm-30) cc_final: 0.6766 (tm-30) REVERT: B 309 GLU cc_start: 0.8658 (mp0) cc_final: 0.8218 (pm20) REVERT: B 434 ILE cc_start: 0.7112 (OUTLIER) cc_final: 0.6512 (pp) REVERT: B 661 GLU cc_start: 0.8811 (tt0) cc_final: 0.8470 (pp20) REVERT: B 773 GLU cc_start: 0.8939 (tt0) cc_final: 0.8604 (tt0) REVERT: B 1001 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9411 (tm) REVERT: B 1002 GLN cc_start: 0.8970 (tp40) cc_final: 0.8252 (tp-100) REVERT: B 1144 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7460 (tm-30) REVERT: C 45 SER cc_start: 0.8068 (OUTLIER) cc_final: 0.7784 (t) REVERT: C 140 PHE cc_start: 0.7903 (p90) cc_final: 0.7282 (p90) REVERT: C 189 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8475 (mt) REVERT: C 237 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7341 (ttp-110) REVERT: C 532 ASN cc_start: 0.9223 (t0) cc_final: 0.8967 (t0) REVERT: C 582 LEU cc_start: 0.9216 (mp) cc_final: 0.8958 (pp) REVERT: C 762 GLN cc_start: 0.9015 (mt0) cc_final: 0.8596 (mt0) REVERT: C 957 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7929 (tm-30) REVERT: C 1002 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8419 (tm-30) REVERT: C 1010 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8716 (mp10) REVERT: C 1145 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7460 (pt) outliers start: 42 outliers final: 14 residues processed: 163 average time/residue: 0.5856 time to fit residues: 113.2003 Evaluate side-chains 137 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 292 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 214 optimal weight: 9.9990 chunk 269 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 255 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 1 optimal weight: 0.0870 chunk 257 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 762 GLN B 957 GLN B1010 GLN C1011 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.123975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.080142 restraints weight = 69934.455| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.72 r_work: 0.3136 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25917 Z= 0.142 Angle : 0.547 10.368 35406 Z= 0.272 Chirality : 0.044 0.255 4158 Planarity : 0.003 0.039 4476 Dihedral : 4.109 31.575 3347 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.39 % Allowed : 9.66 % Favored : 88.95 % 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: 0.33 (0.15), residues: 3072 helix: 1.96 (0.20), residues: 715 sheet: -0.01 (0.19), residues: 695 loop : -0.42 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.019 0.001 TYR A1067 PHE 0.017 0.001 PHE B 392 TRP 0.037 0.002 TRP C 104 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (25815) covalent geometry : angle 0.53031 / 0.27 (35142) SS BOND : bond 0.00115 / 0.07 ( 42) SS BOND : angle 0.61835 / 0.42 ( 84) hydrogen bonds : bond 0.03908 / 2.49 ( 1025) hydrogen bonds : angle 5.43305 / 3.86 ( 2958) link_BETA1-4 : bond 0.00271 / 0.18 ( 18) link_BETA1-4 : angle 0.87467 / 0.61 ( 54) link_NAG-ASN : bond 0.00520 / 0.28 ( 42) link_NAG-ASN : angle 2.23690 / 1.96 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8721 (tm-30) REVERT: A 79 PHE cc_start: 0.6092 (t80) cc_final: 0.5825 (t80) REVERT: A 88 ASP cc_start: 0.8777 (m-30) cc_final: 0.8097 (p0) REVERT: A 188 ASN cc_start: 0.7140 (m110) cc_final: 0.6481 (p0) REVERT: A 304 LYS cc_start: 0.9330 (mmmm) cc_final: 0.9042 (mmmm) REVERT: A 950 ASP cc_start: 0.9015 (t0) cc_final: 0.8768 (t0) REVERT: A 954 GLN cc_start: 0.9128 (mt0) cc_final: 0.8680 (mt0) REVERT: A 1010 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8472 (mp10) REVERT: A 1050 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.8493 (ppp) REVERT: A 1141 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7147 (tm) REVERT: A 1144 GLU cc_start: 0.7587 (mm-30) cc_final: 0.6858 (tm-30) REVERT: B 309 GLU cc_start: 0.8696 (mp0) cc_final: 0.8281 (pm20) REVERT: B 434 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6635 (pp) REVERT: B 661 GLU cc_start: 0.8793 (tt0) cc_final: 0.8491 (pp20) REVERT: B 773 GLU cc_start: 0.8951 (tt0) cc_final: 0.8646 (tt0) REVERT: B 1001 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9412 (tm) REVERT: B 1002 GLN cc_start: 0.9011 (tp40) cc_final: 0.8210 (tp-100) REVERT: B 1010 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8560 (pp30) REVERT: C 45 SER cc_start: 0.8101 (OUTLIER) cc_final: 0.7859 (t) REVERT: C 140 PHE cc_start: 0.7820 (p90) cc_final: 0.7229 (p90) REVERT: C 189 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8532 (mt) REVERT: C 237 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7321 (ttp-110) REVERT: C 532 ASN cc_start: 0.9268 (t0) cc_final: 0.9019 (t0) REVERT: C 582 LEU cc_start: 0.9260 (mp) cc_final: 0.9042 (pp) REVERT: C 762 GLN cc_start: 0.9009 (mt0) cc_final: 0.8578 (mt0) REVERT: C 957 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8062 (tm-30) REVERT: C 1002 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8463 (tm-30) REVERT: C 1010 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8781 (mp10) REVERT: C 1145 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7373 (pt) outliers start: 38 outliers final: 15 residues processed: 150 average time/residue: 0.5481 time to fit residues: 97.2236 Evaluate side-chains 142 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 29 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 chunk 249 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 271 optimal weight: 0.5980 chunk 247 optimal weight: 0.0470 chunk 10 optimal weight: 7.9990 chunk 284 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1002 GLN B 957 GLN B1010 GLN C 314 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.125447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.081212 restraints weight = 70264.139| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.80 r_work: 0.3147 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 25917 Z= 0.108 Angle : 0.527 10.373 35406 Z= 0.264 Chirality : 0.044 0.253 4158 Planarity : 0.003 0.038 4476 Dihedral : 4.012 32.189 3347 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.24 % Allowed : 10.17 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.15), residues: 3072 helix: 2.10 (0.20), residues: 706 sheet: 0.10 (0.19), residues: 669 loop : -0.38 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 567 TYR 0.019 0.001 TYR A1067 PHE 0.023 0.001 PHE C 135 TRP 0.042 0.002 TRP C 104 HIS 0.003 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (25815) covalent geometry : angle 0.51037 / 0.26 (35142) SS BOND : bond 0.00124 / 0.08 ( 42) SS BOND : angle 0.58110 / 0.40 ( 84) hydrogen bonds : bond 0.03736 / 2.38 ( 1025) hydrogen bonds : angle 5.33464 / 3.79 ( 2958) link_BETA1-4 : bond 0.00325 / 0.21 ( 18) link_BETA1-4 : angle 0.80861 / 0.56 ( 54) link_NAG-ASN : bond 0.00508 / 0.26 ( 42) link_NAG-ASN : angle 2.18212 / 1.92 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8733 (tm-30) REVERT: A 88 ASP cc_start: 0.8728 (m-30) cc_final: 0.8090 (p0) REVERT: A 188 ASN cc_start: 0.7079 (m110) cc_final: 0.6459 (p0) REVERT: A 304 LYS cc_start: 0.9320 (mmmm) cc_final: 0.9022 (mmmm) REVERT: A 950 ASP cc_start: 0.8967 (t0) cc_final: 0.8718 (t0) REVERT: A 954 GLN cc_start: 0.9135 (mt0) cc_final: 0.8686 (mt0) REVERT: A 1010 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8452 (mp10) REVERT: A 1050 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.8588 (ppp) REVERT: A 1141 LEU cc_start: 0.7836 (tt) cc_final: 0.7264 (tm) REVERT: A 1144 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7091 (tm-30) REVERT: B 309 GLU cc_start: 0.8680 (mp0) cc_final: 0.8271 (pm20) REVERT: B 434 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.6824 (pp) REVERT: B 661 GLU cc_start: 0.8809 (tt0) cc_final: 0.8447 (pp20) REVERT: B 773 GLU cc_start: 0.8943 (tt0) cc_final: 0.8633 (tt0) REVERT: B 993 ILE cc_start: 0.9297 (mp) cc_final: 0.8978 (mp) REVERT: B 1001 LEU cc_start: 0.9654 (OUTLIER) cc_final: 0.9402 (tm) REVERT: B 1002 GLN cc_start: 0.9001 (tp40) cc_final: 0.8204 (tp-100) REVERT: C 140 PHE cc_start: 0.7781 (p90) cc_final: 0.7199 (p90) REVERT: C 237 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7324 (ttp-110) REVERT: C 532 ASN cc_start: 0.9264 (t0) cc_final: 0.9013 (t0) REVERT: C 582 LEU cc_start: 0.9208 (mp) cc_final: 0.9000 (pp) REVERT: C 762 GLN cc_start: 0.9008 (mt0) cc_final: 0.8591 (mt0) REVERT: C 957 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8079 (tm-30) REVERT: C 1002 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8446 (tm-30) REVERT: C 1010 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8751 (mp10) REVERT: C 1145 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7539 (pt) outliers start: 34 outliers final: 12 residues processed: 152 average time/residue: 0.5963 time to fit residues: 107.5597 Evaluate side-chains 141 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 116 optimal weight: 0.4980 chunk 243 optimal weight: 30.0000 chunk 188 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 259 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 151 optimal weight: 0.6980 chunk 258 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1002 GLN B 196 ASN B 957 GLN B1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.124219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.079949 restraints weight = 69207.078| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.81 r_work: 0.3144 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 25917 Z= 0.136 Angle : 0.543 10.519 35406 Z= 0.271 Chirality : 0.044 0.255 4158 Planarity : 0.003 0.037 4476 Dihedral : 3.965 19.536 3345 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.13 % Allowed : 10.43 % Favored : 88.44 % 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: 0.45 (0.15), residues: 3072 helix: 2.13 (0.20), residues: 712 sheet: 0.06 (0.19), residues: 671 loop : -0.36 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 995 TYR 0.019 0.001 TYR A1067 PHE 0.018 0.001 PHE B 392 TRP 0.031 0.002 TRP C 104 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (25815) covalent geometry : angle 0.52716 / 0.27 (35142) SS BOND : bond 0.00101 / 0.06 ( 42) SS BOND : angle 0.60078 / 0.41 ( 84) hydrogen bonds : bond 0.03786 / 2.41 ( 1025) hydrogen bonds : angle 5.33136 / 3.79 ( 2958) link_BETA1-4 : bond 0.00274 / 0.18 ( 18) link_BETA1-4 : angle 0.85135 / 0.60 ( 54) link_NAG-ASN : bond 0.00506 / 0.27 ( 42) link_NAG-ASN : angle 2.17577 / 1.92 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8742 (tm-30) REVERT: A 104 TRP cc_start: 0.7434 (m-90) cc_final: 0.7093 (m-90) REVERT: A 188 ASN cc_start: 0.7113 (m110) cc_final: 0.6482 (p0) REVERT: A 304 LYS cc_start: 0.9338 (mmmm) cc_final: 0.9044 (mmmm) REVERT: A 950 ASP cc_start: 0.8962 (t0) cc_final: 0.8719 (t0) REVERT: A 954 GLN cc_start: 0.9167 (mt0) cc_final: 0.8750 (mt0) REVERT: A 1010 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8445 (mp10) REVERT: A 1029 MET cc_start: 0.9490 (OUTLIER) cc_final: 0.9254 (tpp) REVERT: A 1050 MET cc_start: 0.9393 (OUTLIER) cc_final: 0.8705 (ppp) REVERT: A 1141 LEU cc_start: 0.7811 (tt) cc_final: 0.7246 (tm) REVERT: A 1144 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7182 (tm-30) REVERT: B 52 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8791 (tp-100) REVERT: B 239 GLN cc_start: 0.7670 (tt0) cc_final: 0.7405 (tm-30) REVERT: B 309 GLU cc_start: 0.8694 (mp0) cc_final: 0.8308 (pm20) REVERT: B 434 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.6862 (pp) REVERT: B 740 MET cc_start: 0.9192 (tpt) cc_final: 0.8836 (mmm) REVERT: B 762 GLN cc_start: 0.8951 (mt0) cc_final: 0.8652 (mt0) REVERT: B 773 GLU cc_start: 0.8943 (tt0) cc_final: 0.8638 (tt0) REVERT: B 993 ILE cc_start: 0.9341 (mp) cc_final: 0.9051 (mp) REVERT: B 1002 GLN cc_start: 0.8970 (tp40) cc_final: 0.8133 (tp-100) REVERT: C 45 SER cc_start: 0.8111 (OUTLIER) cc_final: 0.7903 (t) REVERT: C 140 PHE cc_start: 0.7810 (p90) cc_final: 0.7229 (p90) REVERT: C 532 ASN cc_start: 0.9225 (t0) cc_final: 0.8998 (t0) REVERT: C 565 PHE cc_start: 0.8153 (p90) cc_final: 0.7206 (m-10) REVERT: C 582 LEU cc_start: 0.9218 (mp) cc_final: 0.9003 (pp) REVERT: C 762 GLN cc_start: 0.9014 (mt0) cc_final: 0.8612 (mt0) REVERT: C 957 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8095 (tm-30) REVERT: C 1002 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8471 (tm-30) REVERT: C 1010 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8761 (mp10) REVERT: C 1145 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7352 (pt) outliers start: 31 outliers final: 15 residues processed: 150 average time/residue: 0.6335 time to fit residues: 111.6435 Evaluate side-chains 141 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 254 optimal weight: 7.9990 chunk 311 optimal weight: 0.3980 chunk 212 optimal weight: 3.9990 chunk 267 optimal weight: 5.9990 chunk 292 optimal weight: 2.9990 chunk 100 optimal weight: 0.0170 chunk 270 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 121 optimal weight: 0.0020 chunk 195 optimal weight: 3.9990 overall best weight: 1.4830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1002 GLN B 196 ASN B 957 GLN B1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.123083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.079406 restraints weight = 69741.937| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.69 r_work: 0.3124 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 25917 Z= 0.174 Angle : 0.564 10.729 35406 Z= 0.283 Chirality : 0.045 0.260 4158 Planarity : 0.004 0.053 4476 Dihedral : 4.031 19.664 3345 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.17 % Allowed : 10.61 % Favored : 88.22 % 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: 0.39 (0.15), residues: 3072 helix: 2.08 (0.20), residues: 715 sheet: -0.05 (0.19), residues: 693 loop : -0.37 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 237 TYR 0.019 0.001 TYR A1067 PHE 0.019 0.001 PHE C 135 TRP 0.031 0.002 TRP C 104 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (25815) covalent geometry : angle 0.54821 / 0.28 (35142) SS BOND : bond 0.00136 / 0.08 ( 42) SS BOND : angle 0.68567 / 0.50 ( 84) hydrogen bonds : bond 0.03968 / 2.54 ( 1025) hydrogen bonds : angle 5.38980 / 3.84 ( 2958) link_BETA1-4 : bond 0.00257 / 0.17 ( 18) link_BETA1-4 : angle 0.87708 / 0.62 ( 54) link_NAG-ASN : bond 0.00525 / 0.29 ( 42) link_NAG-ASN : angle 2.19907 / 1.93 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8740 (tm-30) REVERT: A 104 TRP cc_start: 0.7322 (m-90) cc_final: 0.6723 (m-90) REVERT: A 188 ASN cc_start: 0.7123 (m110) cc_final: 0.6464 (p0) REVERT: A 304 LYS cc_start: 0.9345 (mmmm) cc_final: 0.9050 (mmmm) REVERT: A 950 ASP cc_start: 0.8985 (t0) cc_final: 0.8728 (t0) REVERT: A 954 GLN cc_start: 0.9145 (mt0) cc_final: 0.8692 (mt0) REVERT: A 1010 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8464 (mp10) REVERT: A 1050 MET cc_start: 0.9418 (OUTLIER) cc_final: 0.8735 (ppp) REVERT: A 1111 GLU cc_start: 0.8542 (pp20) cc_final: 0.8055 (pp20) REVERT: A 1141 LEU cc_start: 0.7783 (tt) cc_final: 0.7164 (tm) REVERT: A 1144 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7260 (tm-30) REVERT: B 135 PHE cc_start: 0.8464 (m-80) cc_final: 0.8075 (m-80) REVERT: B 309 GLU cc_start: 0.8705 (mp0) cc_final: 0.8330 (pm20) REVERT: B 434 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.6924 (pp) REVERT: B 762 GLN cc_start: 0.8957 (mt0) cc_final: 0.8670 (mt0) REVERT: B 773 GLU cc_start: 0.8961 (tt0) cc_final: 0.8710 (tt0) REVERT: B 1002 GLN cc_start: 0.9039 (tp40) cc_final: 0.8195 (tp-100) REVERT: C 140 PHE cc_start: 0.7794 (p90) cc_final: 0.7233 (p90) REVERT: C 565 PHE cc_start: 0.8192 (p90) cc_final: 0.7230 (m-10) REVERT: C 762 GLN cc_start: 0.9026 (mt0) cc_final: 0.8621 (mt0) REVERT: C 957 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8067 (tm-30) REVERT: C 1002 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8524 (tm-30) REVERT: C 1010 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8741 (mp10) REVERT: C 1145 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7392 (pt) outliers start: 32 outliers final: 13 residues processed: 146 average time/residue: 0.6182 time to fit residues: 106.7123 Evaluate side-chains 136 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 159 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 213 optimal weight: 0.0970 chunk 60 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 239 optimal weight: 20.0000 chunk 222 optimal weight: 0.9980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN B 957 GLN B1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.121690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.077835 restraints weight = 70193.370| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.61 r_work: 0.3093 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 25917 Z= 0.222 Angle : 0.624 15.526 35406 Z= 0.311 Chirality : 0.046 0.269 4158 Planarity : 0.004 0.046 4476 Dihedral : 4.230 21.339 3345 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.84 % Allowed : 11.38 % Favored : 87.78 % 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: 0.30 (0.15), residues: 3072 helix: 1.98 (0.20), residues: 716 sheet: -0.14 (0.19), residues: 682 loop : -0.40 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 237 TYR 0.020 0.001 TYR A1067 PHE 0.029 0.001 PHE C 175 TRP 0.029 0.002 TRP C 104 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 (25815) covalent geometry : angle 0.60923 / 0.31 (35142) SS BOND : bond 0.00130 / 0.07 ( 42) SS BOND : angle 0.75733 / 0.54 ( 84) hydrogen bonds : bond 0.04326 / 2.78 ( 1025) hydrogen bonds : angle 5.56455 / 3.98 ( 2958) link_BETA1-4 : bond 0.00208 / 0.14 ( 18) link_BETA1-4 : angle 0.94551 / 0.67 ( 54) link_NAG-ASN : bond 0.00577 / 0.33 ( 42) link_NAG-ASN : angle 2.27893 / 1.98 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8731 (tm-30) REVERT: A 104 TRP cc_start: 0.7374 (m-90) cc_final: 0.6950 (m-90) REVERT: A 304 LYS cc_start: 0.9320 (mmmm) cc_final: 0.9009 (mmmm) REVERT: A 950 ASP cc_start: 0.9005 (t0) cc_final: 0.8735 (t0) REVERT: A 954 GLN cc_start: 0.9117 (mt0) cc_final: 0.8666 (mt0) REVERT: A 1050 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.8920 (ptp) REVERT: A 1111 GLU cc_start: 0.8547 (pp20) cc_final: 0.8030 (pp20) REVERT: A 1141 LEU cc_start: 0.7813 (tt) cc_final: 0.7219 (tm) REVERT: A 1144 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7394 (mp0) REVERT: A 1145 LEU cc_start: 0.6315 (tm) cc_final: 0.5875 (pp) REVERT: B 135 PHE cc_start: 0.8474 (m-80) cc_final: 0.8082 (m-80) REVERT: B 200 TYR cc_start: 0.8690 (m-80) cc_final: 0.8275 (t80) REVERT: B 309 GLU cc_start: 0.8763 (mp0) cc_final: 0.8414 (pm20) REVERT: B 762 GLN cc_start: 0.8974 (mt0) cc_final: 0.8726 (mt0) REVERT: B 773 GLU cc_start: 0.8993 (tt0) cc_final: 0.8658 (tt0) REVERT: B 988 GLU cc_start: 0.9405 (mp0) cc_final: 0.8871 (pm20) REVERT: B 1002 GLN cc_start: 0.9071 (tp40) cc_final: 0.8172 (tp-100) REVERT: C 140 PHE cc_start: 0.7675 (p90) cc_final: 0.7118 (p90) REVERT: C 582 LEU cc_start: 0.8941 (pp) cc_final: 0.8622 (mm) REVERT: C 762 GLN cc_start: 0.9079 (mt0) cc_final: 0.8680 (mt0) REVERT: C 957 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8090 (tm-30) REVERT: C 1002 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8594 (tm-30) REVERT: C 1010 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8750 (mp10) outliers start: 23 outliers final: 11 residues processed: 140 average time/residue: 0.6041 time to fit residues: 99.9248 Evaluate side-chains 129 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 68 optimal weight: 1.9990 chunk 287 optimal weight: 0.5980 chunk 70 optimal weight: 0.0870 chunk 24 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 273 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 305 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 241 optimal weight: 20.0000 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN B 957 GLN B1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.123010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.078890 restraints weight = 70485.804| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.75 r_work: 0.3123 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25917 Z= 0.129 Angle : 0.568 11.388 35406 Z= 0.283 Chirality : 0.045 0.257 4158 Planarity : 0.004 0.037 4476 Dihedral : 4.067 19.162 3345 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.66 % Allowed : 11.53 % Favored : 87.82 % 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: 0.44 (0.15), residues: 3072 helix: 2.13 (0.20), residues: 713 sheet: -0.00 (0.20), residues: 661 loop : -0.34 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.020 0.001 TYR A1067 PHE 0.019 0.001 PHE B 392 TRP 0.033 0.002 TRP C 104 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (25815) covalent geometry : angle 0.55316 / 0.28 (35142) SS BOND : bond 0.00118 / 0.07 ( 42) SS BOND : angle 0.62641 / 0.44 ( 84) hydrogen bonds : bond 0.03837 / 2.45 ( 1025) hydrogen bonds : angle 5.37072 / 3.83 ( 2958) link_BETA1-4 : bond 0.00310 / 0.20 ( 18) link_BETA1-4 : angle 0.78750 / 0.54 ( 54) link_NAG-ASN : bond 0.00501 / 0.27 ( 42) link_NAG-ASN : angle 2.17803 / 1.91 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10222.14 seconds wall clock time: 174 minutes 41.18 seconds (10481.18 seconds total)