Starting phenix.real_space_refine on Fri Feb 6 15:41:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vg7_65045/02_2026/9vg7_65045.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vg7_65045/02_2026/9vg7_65045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vg7_65045/02_2026/9vg7_65045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vg7_65045/02_2026/9vg7_65045.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vg7_65045/02_2026/9vg7_65045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vg7_65045/02_2026/9vg7_65045.map" } resolution = 2.55 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= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 16290 2.51 5 N 4236 2.21 5 O 5019 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 261 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25665 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8390 Classifications: {'peptide': 1075} Link IDs: {'PTRANS': 49, 'TRANS': 1025} Chain breaks: 2 Chain: "B" Number of atoms: 8390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8390 Classifications: {'peptide': 1075} Link IDs: {'PTRANS': 49, 'TRANS': 1025} Chain breaks: 2 Chain: "C" Number of atoms: 8390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8390 Classifications: {'peptide': 1075} Link IDs: {'PTRANS': 49, 'TRANS': 1025} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.68, per 1000 atoms: 0.26 Number of scatterers: 25665 At special positions: 0 Unit cell: (132.804, 138.337, 164.898, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5019 8.00 N 4236 7.00 C 16290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 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 516 " distance=2.02 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 581 " distance=2.04 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 640 " distance=2.03 Simple disulfide: pdb=" SG CYS A 653 " - pdb=" SG CYS A 662 " distance=2.04 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG CYS A 748 " distance=2.04 Simple disulfide: pdb=" SG CYS A 731 " - pdb=" SG CYS A 737 " distance=2.04 Simple disulfide: pdb=" SG CYS A 828 " - pdb=" SG CYS A 839 " distance=2.03 Simple disulfide: pdb=" SG CYS A1020 " - pdb=" SG CYS A1031 " distance=2.01 Simple disulfide: pdb=" SG CYS A1070 " - pdb=" SG CYS A1114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 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 516 " distance=2.02 Simple disulfide: pdb=" SG CYS B 529 " - pdb=" SG CYS B 581 " distance=2.04 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 640 " distance=2.03 Simple disulfide: pdb=" SG CYS B 653 " - pdb=" SG CYS B 662 " distance=2.04 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG CYS B 748 " distance=2.04 Simple disulfide: pdb=" SG CYS B 731 " - pdb=" SG CYS B 737 " distance=2.04 Simple disulfide: pdb=" SG CYS B 828 " - pdb=" SG CYS B 839 " distance=2.03 Simple disulfide: pdb=" SG CYS B1020 " - pdb=" SG CYS B1031 " distance=2.02 Simple disulfide: pdb=" SG CYS B1070 " - pdb=" SG CYS B1114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 172 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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 516 " distance=2.02 Simple disulfide: pdb=" SG CYS C 529 " - pdb=" SG CYS C 581 " distance=2.04 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 640 " distance=2.03 Simple disulfide: pdb=" SG CYS C 653 " - pdb=" SG CYS C 662 " distance=2.04 Simple disulfide: pdb=" SG CYS C 726 " - pdb=" SG CYS C 748 " distance=2.04 Simple disulfide: pdb=" SG CYS C 731 " - pdb=" SG CYS C 737 " distance=2.04 Simple disulfide: pdb=" SG CYS C 828 " - pdb=" SG CYS C 839 " distance=2.03 Simple disulfide: pdb=" SG CYS C1020 " - pdb=" SG CYS C1031 " distance=2.02 Simple disulfide: pdb=" SG CYS C1070 " - pdb=" SG CYS C1114 " 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 E 2 " - " BMA E 3 " " 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 I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 175 " " NAG A1302 " - " ASN A 370 " " NAG A1303 " - " ASN A 705 " " NAG B1301 " - " ASN B 175 " " NAG B1302 " - " ASN B 370 " " NAG B1303 " - " ASN B 705 " " NAG C1301 " - " ASN C 175 " " NAG C1302 " - " ASN C 370 " " NAG C1303 " - " ASN C 705 " " NAG D 1 " - " ASN A 85 " " NAG E 1 " - " ASN A 244 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 789 " " NAG H 1 " - " ASN B 85 " " NAG I 1 " - " ASN B 244 " " NAG J 1 " - " ASN B 331 " " NAG K 1 " - " ASN B 789 " " NAG L 1 " - " ASN C 85 " " NAG M 1 " - " ASN C 244 " " NAG N 1 " - " ASN C 331 " " NAG O 1 " - " ASN C 789 " Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6054 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 51 sheets defined 27.7% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.519A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.180A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.561A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.865A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 493 through 496 Processing helix chain 'A' and resid 610 through 615 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 734 through 742 Processing helix chain 'A' and resid 743 through 745 No H-bonds generated for 'chain 'A' and resid 743 through 745' Processing helix chain 'A' and resid 746 through 771 removed outlier: 3.558A pdb=" N ASP A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 removed outlier: 3.540A pdb=" N VAL A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 829 removed outlier: 3.879A pdb=" N CYS A 828 " --> pdb=" O TYR A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 844 Processing helix chain 'A' and resid 854 through 872 Processing helix chain 'A' and resid 874 through 878 removed outlier: 3.808A pdb=" N GLY A 877 " --> pdb=" O TRP A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 897 Processing helix chain 'A' and resid 900 through 907 removed outlier: 3.939A pdb=" N LEU A 904 " --> pdb=" O THR A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 928 removed outlier: 3.786A pdb=" N GLU A 924 " --> pdb=" O GLY A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 953 Processing helix chain 'A' and resid 954 through 956 No H-bonds generated for 'chain 'A' and resid 954 through 956' Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 973 through 1021 removed outlier: 3.976A pdb=" N VAL A 979 " --> pdb=" O PRO A 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.519A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.180A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.561A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.866A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 493 through 496 Processing helix chain 'B' and resid 610 through 615 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 725 through 732 Processing helix chain 'B' and resid 734 through 742 Processing helix chain 'B' and resid 743 through 745 No H-bonds generated for 'chain 'B' and resid 743 through 745' Processing helix chain 'B' and resid 746 through 771 removed outlier: 3.558A pdb=" N ASP B 763 " --> pdb=" O ALA B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 814 removed outlier: 3.540A pdb=" N VAL B 814 " --> pdb=" O LEU B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 829 removed outlier: 3.879A pdb=" N CYS B 828 " --> pdb=" O TYR B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 844 Processing helix chain 'B' and resid 854 through 872 Processing helix chain 'B' and resid 874 through 878 removed outlier: 3.808A pdb=" N GLY B 877 " --> pdb=" O TRP B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 897 Processing helix chain 'B' and resid 900 through 907 removed outlier: 3.939A pdb=" N LEU B 904 " --> pdb=" O THR B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 928 removed outlier: 3.786A pdb=" N GLU B 924 " --> pdb=" O GLY B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 953 Processing helix chain 'B' and resid 954 through 956 No H-bonds generated for 'chain 'B' and resid 954 through 956' Processing helix chain 'B' and resid 964 through 972 Processing helix chain 'B' and resid 973 through 1021 removed outlier: 3.976A pdb=" N VAL B 979 " --> pdb=" O PRO B 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.519A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 removed outlier: 4.181A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.561A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.866A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 493 through 496 Processing helix chain 'C' and resid 610 through 615 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 725 through 732 Processing helix chain 'C' and resid 734 through 742 Processing helix chain 'C' and resid 743 through 745 No H-bonds generated for 'chain 'C' and resid 743 through 745' Processing helix chain 'C' and resid 746 through 771 removed outlier: 3.558A pdb=" N ASP C 763 " --> pdb=" O ALA C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 removed outlier: 3.540A pdb=" N VAL C 814 " --> pdb=" O LEU C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 829 removed outlier: 3.879A pdb=" N CYS C 828 " --> pdb=" O TYR C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 844 Processing helix chain 'C' and resid 854 through 872 Processing helix chain 'C' and resid 874 through 878 removed outlier: 3.807A pdb=" N GLY C 877 " --> pdb=" O TRP C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 897 Processing helix chain 'C' and resid 900 through 907 removed outlier: 3.939A pdb=" N LEU C 904 " --> pdb=" O THR C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 928 removed outlier: 3.786A pdb=" N GLU C 924 " --> pdb=" O GLY C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 953 Processing helix chain 'C' and resid 954 through 956 No H-bonds generated for 'chain 'C' and resid 954 through 956' Processing helix chain 'C' and resid 964 through 972 Processing helix chain 'C' and resid 973 through 1021 removed outlier: 3.976A pdb=" N VAL C 979 " --> pdb=" O PRO C 975 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 54 removed outlier: 4.527A pdb=" N HIS A 49 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ASN A 85 " --> pdb=" O HIS A 269 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N HIS A 269 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 113 " --> pdb=" O THR A 194 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR A 194 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 193 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU A 207 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS A 238 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 209 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 79 removed outlier: 7.479A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N MET A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA A 288 " --> pdb=" O MET A 276 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS A 278 " --> pdb=" O VAL A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.569A pdb=" N GLY A 120 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR A 253 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 118 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG A 119 " --> pdb=" O ASN A 138 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 143 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 174 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR A 149 " --> pdb=" O CYS A 172 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N CYS A 172 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N HIS A 151 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N PHE A 170 " --> pdb=" O HIS A 151 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N CYS A 153 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N SER A 168 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N THR A 155 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TYR A 166 " --> pdb=" O THR A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 102 removed outlier: 12.994A pdb=" N PHE A 248 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 12.989A pdb=" N PHE A 152 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 12.765A pdb=" N THR A 250 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N VAL A 252 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N LEU A 254 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE A 158 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 143 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 174 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR A 149 " --> pdb=" O CYS A 172 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N CYS A 172 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N HIS A 151 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N PHE A 170 " --> pdb=" O HIS A 151 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N CYS A 153 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N SER A 168 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N THR A 155 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TYR A 166 " --> pdb=" O THR A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.983A pdb=" N VAL A 586 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.844A pdb=" N ASP A 565 " --> pdb=" O ILE A 578 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.672A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.729A pdb=" N CYS A 361 " --> pdb=" O CYS A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 472 through 475 Processing sheet with id=AB2, first strand: chain 'A' and resid 645 through 646 removed outlier: 6.073A pdb=" N GLU A 645 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N VAL A 684 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE A 661 " --> pdb=" O ILE A 657 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 689 through 691 removed outlier: 6.915A pdb=" N ALA A 689 " --> pdb=" O ILE B 776 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 699 through 716 removed outlier: 6.265A pdb=" N GLN A1059 " --> pdb=" O THR A 704 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE A 706 " --> pdb=" O PRO A1057 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE A 708 " --> pdb=" O TYR A1055 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR A1055 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 710 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A1053 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR A 712 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU A1051 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 714 " --> pdb=" O VAL A1049 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A1049 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY A1047 " --> pdb=" O PRO A 716 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR A1055 " --> pdb=" O HIS A1036 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N HIS A1036 " --> pdb=" O TYR A1055 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 699 through 716 removed outlier: 6.265A pdb=" N GLN A1059 " --> pdb=" O THR A 704 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE A 706 " --> pdb=" O PRO A1057 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE A 708 " --> pdb=" O TYR A1055 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR A1055 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 710 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A1053 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR A 712 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU A1051 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 714 " --> pdb=" O VAL A1049 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A1049 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY A1047 " --> pdb=" O PRO A 716 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR A1064 " --> pdb=" O SER A1085 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A1066 " --> pdb=" O PHE A1083 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE A1083 " --> pdb=" O ALA A1066 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 721 through 724 removed outlier: 4.267A pdb=" N LYS A 721 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 775 through 777 Processing sheet with id=AB8, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AB9, first strand: chain 'A' and resid 1108 through 1113 removed outlier: 4.297A pdb=" N ALA A1075 " --> pdb=" O SER A1111 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 49 through 54 removed outlier: 4.527A pdb=" N HIS B 49 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ASN B 85 " --> pdb=" O HIS B 269 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N HIS B 269 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP B 113 " --> pdb=" O THR B 194 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR B 194 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 193 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU B 207 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS B 238 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 209 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 71 through 79 removed outlier: 7.478A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N MET B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA B 288 " --> pdb=" O MET B 276 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS B 278 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 101 through 102 removed outlier: 3.570A pdb=" N GLY B 120 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR B 253 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL B 118 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG B 119 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 143 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 174 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR B 149 " --> pdb=" O CYS B 172 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N CYS B 172 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N HIS B 151 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N PHE B 170 " --> pdb=" O HIS B 151 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N CYS B 153 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N SER B 168 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N THR B 155 " --> pdb=" O TYR B 166 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TYR B 166 " --> pdb=" O THR B 155 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 101 through 102 removed outlier: 12.994A pdb=" N PHE B 248 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 12.989A pdb=" N PHE B 152 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 12.765A pdb=" N THR B 250 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N VAL B 252 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N LEU B 254 " --> pdb=" O PRO B 156 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE B 158 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 143 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 174 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR B 149 " --> pdb=" O CYS B 172 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N CYS B 172 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N HIS B 151 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N PHE B 170 " --> pdb=" O HIS B 151 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N CYS B 153 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N SER B 168 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N THR B 155 " --> pdb=" O TYR B 166 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TYR B 166 " --> pdb=" O THR B 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.984A pdb=" N VAL B 586 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 4.844A pdb=" N ASP B 565 " --> pdb=" O ILE B 578 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.672A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.729A pdb=" N CYS B 361 " --> pdb=" O CYS B 516 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 472 through 475 Processing sheet with id=AD2, first strand: chain 'B' and resid 645 through 646 removed outlier: 6.074A pdb=" N GLU B 645 " --> pdb=" O ALA B 682 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N VAL B 684 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 661 " --> pdb=" O ILE B 657 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 689 through 691 removed outlier: 6.908A pdb=" N ALA B 689 " --> pdb=" O ILE C 776 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 699 through 716 removed outlier: 6.265A pdb=" N GLN B1059 " --> pdb=" O THR B 704 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE B 706 " --> pdb=" O PRO B1057 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE B 708 " --> pdb=" O TYR B1055 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR B1055 " --> pdb=" O ILE B 708 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 710 " --> pdb=" O VAL B1053 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL B1053 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR B 712 " --> pdb=" O LEU B1051 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU B1051 " --> pdb=" O THR B 712 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 714 " --> pdb=" O VAL B1049 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B1049 " --> pdb=" O VAL B 714 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY B1047 " --> pdb=" O PRO B 716 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR B1055 " --> pdb=" O HIS B1036 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N HIS B1036 " --> pdb=" O TYR B1055 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 699 through 716 removed outlier: 6.265A pdb=" N GLN B1059 " --> pdb=" O THR B 704 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE B 706 " --> pdb=" O PRO B1057 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE B 708 " --> pdb=" O TYR B1055 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR B1055 " --> pdb=" O ILE B 708 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 710 " --> pdb=" O VAL B1053 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL B1053 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR B 712 " --> pdb=" O LEU B1051 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU B1051 " --> pdb=" O THR B 712 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 714 " --> pdb=" O VAL B1049 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B1049 " --> pdb=" O VAL B 714 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY B1047 " --> pdb=" O PRO B 716 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B1064 " --> pdb=" O SER B1085 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B1066 " --> pdb=" O PHE B1083 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE B1083 " --> pdb=" O ALA B1066 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 721 through 724 removed outlier: 4.267A pdb=" N LYS B 721 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 784 through 785 Processing sheet with id=AD8, first strand: chain 'B' and resid 1108 through 1113 removed outlier: 4.296A pdb=" N ALA B1075 " --> pdb=" O SER B1111 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 49 through 54 removed outlier: 4.527A pdb=" N HIS C 49 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ASN C 85 " --> pdb=" O HIS C 269 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N HIS C 269 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP C 113 " --> pdb=" O THR C 194 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR C 194 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS C 193 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU C 207 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS C 238 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL C 209 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 71 through 79 removed outlier: 7.479A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N MET C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA C 288 " --> pdb=" O MET C 276 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS C 278 " --> pdb=" O VAL C 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 101 through 102 removed outlier: 3.570A pdb=" N GLY C 120 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR C 253 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 118 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG C 119 " --> pdb=" O ASN C 138 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 174 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR C 149 " --> pdb=" O CYS C 172 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N CYS C 172 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N HIS C 151 " --> pdb=" O PHE C 170 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N PHE C 170 " --> pdb=" O HIS C 151 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N CYS C 153 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N SER C 168 " --> pdb=" O CYS C 153 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N THR C 155 " --> pdb=" O TYR C 166 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TYR C 166 " --> pdb=" O THR C 155 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 101 through 102 removed outlier: 12.994A pdb=" N PHE C 248 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 12.989A pdb=" N PHE C 152 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 12.765A pdb=" N THR C 250 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N VAL C 252 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N LEU C 254 " --> pdb=" O PRO C 156 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE C 158 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 174 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR C 149 " --> pdb=" O CYS C 172 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N CYS C 172 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N HIS C 151 " --> pdb=" O PHE C 170 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N PHE C 170 " --> pdb=" O HIS C 151 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N CYS C 153 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N SER C 168 " --> pdb=" O CYS C 153 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N THR C 155 " --> pdb=" O TYR C 166 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TYR C 166 " --> pdb=" O THR C 155 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.984A pdb=" N VAL C 586 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 325 through 328 removed outlier: 4.843A pdb=" N ASP C 565 " --> pdb=" O ILE C 578 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.672A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.730A pdb=" N CYS C 361 " --> pdb=" O CYS C 516 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 472 through 475 Processing sheet with id=AF1, first strand: chain 'C' and resid 645 through 646 removed outlier: 6.073A pdb=" N GLU C 645 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N VAL C 684 " --> pdb=" O GLU C 645 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 661 " --> pdb=" O ILE C 657 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 699 through 716 removed outlier: 6.265A pdb=" N GLN C1059 " --> pdb=" O THR C 704 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE C 706 " --> pdb=" O PRO C1057 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE C 708 " --> pdb=" O TYR C1055 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR C1055 " --> pdb=" O ILE C 708 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL C 710 " --> pdb=" O VAL C1053 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL C1053 " --> pdb=" O VAL C 710 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR C 712 " --> pdb=" O LEU C1051 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU C1051 " --> pdb=" O THR C 712 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C 714 " --> pdb=" O VAL C1049 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL C1049 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY C1047 " --> pdb=" O PRO C 716 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR C1055 " --> pdb=" O HIS C1036 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N HIS C1036 " --> pdb=" O TYR C1055 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 699 through 716 removed outlier: 6.265A pdb=" N GLN C1059 " --> pdb=" O THR C 704 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE C 706 " --> pdb=" O PRO C1057 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE C 708 " --> pdb=" O TYR C1055 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR C1055 " --> pdb=" O ILE C 708 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL C 710 " --> pdb=" O VAL C1053 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL C1053 " --> pdb=" O VAL C 710 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR C 712 " --> pdb=" O LEU C1051 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU C1051 " --> pdb=" O THR C 712 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C 714 " --> pdb=" O VAL C1049 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL C1049 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY C1047 " --> pdb=" O PRO C 716 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR C1064 " --> pdb=" O SER C1085 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA C1066 " --> pdb=" O PHE C1083 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE C1083 " --> pdb=" O ALA C1066 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 721 through 724 removed outlier: 4.266A pdb=" N LYS C 721 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 784 through 785 Processing sheet with id=AF6, first strand: chain 'C' and resid 1108 through 1113 removed outlier: 4.297A pdb=" N ALA C1075 " --> pdb=" O SER C1111 " (cutoff:3.500A) 1154 hydrogen bonds defined for protein. 3048 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: 6.08 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7899 1.34 - 1.46: 4021 1.46 - 1.58: 14186 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 26262 Sorted by residual: bond pdb=" N ILE B1056 " pdb=" CA ILE B1056 " ideal model delta sigma weight residual 1.454 1.493 -0.038 7.70e-03 1.69e+04 2.44e+01 bond pdb=" N ILE A1056 " pdb=" CA ILE A1056 " ideal model delta sigma weight residual 1.454 1.492 -0.038 7.70e-03 1.69e+04 2.43e+01 bond pdb=" N ILE C1056 " pdb=" CA ILE C1056 " ideal model delta sigma weight residual 1.454 1.492 -0.037 7.70e-03 1.69e+04 2.34e+01 bond pdb=" N ILE C 655 " pdb=" CA ILE C 655 " ideal model delta sigma weight residual 1.458 1.493 -0.035 7.70e-03 1.69e+04 2.08e+01 bond pdb=" N ILE B 655 " pdb=" CA ILE B 655 " ideal model delta sigma weight residual 1.458 1.493 -0.035 7.70e-03 1.69e+04 2.08e+01 ... (remaining 26257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 30525 2.19 - 4.38: 4887 4.38 - 6.58: 336 6.58 - 8.77: 24 8.77 - 10.96: 21 Bond angle restraints: 35793 Sorted by residual: angle pdb=" CG GLN C 792 " pdb=" CD GLN C 792 " pdb=" NE2 GLN C 792 " ideal model delta sigma weight residual 116.40 106.67 9.73 1.50e+00 4.44e-01 4.21e+01 angle pdb=" CG GLN A 792 " pdb=" CD GLN A 792 " pdb=" NE2 GLN A 792 " ideal model delta sigma weight residual 116.40 106.71 9.69 1.50e+00 4.44e-01 4.17e+01 angle pdb=" CG GLN B 792 " pdb=" CD GLN B 792 " pdb=" NE2 GLN B 792 " ideal model delta sigma weight residual 116.40 106.73 9.67 1.50e+00 4.44e-01 4.15e+01 angle pdb=" CA THR B1105 " pdb=" CB THR B1105 " pdb=" OG1 THR B1105 " ideal model delta sigma weight residual 109.60 100.30 9.30 1.50e+00 4.44e-01 3.84e+01 angle pdb=" CA THR A1105 " pdb=" CB THR A1105 " pdb=" OG1 THR A1105 " ideal model delta sigma weight residual 109.60 100.31 9.29 1.50e+00 4.44e-01 3.83e+01 ... (remaining 35788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.88: 15275 20.88 - 41.77: 577 41.77 - 62.65: 156 62.65 - 83.53: 33 83.53 - 104.42: 18 Dihedral angle restraints: 16059 sinusoidal: 6636 harmonic: 9423 Sorted by residual: dihedral pdb=" CD ARG C 457 " pdb=" NE ARG C 457 " pdb=" CZ ARG C 457 " pdb=" NH1 ARG C 457 " ideal model delta sinusoidal sigma weight residual 0.00 49.86 -49.86 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CD ARG B 457 " pdb=" NE ARG B 457 " pdb=" CZ ARG B 457 " pdb=" NH1 ARG B 457 " ideal model delta sinusoidal sigma weight residual 0.00 49.85 -49.85 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CD ARG A 457 " pdb=" NE ARG A 457 " pdb=" CZ ARG A 457 " pdb=" NH1 ARG A 457 " ideal model delta sinusoidal sigma weight residual 0.00 49.85 -49.85 1 1.00e+01 1.00e-02 3.41e+01 ... (remaining 16056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1859 0.063 - 0.125: 1472 0.125 - 0.188: 647 0.188 - 0.251: 189 0.251 - 0.313: 15 Chirality restraints: 4182 Sorted by residual: chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.20e+01 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.12e+01 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.94e+01 ... (remaining 4179 not shown) Planarity restraints: 4596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 457 " -0.829 9.50e-02 1.11e+02 3.71e-01 8.40e+01 pdb=" NE ARG C 457 " 0.050 2.00e-02 2.50e+03 pdb=" CZ ARG C 457 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 457 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 457 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 457 " 0.828 9.50e-02 1.11e+02 3.71e-01 8.39e+01 pdb=" NE ARG A 457 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG A 457 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 457 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 457 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 457 " 0.828 9.50e-02 1.11e+02 3.71e-01 8.38e+01 pdb=" NE ARG B 457 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG B 457 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 457 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 457 " 0.024 2.00e-02 2.50e+03 ... (remaining 4593 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 427 2.65 - 3.21: 22754 3.21 - 3.78: 40325 3.78 - 4.34: 59182 4.34 - 4.90: 92395 Nonbonded interactions: 215083 Sorted by model distance: nonbonded pdb=" C ASN A 547 " pdb=" CD1 ILE B 832 " model vdw 2.090 3.690 nonbonded pdb=" CD1 ILE A 832 " pdb=" C ASN C 547 " model vdw 2.090 3.690 nonbonded pdb=" C ASN B 547 " pdb=" CD1 ILE C 832 " model vdw 2.093 3.690 nonbonded pdb=" CD2 LEU A 882 " pdb=" OE1 GLU C1060 " model vdw 2.212 3.460 nonbonded pdb=" OE1 GLU B1060 " pdb=" CD2 LEU C 882 " model vdw 2.217 3.460 ... (remaining 215078 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.910 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.014 0.047 26340 Z= 1.044 Angle : 1.588 12.914 35985 Z= 1.146 Chirality : 0.097 0.313 4182 Planarity : 0.022 0.371 4575 Dihedral : 12.948 104.417 9879 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Cbeta Deviations : 0.30 % 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: -0.34 (0.13), residues: 3207 helix: 0.69 (0.19), residues: 732 sheet: 0.43 (0.19), residues: 612 loop : -0.83 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 403 TYR 0.029 0.003 TYR B 651 PHE 0.027 0.003 PHE B 91 TRP 0.018 0.003 TRP A 92 HIS 0.008 0.002 HIS A1076 Details of bonding type rmsd covalent geometry : bond 0.01389 (26262) covalent geometry : angle 1.56003 (35793) SS BOND : bond 0.00808 ( 42) SS BOND : angle 1.59925 ( 84) hydrogen bonds : bond 0.18390 ( 1109) hydrogen bonds : angle 8.31495 ( 3048) link_BETA1-4 : bond 0.04628 ( 15) link_BETA1-4 : angle 6.73624 ( 45) link_NAG-ASN : bond 0.00842 ( 21) link_NAG-ASN : angle 4.64346 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 534 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.9329 (ttp) cc_final: 0.9124 (ttm) REVERT: A 764 LYS cc_start: 0.7971 (tttt) cc_final: 0.7699 (tttp) REVERT: A 768 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7124 (mt-10) REVERT: B 276 MET cc_start: 0.9310 (ttp) cc_final: 0.9065 (ttp) REVERT: B 764 LYS cc_start: 0.7863 (tttt) cc_final: 0.7501 (ttpp) REVERT: B 768 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6775 (mt-10) REVERT: C 276 MET cc_start: 0.9272 (ttp) cc_final: 0.8972 (ttp) REVERT: C 764 LYS cc_start: 0.7928 (tttt) cc_final: 0.7721 (tttm) REVERT: C 825 TYR cc_start: 0.7685 (t80) cc_final: 0.7429 (t80) outliers start: 0 outliers final: 3 residues processed: 534 average time/residue: 0.7309 time to fit residues: 440.9734 Evaluate side-chains 264 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 261 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain C residue 957 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0570 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.0770 chunk 298 optimal weight: 0.8980 overall best weight: 0.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 258 ASN A 314 GLN A 317 ASN A 598 GLN A 637 GLN A 648 ASN A 649 ASN B 317 ASN ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 ASN B 943 ASN C 317 ASN C 323 GLN C 485 ASN C 637 GLN C 648 ASN C 666 HIS C 752 ASN C 957 ASN C 993 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.094206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.070954 restraints weight = 40849.978| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.60 r_work: 0.2692 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26340 Z= 0.125 Angle : 0.584 13.141 35985 Z= 0.307 Chirality : 0.045 0.381 4182 Planarity : 0.004 0.056 4575 Dihedral : 6.812 72.125 4242 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.81 % Allowed : 10.69 % Favored : 87.50 % 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: 0.52 (0.14), residues: 3207 helix: 2.11 (0.20), residues: 696 sheet: 0.77 (0.19), residues: 672 loop : -0.52 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 304 TYR 0.025 0.001 TYR A 651 PHE 0.023 0.001 PHE A1109 TRP 0.020 0.001 TRP A 88 HIS 0.003 0.001 HIS C 269 Details of bonding type rmsd covalent geometry : bond 0.00255 (26262) covalent geometry : angle 0.56021 (35793) SS BOND : bond 0.00186 ( 42) SS BOND : angle 0.73475 ( 84) hydrogen bonds : bond 0.05281 ( 1109) hydrogen bonds : angle 6.28604 ( 3048) link_BETA1-4 : bond 0.00846 ( 15) link_BETA1-4 : angle 2.63435 ( 45) link_NAG-ASN : bond 0.00349 ( 21) link_NAG-ASN : angle 3.32206 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 275 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.7663 (p90) cc_final: 0.7270 (p90) REVERT: A 94 GLN cc_start: 0.9288 (mm-40) cc_final: 0.8888 (mp10) REVERT: A 182 ARG cc_start: 0.8598 (mmm-85) cc_final: 0.8243 (tpt-90) REVERT: A 276 MET cc_start: 0.9372 (ttp) cc_final: 0.9077 (ttp) REVERT: A 719 MET cc_start: 0.9297 (ptp) cc_final: 0.8932 (ptm) REVERT: B 93 ASN cc_start: 0.8859 (p0) cc_final: 0.8623 (m-40) REVERT: B 276 MET cc_start: 0.9352 (ttp) cc_final: 0.9025 (ttp) REVERT: B 752 ASN cc_start: 0.8506 (m110) cc_final: 0.8183 (m110) REVERT: B 768 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8294 (mt-10) REVERT: B 782 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7136 (pp) REVERT: B 1123 ASN cc_start: 0.8546 (t0) cc_final: 0.8040 (t0) REVERT: C 68 ARG cc_start: 0.8048 (mtt-85) cc_final: 0.7653 (mtt-85) REVERT: C 276 MET cc_start: 0.9341 (ttp) cc_final: 0.9075 (ttp) REVERT: C 439 ARG cc_start: 0.8571 (ttp80) cc_final: 0.8272 (ttt-90) REVERT: C 478 GLN cc_start: 0.7832 (mp10) cc_final: 0.7503 (pm20) REVERT: C 719 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.9077 (ptm) REVERT: C 768 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8170 (mt-10) REVERT: C 809 LEU cc_start: 0.7735 (mp) cc_final: 0.7471 (tp) REVERT: C 895 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8363 (p0) outliers start: 51 outliers final: 9 residues processed: 304 average time/residue: 0.6609 time to fit residues: 230.6183 Evaluate side-chains 239 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 227 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 719 MET Chi-restraints excluded: chain C residue 895 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 160 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 239 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 286 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 649 ASN A 945 GLN A 993 GLN ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 GLN B 990 GLN C 594 ASN C 990 GLN C 993 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.086861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.063327 restraints weight = 41896.698| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 2.61 r_work: 0.2536 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 26340 Z= 0.236 Angle : 0.615 13.041 35985 Z= 0.320 Chirality : 0.049 0.546 4182 Planarity : 0.004 0.048 4575 Dihedral : 6.137 58.813 4236 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.02 % Allowed : 10.90 % Favored : 87.08 % 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: 0.54 (0.14), residues: 3207 helix: 2.08 (0.20), residues: 699 sheet: 0.88 (0.19), residues: 642 loop : -0.50 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 304 TYR 0.031 0.002 TYR B 486 PHE 0.019 0.002 PHE A1109 TRP 0.020 0.002 TRP B 874 HIS 0.007 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00562 (26262) covalent geometry : angle 0.59107 (35793) SS BOND : bond 0.00235 ( 42) SS BOND : angle 0.81994 ( 84) hydrogen bonds : bond 0.05616 ( 1109) hydrogen bonds : angle 6.00660 ( 3048) link_BETA1-4 : bond 0.00447 ( 15) link_BETA1-4 : angle 2.35876 ( 45) link_NAG-ASN : bond 0.00660 ( 21) link_NAG-ASN : angle 3.55631 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 235 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.7811 (p90) cc_final: 0.7528 (p90) REVERT: A 182 ARG cc_start: 0.8673 (mmm-85) cc_final: 0.8277 (tpt-90) REVERT: A 276 MET cc_start: 0.9429 (ttp) cc_final: 0.9182 (ttp) REVERT: A 478 GLN cc_start: 0.7813 (mp10) cc_final: 0.7455 (pm20) REVERT: A 719 MET cc_start: 0.9292 (ptp) cc_final: 0.8929 (ptm) REVERT: A 924 GLU cc_start: 0.8148 (mp0) cc_final: 0.7762 (mp0) REVERT: A 1074 LYS cc_start: 0.8186 (mtmm) cc_final: 0.7968 (mtmm) REVERT: A 1123 ASN cc_start: 0.8747 (t0) cc_final: 0.8383 (t0) REVERT: B 93 ASN cc_start: 0.8831 (p0) cc_final: 0.8494 (p0) REVERT: B 276 MET cc_start: 0.9416 (ttp) cc_final: 0.9169 (ttp) REVERT: B 386 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8029 (mmpt) REVERT: B 478 GLN cc_start: 0.7850 (mp10) cc_final: 0.7575 (pm20) REVERT: B 551 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7650 (mt0) REVERT: B 752 ASN cc_start: 0.8749 (m110) cc_final: 0.8384 (m-40) REVERT: B 782 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7400 (pp) REVERT: B 815 THR cc_start: 0.8771 (OUTLIER) cc_final: 0.8340 (p) REVERT: B 924 GLU cc_start: 0.8244 (mp0) cc_final: 0.8036 (mp0) REVERT: B 1123 ASN cc_start: 0.8763 (t0) cc_final: 0.8146 (t0) REVERT: C 68 ARG cc_start: 0.8254 (mtt-85) cc_final: 0.7984 (mtt-85) REVERT: C 276 MET cc_start: 0.9437 (ttp) cc_final: 0.9185 (ttp) REVERT: C 304 ARG cc_start: 0.8751 (mtt90) cc_final: 0.8512 (mpt-90) REVERT: C 424 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8524 (tttm) REVERT: C 719 MET cc_start: 0.9331 (ptp) cc_final: 0.9047 (ptm) REVERT: C 782 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7587 (pp) REVERT: C 809 LEU cc_start: 0.7985 (mp) cc_final: 0.7769 (tp) REVERT: C 815 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8231 (p) REVERT: C 895 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8497 (p0) REVERT: C 924 GLU cc_start: 0.8128 (mp0) cc_final: 0.7797 (mp0) REVERT: C 1074 LYS cc_start: 0.8240 (mtmm) cc_final: 0.8037 (mppt) REVERT: C 1123 ASN cc_start: 0.8806 (t0) cc_final: 0.8539 (t0) outliers start: 57 outliers final: 17 residues processed: 269 average time/residue: 0.7271 time to fit residues: 223.7909 Evaluate side-chains 249 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 677 ASN Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 895 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 276 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 144 optimal weight: 0.7980 chunk 259 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 485 ASN B 604 GLN B 649 ASN B 990 GLN C 649 ASN C 993 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.086703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.062964 restraints weight = 41456.257| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 2.63 r_work: 0.2527 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26340 Z= 0.178 Angle : 0.551 13.315 35985 Z= 0.289 Chirality : 0.045 0.369 4182 Planarity : 0.004 0.037 4575 Dihedral : 5.238 54.105 4236 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.85 % Allowed : 11.61 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.14), residues: 3207 helix: 2.19 (0.20), residues: 702 sheet: 0.82 (0.19), residues: 645 loop : -0.40 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 68 TYR 0.020 0.002 TYR B 486 PHE 0.016 0.001 PHE A1109 TRP 0.021 0.001 TRP B 874 HIS 0.005 0.001 HIS C 616 Details of bonding type rmsd covalent geometry : bond 0.00419 (26262) covalent geometry : angle 0.52809 (35793) SS BOND : bond 0.00186 ( 42) SS BOND : angle 0.71726 ( 84) hydrogen bonds : bond 0.04946 ( 1109) hydrogen bonds : angle 5.79561 ( 3048) link_BETA1-4 : bond 0.00443 ( 15) link_BETA1-4 : angle 2.08676 ( 45) link_NAG-ASN : bond 0.00430 ( 21) link_NAG-ASN : angle 3.32012 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 234 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.7822 (p90) cc_final: 0.7544 (p90) REVERT: A 182 ARG cc_start: 0.8667 (mmm-85) cc_final: 0.8251 (tpt-90) REVERT: A 478 GLN cc_start: 0.7802 (mp10) cc_final: 0.7427 (pm20) REVERT: A 679 ARG cc_start: 0.8758 (pmm-80) cc_final: 0.8380 (pmm-80) REVERT: A 719 MET cc_start: 0.9309 (ptp) cc_final: 0.8967 (ptm) REVERT: A 809 LEU cc_start: 0.8178 (mp) cc_final: 0.7857 (tp) REVERT: A 847 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8725 (p) REVERT: A 924 GLU cc_start: 0.8018 (mp0) cc_final: 0.7752 (mp0) REVERT: A 1123 ASN cc_start: 0.8823 (t0) cc_final: 0.8420 (t0) REVERT: B 76 GLU cc_start: 0.8686 (tp30) cc_final: 0.8465 (tm-30) REVERT: B 93 ASN cc_start: 0.8813 (p0) cc_final: 0.8490 (p0) REVERT: B 272 ARG cc_start: 0.8918 (ttm-80) cc_final: 0.8507 (ttm-80) REVERT: B 475 VAL cc_start: 0.8247 (t) cc_final: 0.7756 (m) REVERT: B 478 GLN cc_start: 0.7960 (mp10) cc_final: 0.7505 (pm20) REVERT: B 633 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8736 (mtm) REVERT: B 679 ARG cc_start: 0.8456 (ptp-170) cc_final: 0.8040 (ptt-90) REVERT: B 690 GLU cc_start: 0.8802 (tp30) cc_final: 0.8586 (tp30) REVERT: B 752 ASN cc_start: 0.8722 (m110) cc_final: 0.8372 (m-40) REVERT: B 782 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7470 (pp) REVERT: B 815 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8500 (p) REVERT: B 847 THR cc_start: 0.8971 (m) cc_final: 0.8584 (p) REVERT: B 924 GLU cc_start: 0.8105 (mp0) cc_final: 0.7784 (mp0) REVERT: B 998 GLN cc_start: 0.8617 (tp40) cc_final: 0.7946 (tt0) REVERT: B 1123 ASN cc_start: 0.8853 (t0) cc_final: 0.8355 (t0) REVERT: C 76 GLU cc_start: 0.8608 (tp30) cc_final: 0.8397 (tm-30) REVERT: C 184 ASP cc_start: 0.8719 (m-30) cc_final: 0.8256 (m-30) REVERT: C 276 MET cc_start: 0.9424 (ttp) cc_final: 0.9145 (ttp) REVERT: C 424 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8474 (tttm) REVERT: C 475 VAL cc_start: 0.8256 (t) cc_final: 0.7794 (m) REVERT: C 478 GLN cc_start: 0.7907 (mp10) cc_final: 0.7516 (pm20) REVERT: C 719 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.9029 (ptm) REVERT: C 809 LEU cc_start: 0.8054 (mp) cc_final: 0.7843 (tp) REVERT: C 815 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8440 (p) REVERT: C 924 GLU cc_start: 0.8013 (mp0) cc_final: 0.7680 (mp0) REVERT: C 1123 ASN cc_start: 0.8848 (t0) cc_final: 0.8587 (t0) outliers start: 52 outliers final: 18 residues processed: 270 average time/residue: 0.7504 time to fit residues: 230.4560 Evaluate side-chains 250 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 1121 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 719 MET Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 922 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 225 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 156 optimal weight: 0.3980 chunk 263 optimal weight: 1.9990 chunk 304 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 604 GLN C 993 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.086631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.062916 restraints weight = 41333.728| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 2.63 r_work: 0.2583 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 26340 Z= 0.161 Angle : 0.531 11.558 35985 Z= 0.281 Chirality : 0.045 0.359 4182 Planarity : 0.004 0.039 4575 Dihedral : 4.775 54.091 4236 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.85 % Allowed : 11.96 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.14), residues: 3207 helix: 2.14 (0.20), residues: 720 sheet: 0.93 (0.19), residues: 672 loop : -0.30 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 68 TYR 0.018 0.001 TYR A 265 PHE 0.019 0.001 PHE B 634 TRP 0.025 0.001 TRP B 874 HIS 0.004 0.001 HIS C 616 Details of bonding type rmsd covalent geometry : bond 0.00375 (26262) covalent geometry : angle 0.50859 (35793) SS BOND : bond 0.00173 ( 42) SS BOND : angle 0.66855 ( 84) hydrogen bonds : bond 0.04721 ( 1109) hydrogen bonds : angle 5.68506 ( 3048) link_BETA1-4 : bond 0.00404 ( 15) link_BETA1-4 : angle 1.93508 ( 45) link_NAG-ASN : bond 0.00429 ( 21) link_NAG-ASN : angle 3.33413 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 240 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.7810 (p90) cc_final: 0.7532 (p90) REVERT: A 182 ARG cc_start: 0.8663 (mmm-85) cc_final: 0.8236 (tpt-90) REVERT: A 424 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8412 (tttp) REVERT: A 475 VAL cc_start: 0.8413 (t) cc_final: 0.7899 (m) REVERT: A 478 GLN cc_start: 0.7826 (mp10) cc_final: 0.7307 (pm20) REVERT: A 679 ARG cc_start: 0.8684 (pmm-80) cc_final: 0.8163 (pmm-80) REVERT: A 690 GLU cc_start: 0.8876 (tp30) cc_final: 0.8476 (tm-30) REVERT: A 719 MET cc_start: 0.9285 (ptp) cc_final: 0.8845 (ptm) REVERT: A 809 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7796 (tp) REVERT: A 815 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8492 (p) REVERT: A 835 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7519 (mtt180) REVERT: A 847 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8728 (p) REVERT: A 923 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8715 (mm-40) REVERT: A 924 GLU cc_start: 0.7980 (mp0) cc_final: 0.7709 (mp0) REVERT: A 973 ASP cc_start: 0.7680 (p0) cc_final: 0.7176 (p0) REVERT: A 976 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8024 (mp0) REVERT: A 1123 ASN cc_start: 0.8854 (t0) cc_final: 0.8440 (t0) REVERT: B 76 GLU cc_start: 0.8732 (tp30) cc_final: 0.8247 (tm-30) REVERT: B 93 ASN cc_start: 0.8811 (p0) cc_final: 0.8514 (p0) REVERT: B 272 ARG cc_start: 0.8931 (ttm-80) cc_final: 0.8333 (ttm-80) REVERT: B 386 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.7890 (mmpt) REVERT: B 475 VAL cc_start: 0.8251 (t) cc_final: 0.7914 (m) REVERT: B 478 GLN cc_start: 0.7979 (mp10) cc_final: 0.7559 (pm20) REVERT: B 633 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8778 (mtm) REVERT: B 679 ARG cc_start: 0.8368 (ptp-170) cc_final: 0.7894 (ptt-90) REVERT: B 690 GLU cc_start: 0.8827 (tp30) cc_final: 0.8586 (tp30) REVERT: B 752 ASN cc_start: 0.8666 (m110) cc_final: 0.8349 (m-40) REVERT: B 782 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7465 (pp) REVERT: B 802 LYS cc_start: 0.8655 (ttmt) cc_final: 0.8439 (ttmm) REVERT: B 815 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8578 (p) REVERT: B 847 THR cc_start: 0.8917 (m) cc_final: 0.8606 (p) REVERT: B 924 GLU cc_start: 0.8093 (mp0) cc_final: 0.7731 (mp0) REVERT: B 998 GLN cc_start: 0.8531 (tp40) cc_final: 0.7862 (tt0) REVERT: B 1123 ASN cc_start: 0.8920 (t0) cc_final: 0.8504 (t0) REVERT: C 68 ARG cc_start: 0.8297 (mtt-85) cc_final: 0.7968 (mtt90) REVERT: C 184 ASP cc_start: 0.8740 (m-30) cc_final: 0.8270 (m-30) REVERT: C 276 MET cc_start: 0.9393 (ttp) cc_final: 0.9096 (ttp) REVERT: C 408 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8004 (ppt170) REVERT: C 424 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8361 (tttm) REVERT: C 475 VAL cc_start: 0.8305 (t) cc_final: 0.7785 (m) REVERT: C 478 GLN cc_start: 0.7894 (mp10) cc_final: 0.7439 (pm20) REVERT: C 719 MET cc_start: 0.9188 (ptp) cc_final: 0.8882 (ptm) REVERT: C 815 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8488 (p) REVERT: C 847 THR cc_start: 0.8974 (m) cc_final: 0.8489 (p) REVERT: C 924 GLU cc_start: 0.8046 (mp0) cc_final: 0.7693 (mp0) REVERT: C 976 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7721 (mp0) REVERT: C 998 GLN cc_start: 0.8573 (tp40) cc_final: 0.7956 (tt0) REVERT: C 1123 ASN cc_start: 0.8875 (t0) cc_final: 0.8493 (t0) outliers start: 52 outliers final: 18 residues processed: 275 average time/residue: 0.7418 time to fit residues: 231.6856 Evaluate side-chains 256 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 677 ASN Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 923 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 1121 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 135 optimal weight: 4.9990 chunk 312 optimal weight: 0.7980 chunk 268 optimal weight: 3.9990 chunk 184 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 316 optimal weight: 5.9990 chunk 77 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 238 optimal weight: 9.9990 chunk 269 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 132 GLN A 945 GLN B 75 HIS B 604 GLN B 943 ASN B 990 GLN C 75 HIS C 677 ASN C 993 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.086245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.062499 restraints weight = 41538.697| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 2.64 r_work: 0.2571 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2443 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 26340 Z= 0.159 Angle : 0.529 12.270 35985 Z= 0.278 Chirality : 0.045 0.632 4182 Planarity : 0.004 0.042 4575 Dihedral : 4.823 54.264 4236 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.85 % Allowed : 12.53 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.14), residues: 3207 helix: 2.18 (0.20), residues: 720 sheet: 0.83 (0.19), residues: 642 loop : -0.25 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 68 TYR 0.018 0.001 TYR A 265 PHE 0.012 0.001 PHE A1109 TRP 0.028 0.001 TRP B 874 HIS 0.004 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00372 (26262) covalent geometry : angle 0.50678 (35793) SS BOND : bond 0.00165 ( 42) SS BOND : angle 0.64480 ( 84) hydrogen bonds : bond 0.04655 ( 1109) hydrogen bonds : angle 5.63576 ( 3048) link_BETA1-4 : bond 0.00396 ( 15) link_BETA1-4 : angle 1.84713 ( 45) link_NAG-ASN : bond 0.00313 ( 21) link_NAG-ASN : angle 3.31241 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 235 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 92 TRP cc_start: 0.7837 (p90) cc_final: 0.7554 (p90) REVERT: A 182 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.8229 (tpt-90) REVERT: A 238 LYS cc_start: 0.9179 (mtpm) cc_final: 0.8965 (mtmt) REVERT: A 424 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8446 (tttp) REVERT: A 475 VAL cc_start: 0.8444 (t) cc_final: 0.7971 (m) REVERT: A 478 GLN cc_start: 0.7840 (mp10) cc_final: 0.7374 (pm20) REVERT: A 679 ARG cc_start: 0.8685 (pmm-80) cc_final: 0.8188 (pmm-80) REVERT: A 690 GLU cc_start: 0.8900 (tp30) cc_final: 0.8475 (tm-30) REVERT: A 719 MET cc_start: 0.9292 (ptp) cc_final: 0.8851 (ptm) REVERT: A 809 LEU cc_start: 0.8061 (mp) cc_final: 0.7798 (tp) REVERT: A 813 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8120 (mmmt) REVERT: A 815 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8586 (p) REVERT: A 835 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7434 (mtt180) REVERT: A 923 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8674 (mm-40) REVERT: A 924 GLU cc_start: 0.8001 (mp0) cc_final: 0.7683 (mp0) REVERT: A 973 ASP cc_start: 0.7625 (p0) cc_final: 0.7136 (p0) REVERT: A 976 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8016 (mp0) REVERT: A 1123 ASN cc_start: 0.8844 (t0) cc_final: 0.8460 (t0) REVERT: B 76 GLU cc_start: 0.8769 (tp30) cc_final: 0.8336 (tm-30) REVERT: B 93 ASN cc_start: 0.8817 (p0) cc_final: 0.8539 (p0) REVERT: B 272 ARG cc_start: 0.8968 (ttm-80) cc_final: 0.8380 (ttm-80) REVERT: B 386 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.7881 (mmpt) REVERT: B 478 GLN cc_start: 0.7946 (mp10) cc_final: 0.7694 (mp10) REVERT: B 633 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8813 (mtm) REVERT: B 679 ARG cc_start: 0.8383 (ptp-170) cc_final: 0.7914 (ptt-90) REVERT: B 690 GLU cc_start: 0.8862 (tp30) cc_final: 0.8617 (tp30) REVERT: B 752 ASN cc_start: 0.8648 (m110) cc_final: 0.8269 (m-40) REVERT: B 782 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7480 (pp) REVERT: B 815 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8666 (p) REVERT: B 847 THR cc_start: 0.8905 (m) cc_final: 0.8612 (p) REVERT: B 924 GLU cc_start: 0.8148 (mp0) cc_final: 0.7871 (mp0) REVERT: B 998 GLN cc_start: 0.8522 (tp40) cc_final: 0.7868 (tt0) REVERT: B 1123 ASN cc_start: 0.8967 (t0) cc_final: 0.8579 (t0) REVERT: C 68 ARG cc_start: 0.8293 (mtt-85) cc_final: 0.7956 (mtt90) REVERT: C 184 ASP cc_start: 0.8776 (m-30) cc_final: 0.8320 (m-30) REVERT: C 276 MET cc_start: 0.9392 (ttp) cc_final: 0.9109 (ttp) REVERT: C 408 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8030 (ppt170) REVERT: C 424 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8343 (tttm) REVERT: C 475 VAL cc_start: 0.8303 (t) cc_final: 0.7813 (m) REVERT: C 478 GLN cc_start: 0.7917 (mp10) cc_final: 0.7443 (pm20) REVERT: C 690 GLU cc_start: 0.8817 (tt0) cc_final: 0.8369 (tp30) REVERT: C 719 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8882 (ptm) REVERT: C 815 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8529 (p) REVERT: C 847 THR cc_start: 0.8979 (m) cc_final: 0.8505 (p) REVERT: C 923 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8517 (mm-40) REVERT: C 924 GLU cc_start: 0.8079 (mp0) cc_final: 0.7755 (mp0) REVERT: C 976 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7701 (mp0) REVERT: C 998 GLN cc_start: 0.8591 (tp40) cc_final: 0.7982 (tt0) REVERT: C 1123 ASN cc_start: 0.8856 (t0) cc_final: 0.8548 (t0) outliers start: 52 outliers final: 20 residues processed: 269 average time/residue: 0.7123 time to fit residues: 218.9010 Evaluate side-chains 265 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 923 GLN Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 719 MET Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 923 GLN Chi-restraints excluded: chain C residue 1121 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 106 optimal weight: 10.0000 chunk 242 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 264 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 HIS A 677 ASN A 945 GLN B 990 GLN C 677 ASN C 993 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.086674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.063018 restraints weight = 41375.646| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.63 r_work: 0.2579 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26340 Z= 0.140 Angle : 0.527 13.584 35985 Z= 0.276 Chirality : 0.045 0.502 4182 Planarity : 0.004 0.039 4575 Dihedral : 4.793 54.062 4236 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.70 % Allowed : 12.82 % Favored : 85.48 % 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: 0.87 (0.14), residues: 3207 helix: 2.24 (0.20), residues: 720 sheet: 0.92 (0.19), residues: 678 loop : -0.22 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 272 TYR 0.017 0.001 TYR A 265 PHE 0.019 0.001 PHE B 634 TRP 0.032 0.001 TRP B 874 HIS 0.003 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00322 (26262) covalent geometry : angle 0.50311 (35793) SS BOND : bond 0.00156 ( 42) SS BOND : angle 0.61982 ( 84) hydrogen bonds : bond 0.04493 ( 1109) hydrogen bonds : angle 5.57856 ( 3048) link_BETA1-4 : bond 0.00402 ( 15) link_BETA1-4 : angle 1.77489 ( 45) link_NAG-ASN : bond 0.00374 ( 21) link_NAG-ASN : angle 3.47496 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 241 time to evaluate : 0.887 Fit side-chains REVERT: A 92 TRP cc_start: 0.7829 (p90) cc_final: 0.7543 (p90) REVERT: A 182 ARG cc_start: 0.8673 (mmm-85) cc_final: 0.8241 (tpt-90) REVERT: A 238 LYS cc_start: 0.9169 (mtpm) cc_final: 0.8956 (mtmt) REVERT: A 424 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8467 (tttp) REVERT: A 475 VAL cc_start: 0.8490 (t) cc_final: 0.8018 (m) REVERT: A 478 GLN cc_start: 0.7854 (mp10) cc_final: 0.7369 (pm20) REVERT: A 679 ARG cc_start: 0.8680 (pmm-80) cc_final: 0.8210 (pmm-80) REVERT: A 690 GLU cc_start: 0.8917 (tp30) cc_final: 0.8475 (tm-30) REVERT: A 719 MET cc_start: 0.9293 (ptp) cc_final: 0.8859 (ptm) REVERT: A 809 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7768 (tp) REVERT: A 813 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8102 (mmmt) REVERT: A 815 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8637 (p) REVERT: A 835 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7452 (mtt180) REVERT: A 924 GLU cc_start: 0.8032 (mp0) cc_final: 0.7685 (mp0) REVERT: A 973 ASP cc_start: 0.7580 (p0) cc_final: 0.7120 (p0) REVERT: A 976 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8016 (mp0) REVERT: A 1123 ASN cc_start: 0.8875 (t0) cc_final: 0.8473 (t0) REVERT: B 76 GLU cc_start: 0.8783 (tp30) cc_final: 0.8464 (tm-30) REVERT: B 93 ASN cc_start: 0.8825 (p0) cc_final: 0.8555 (p0) REVERT: B 272 ARG cc_start: 0.8982 (ttm-80) cc_final: 0.8302 (ttm-80) REVERT: B 386 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7875 (mmpt) REVERT: B 478 GLN cc_start: 0.7922 (mp10) cc_final: 0.7599 (pm20) REVERT: B 604 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8566 (mt0) REVERT: B 633 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8828 (mtm) REVERT: B 679 ARG cc_start: 0.8412 (ptp-170) cc_final: 0.7897 (ptt-90) REVERT: B 690 GLU cc_start: 0.8908 (tp30) cc_final: 0.8676 (tp30) REVERT: B 752 ASN cc_start: 0.8636 (m110) cc_final: 0.8261 (m-40) REVERT: B 782 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7527 (pp) REVERT: B 815 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8706 (p) REVERT: B 847 THR cc_start: 0.8909 (m) cc_final: 0.8638 (p) REVERT: B 924 GLU cc_start: 0.8187 (mp0) cc_final: 0.7867 (mp0) REVERT: B 998 GLN cc_start: 0.8530 (tp40) cc_final: 0.7880 (tt0) REVERT: B 1123 ASN cc_start: 0.9002 (t0) cc_final: 0.8576 (t0) REVERT: C 68 ARG cc_start: 0.8324 (mtt-85) cc_final: 0.8035 (mtt90) REVERT: C 184 ASP cc_start: 0.8779 (m-30) cc_final: 0.8318 (m-30) REVERT: C 408 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8038 (ppt170) REVERT: C 424 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8339 (tttm) REVERT: C 475 VAL cc_start: 0.8316 (t) cc_final: 0.7885 (m) REVERT: C 478 GLN cc_start: 0.7914 (mp10) cc_final: 0.7468 (pm20) REVERT: C 690 GLU cc_start: 0.8835 (tt0) cc_final: 0.8376 (tp30) REVERT: C 719 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8877 (ptm) REVERT: C 809 LEU cc_start: 0.8334 (tp) cc_final: 0.8132 (tt) REVERT: C 815 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8584 (p) REVERT: C 847 THR cc_start: 0.8971 (m) cc_final: 0.8553 (p) REVERT: C 924 GLU cc_start: 0.8070 (mp0) cc_final: 0.7726 (mp0) REVERT: C 973 ASP cc_start: 0.7449 (p0) cc_final: 0.6920 (p0) REVERT: C 976 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7928 (mp0) REVERT: C 998 GLN cc_start: 0.8581 (tp40) cc_final: 0.7983 (tt0) REVERT: C 1123 ASN cc_start: 0.8855 (t0) cc_final: 0.8549 (t0) outliers start: 48 outliers final: 17 residues processed: 274 average time/residue: 0.7689 time to fit residues: 239.2308 Evaluate side-chains 264 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 604 GLN Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 1121 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 719 MET Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 922 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 44 optimal weight: 4.9990 chunk 290 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 282 optimal weight: 2.9990 chunk 305 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN A 945 GLN B 990 GLN C 993 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.086483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.062725 restraints weight = 41722.747| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.64 r_work: 0.2578 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 26340 Z= 0.153 Angle : 0.529 12.522 35985 Z= 0.276 Chirality : 0.047 0.740 4182 Planarity : 0.004 0.040 4575 Dihedral : 4.877 54.396 4236 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.56 % Allowed : 13.17 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.15), residues: 3207 helix: 2.22 (0.20), residues: 720 sheet: 0.86 (0.19), residues: 690 loop : -0.19 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 182 TYR 0.018 0.001 TYR A 265 PHE 0.020 0.001 PHE B 634 TRP 0.040 0.002 TRP B 874 HIS 0.003 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00357 (26262) covalent geometry : angle 0.50663 (35793) SS BOND : bond 0.00163 ( 42) SS BOND : angle 0.63142 ( 84) hydrogen bonds : bond 0.04544 ( 1109) hydrogen bonds : angle 5.57478 ( 3048) link_BETA1-4 : bond 0.00371 ( 15) link_BETA1-4 : angle 1.75548 ( 45) link_NAG-ASN : bond 0.00384 ( 21) link_NAG-ASN : angle 3.39288 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 0.965 Fit side-chains REVERT: A 92 TRP cc_start: 0.7791 (p90) cc_final: 0.7532 (p90) REVERT: A 182 ARG cc_start: 0.8670 (mmm-85) cc_final: 0.8226 (tpt-90) REVERT: A 238 LYS cc_start: 0.9189 (mtpm) cc_final: 0.8969 (mtmt) REVERT: A 424 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8452 (tttp) REVERT: A 475 VAL cc_start: 0.8435 (t) cc_final: 0.7893 (m) REVERT: A 478 GLN cc_start: 0.7853 (mp10) cc_final: 0.7359 (pm20) REVERT: A 679 ARG cc_start: 0.8683 (pmm-80) cc_final: 0.8210 (pmm-80) REVERT: A 690 GLU cc_start: 0.8922 (tp30) cc_final: 0.8487 (tm-30) REVERT: A 719 MET cc_start: 0.9290 (ptp) cc_final: 0.8855 (ptm) REVERT: A 809 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7862 (tp) REVERT: A 813 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8246 (mmmt) REVERT: A 815 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8636 (p) REVERT: A 835 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7482 (mtt180) REVERT: A 924 GLU cc_start: 0.8024 (mp0) cc_final: 0.7764 (mm-30) REVERT: A 973 ASP cc_start: 0.7547 (p0) cc_final: 0.7076 (p0) REVERT: A 976 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8009 (mp0) REVERT: A 1123 ASN cc_start: 0.8870 (t0) cc_final: 0.8472 (t0) REVERT: B 93 ASN cc_start: 0.8813 (p0) cc_final: 0.8539 (p0) REVERT: B 386 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7854 (mmpt) REVERT: B 478 GLN cc_start: 0.7924 (mp10) cc_final: 0.7640 (pm20) REVERT: B 604 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8538 (mt0) REVERT: B 633 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8809 (mtm) REVERT: B 679 ARG cc_start: 0.8439 (ptp-170) cc_final: 0.7890 (ptt-90) REVERT: B 690 GLU cc_start: 0.8931 (tp30) cc_final: 0.8611 (tm-30) REVERT: B 752 ASN cc_start: 0.8622 (m110) cc_final: 0.8247 (m-40) REVERT: B 782 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7557 (pp) REVERT: B 815 THR cc_start: 0.9000 (OUTLIER) cc_final: 0.8740 (p) REVERT: B 847 THR cc_start: 0.8901 (m) cc_final: 0.8631 (p) REVERT: B 924 GLU cc_start: 0.8200 (mp0) cc_final: 0.7862 (mp0) REVERT: B 998 GLN cc_start: 0.8515 (tp40) cc_final: 0.7870 (tt0) REVERT: B 1123 ASN cc_start: 0.8999 (t0) cc_final: 0.8581 (t0) REVERT: C 68 ARG cc_start: 0.8331 (mtt-85) cc_final: 0.8050 (mtt90) REVERT: C 184 ASP cc_start: 0.8785 (m-30) cc_final: 0.8322 (m-30) REVERT: C 408 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8013 (ppt170) REVERT: C 424 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8318 (tttm) REVERT: C 475 VAL cc_start: 0.8297 (t) cc_final: 0.7838 (m) REVERT: C 478 GLN cc_start: 0.7909 (mp10) cc_final: 0.7437 (pm20) REVERT: C 679 ARG cc_start: 0.7851 (mtt90) cc_final: 0.7620 (ptp90) REVERT: C 690 GLU cc_start: 0.8865 (tt0) cc_final: 0.8447 (tp30) REVERT: C 719 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8857 (ptm) REVERT: C 815 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8620 (p) REVERT: C 847 THR cc_start: 0.8922 (m) cc_final: 0.8521 (p) REVERT: C 924 GLU cc_start: 0.8013 (mp0) cc_final: 0.7626 (mp0) REVERT: C 973 ASP cc_start: 0.7519 (p0) cc_final: 0.6978 (p0) REVERT: C 976 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7856 (mp0) REVERT: C 998 GLN cc_start: 0.8632 (tp40) cc_final: 0.8003 (tt0) REVERT: C 1111 SER cc_start: 0.8438 (t) cc_final: 0.8234 (m) REVERT: C 1123 ASN cc_start: 0.8879 (t0) cc_final: 0.8561 (t0) outliers start: 44 outliers final: 20 residues processed: 269 average time/residue: 0.7818 time to fit residues: 238.9892 Evaluate side-chains 268 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 604 GLN Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 1121 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 719 MET Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 1121 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 215 optimal weight: 5.9990 chunk 311 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN A 945 GLN B 646 HIS ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.084706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.060796 restraints weight = 42062.120| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 2.66 r_work: 0.2495 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2372 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26340 Z= 0.219 Angle : 0.572 12.697 35985 Z= 0.298 Chirality : 0.048 0.664 4182 Planarity : 0.004 0.040 4575 Dihedral : 5.066 55.845 4236 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.46 % Allowed : 13.49 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.15), residues: 3207 helix: 1.93 (0.19), residues: 741 sheet: 0.80 (0.19), residues: 684 loop : -0.18 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 182 TYR 0.024 0.002 TYR A 486 PHE 0.020 0.002 PHE B 634 TRP 0.053 0.002 TRP B 874 HIS 0.005 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00520 (26262) covalent geometry : angle 0.54999 (35793) SS BOND : bond 0.00209 ( 42) SS BOND : angle 0.71928 ( 84) hydrogen bonds : bond 0.05067 ( 1109) hydrogen bonds : angle 5.70002 ( 3048) link_BETA1-4 : bond 0.00295 ( 15) link_BETA1-4 : angle 1.86829 ( 45) link_NAG-ASN : bond 0.00440 ( 21) link_NAG-ASN : angle 3.40420 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 0.984 Fit side-chains REVERT: A 92 TRP cc_start: 0.7972 (p90) cc_final: 0.7743 (p90) REVERT: A 182 ARG cc_start: 0.8679 (mmm-85) cc_final: 0.8224 (tpt-90) REVERT: A 424 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8481 (tttp) REVERT: A 475 VAL cc_start: 0.8500 (t) cc_final: 0.7915 (m) REVERT: A 478 GLN cc_start: 0.7886 (mp10) cc_final: 0.7370 (pm20) REVERT: A 679 ARG cc_start: 0.8684 (pmm-80) cc_final: 0.8186 (pmm-80) REVERT: A 690 GLU cc_start: 0.8942 (tp30) cc_final: 0.8506 (tm-30) REVERT: A 719 MET cc_start: 0.9336 (ptp) cc_final: 0.9042 (ptm) REVERT: A 778 LYS cc_start: 0.9233 (mtpp) cc_final: 0.8987 (mtpp) REVERT: A 809 LEU cc_start: 0.8330 (mp) cc_final: 0.7979 (tp) REVERT: A 813 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8232 (mmmt) REVERT: A 815 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8667 (p) REVERT: A 835 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7546 (mtt180) REVERT: A 924 GLU cc_start: 0.8104 (mp0) cc_final: 0.7833 (mm-30) REVERT: A 973 ASP cc_start: 0.7703 (p0) cc_final: 0.7237 (p0) REVERT: A 976 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8067 (mp0) REVERT: A 1123 ASN cc_start: 0.8920 (t0) cc_final: 0.8529 (t0) REVERT: B 93 ASN cc_start: 0.8855 (p0) cc_final: 0.8577 (p0) REVERT: B 272 ARG cc_start: 0.9106 (ttm-80) cc_final: 0.8625 (ttm-80) REVERT: B 386 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.7972 (mmpt) REVERT: B 478 GLN cc_start: 0.7924 (mp10) cc_final: 0.7625 (pm20) REVERT: B 604 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8658 (mt0) REVERT: B 679 ARG cc_start: 0.8453 (ptp-170) cc_final: 0.7914 (ptt-90) REVERT: B 690 GLU cc_start: 0.8946 (tp30) cc_final: 0.8577 (tm-30) REVERT: B 752 ASN cc_start: 0.8730 (m110) cc_final: 0.8407 (m-40) REVERT: B 782 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7611 (pp) REVERT: B 815 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8792 (p) REVERT: B 847 THR cc_start: 0.8965 (m) cc_final: 0.8669 (p) REVERT: B 924 GLU cc_start: 0.8251 (mp0) cc_final: 0.7915 (mp0) REVERT: B 998 GLN cc_start: 0.8613 (tp40) cc_final: 0.8010 (tt0) REVERT: B 1123 ASN cc_start: 0.9020 (t0) cc_final: 0.8596 (t0) REVERT: C 68 ARG cc_start: 0.8376 (mtt-85) cc_final: 0.8099 (mtt90) REVERT: C 184 ASP cc_start: 0.8833 (m-30) cc_final: 0.8368 (m-30) REVERT: C 408 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8110 (ppt170) REVERT: C 424 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8533 (tttm) REVERT: C 475 VAL cc_start: 0.8472 (t) cc_final: 0.7929 (m) REVERT: C 478 GLN cc_start: 0.7947 (mp10) cc_final: 0.7458 (pm20) REVERT: C 679 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7683 (ptp90) REVERT: C 690 GLU cc_start: 0.8914 (tt0) cc_final: 0.8471 (tp30) REVERT: C 719 MET cc_start: 0.9225 (ptp) cc_final: 0.8907 (ptm) REVERT: C 815 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8649 (p) REVERT: C 847 THR cc_start: 0.8992 (m) cc_final: 0.8645 (p) REVERT: C 924 GLU cc_start: 0.8048 (mp0) cc_final: 0.7671 (mp0) REVERT: C 973 ASP cc_start: 0.7525 (p0) cc_final: 0.7032 (p0) REVERT: C 976 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7904 (mp0) REVERT: C 998 GLN cc_start: 0.8723 (tp40) cc_final: 0.8118 (tt0) outliers start: 41 outliers final: 22 residues processed: 257 average time/residue: 0.7781 time to fit residues: 226.9149 Evaluate side-chains 257 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 604 GLN Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 1121 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 1121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 110 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 chunk 310 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 189 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 198 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 221 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN A 945 GLN ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.087933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.064306 restraints weight = 41506.727| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.63 r_work: 0.2607 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26340 Z= 0.103 Angle : 0.504 11.242 35985 Z= 0.263 Chirality : 0.044 0.479 4182 Planarity : 0.004 0.039 4575 Dihedral : 4.742 52.671 4236 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.89 % Allowed : 14.06 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.15), residues: 3207 helix: 2.29 (0.20), residues: 726 sheet: 0.86 (0.19), residues: 690 loop : -0.16 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 182 TYR 0.014 0.001 TYR C 265 PHE 0.019 0.001 PHE B 634 TRP 0.045 0.002 TRP B 874 HIS 0.002 0.001 HIS C 616 Details of bonding type rmsd covalent geometry : bond 0.00223 (26262) covalent geometry : angle 0.48562 (35793) SS BOND : bond 0.00142 ( 42) SS BOND : angle 0.59995 ( 84) hydrogen bonds : bond 0.04037 ( 1109) hydrogen bonds : angle 5.45917 ( 3048) link_BETA1-4 : bond 0.00457 ( 15) link_BETA1-4 : angle 1.55227 ( 45) link_NAG-ASN : bond 0.00233 ( 21) link_NAG-ASN : angle 2.97972 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 1.009 Fit side-chains REVERT: A 92 TRP cc_start: 0.7762 (p90) cc_final: 0.7531 (p90) REVERT: A 182 ARG cc_start: 0.8682 (mmm-85) cc_final: 0.8231 (tpt-90) REVERT: A 238 LYS cc_start: 0.9182 (mtpm) cc_final: 0.8969 (mtmt) REVERT: A 475 VAL cc_start: 0.8480 (t) cc_final: 0.8039 (m) REVERT: A 478 GLN cc_start: 0.7846 (mp10) cc_final: 0.7374 (pm20) REVERT: A 679 ARG cc_start: 0.8673 (pmm-80) cc_final: 0.8187 (pmm-80) REVERT: A 690 GLU cc_start: 0.8956 (tp30) cc_final: 0.8570 (tm-30) REVERT: A 719 MET cc_start: 0.9306 (ptp) cc_final: 0.9023 (ptm) REVERT: A 809 LEU cc_start: 0.8036 (mp) cc_final: 0.7778 (tp) REVERT: A 813 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8203 (mmmt) REVERT: A 815 THR cc_start: 0.8984 (m) cc_final: 0.8686 (p) REVERT: A 835 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7443 (mtt180) REVERT: A 924 GLU cc_start: 0.7974 (mp0) cc_final: 0.7703 (mm-30) REVERT: A 973 ASP cc_start: 0.7515 (p0) cc_final: 0.7271 (p0) REVERT: A 990 GLN cc_start: 0.8863 (tt0) cc_final: 0.8573 (tp40) REVERT: A 1123 ASN cc_start: 0.8847 (t0) cc_final: 0.8438 (t0) REVERT: B 93 ASN cc_start: 0.8870 (p0) cc_final: 0.8602 (p0) REVERT: B 271 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8430 (mmtt) REVERT: B 272 ARG cc_start: 0.9097 (ttm-80) cc_final: 0.8586 (ttm-80) REVERT: B 386 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7860 (mmpt) REVERT: B 478 GLN cc_start: 0.7892 (mp10) cc_final: 0.7597 (pm20) REVERT: B 604 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8499 (mt0) REVERT: B 633 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8820 (mtm) REVERT: B 679 ARG cc_start: 0.8444 (ptp-170) cc_final: 0.7911 (ptt-90) REVERT: B 690 GLU cc_start: 0.8978 (tp30) cc_final: 0.8648 (tm-30) REVERT: B 752 ASN cc_start: 0.8681 (m110) cc_final: 0.8327 (m-40) REVERT: B 782 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7565 (pp) REVERT: B 847 THR cc_start: 0.8967 (m) cc_final: 0.8758 (p) REVERT: B 924 GLU cc_start: 0.8224 (mp0) cc_final: 0.7963 (mp0) REVERT: B 998 GLN cc_start: 0.8562 (tp40) cc_final: 0.7930 (tt0) REVERT: B 1060 GLU cc_start: 0.9073 (pm20) cc_final: 0.8392 (pm20) REVERT: B 1123 ASN cc_start: 0.9041 (t0) cc_final: 0.8623 (t0) REVERT: C 68 ARG cc_start: 0.8362 (mtt-85) cc_final: 0.8085 (mtt90) REVERT: C 184 ASP cc_start: 0.8853 (m-30) cc_final: 0.8319 (m-30) REVERT: C 408 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8041 (ppt170) REVERT: C 439 ARG cc_start: 0.8722 (ttp80) cc_final: 0.8474 (ttt-90) REVERT: C 475 VAL cc_start: 0.8484 (t) cc_final: 0.7983 (m) REVERT: C 478 GLN cc_start: 0.7898 (mp10) cc_final: 0.7419 (pm20) REVERT: C 679 ARG cc_start: 0.7946 (mtt90) cc_final: 0.7712 (ptp90) REVERT: C 690 GLU cc_start: 0.8909 (tt0) cc_final: 0.8483 (tp30) REVERT: C 719 MET cc_start: 0.9179 (ptp) cc_final: 0.8913 (ptm) REVERT: C 815 THR cc_start: 0.8968 (m) cc_final: 0.8711 (p) REVERT: C 847 THR cc_start: 0.8987 (m) cc_final: 0.8635 (p) REVERT: C 973 ASP cc_start: 0.7449 (p0) cc_final: 0.7009 (p0) REVERT: C 976 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7931 (mp0) REVERT: C 998 GLN cc_start: 0.8612 (tp40) cc_final: 0.7991 (tt0) REVERT: C 1123 ASN cc_start: 0.8876 (t0) cc_final: 0.8579 (t0) outliers start: 25 outliers final: 11 residues processed: 256 average time/residue: 0.8268 time to fit residues: 239.6783 Evaluate side-chains 249 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 604 GLN Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 895 ASN Chi-restraints excluded: chain C residue 922 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 231 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 249 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN A 945 GLN B 990 GLN ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 993 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.086888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.063042 restraints weight = 41521.952| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.66 r_work: 0.2594 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26340 Z= 0.140 Angle : 0.520 10.859 35985 Z= 0.273 Chirality : 0.044 0.444 4182 Planarity : 0.004 0.040 4575 Dihedral : 4.808 54.455 4236 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.75 % Allowed : 14.13 % Favored : 85.13 % 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: 0.94 (0.15), residues: 3207 helix: 2.25 (0.20), residues: 729 sheet: 0.89 (0.19), residues: 690 loop : -0.13 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 272 TYR 0.025 0.001 TYR C 253 PHE 0.021 0.001 PHE B 634 TRP 0.064 0.002 TRP B 874 HIS 0.003 0.001 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00323 (26262) covalent geometry : angle 0.50205 (35793) SS BOND : bond 0.00150 ( 42) SS BOND : angle 0.62118 ( 84) hydrogen bonds : bond 0.04344 ( 1109) hydrogen bonds : angle 5.48934 ( 3048) link_BETA1-4 : bond 0.00353 ( 15) link_BETA1-4 : angle 1.64650 ( 45) link_NAG-ASN : bond 0.00270 ( 21) link_NAG-ASN : angle 2.92532 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8776.41 seconds wall clock time: 150 minutes 21.79 seconds (9021.79 seconds total)