Starting phenix.real_space_refine on Mon May 4 14:54:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hek_52079/05_2026/9hek_52079.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hek_52079/05_2026/9hek_52079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hek_52079/05_2026/9hek_52079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hek_52079/05_2026/9hek_52079.map" model { file = "/net/cci-nas-00/data/ceres_data/9hek_52079/05_2026/9hek_52079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hek_52079/05_2026/9hek_52079.cif" } resolution = 3.15 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= 0.017 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: 6 Type Number sf(0) Gaussians Ca 19 9.91 5 Fe 2 7.16 5 S 209 5.16 5 C 13643 2.51 5 N 3927 2.21 5 O 4264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22064 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 6451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6451 Classifications: {'peptide': 852} Link IDs: {'PTRANS': 24, 'TRANS': 827} Chain breaks: 1 Chain: "C" Number of atoms: 5591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5591 Classifications: {'peptide': 737} Link IDs: {'PTRANS': 23, 'TRANS': 713} Chain breaks: 1 Chain: "B" Number of atoms: 5574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5574 Classifications: {'peptide': 735} Link IDs: {'PTRANS': 23, 'TRANS': 711} Chain breaks: 1 Chain: "D" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "E" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1084 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "F" Number of atoms: 1951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1951 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 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: 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: "J" 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: "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: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 37 Unusual residues: {' CA': 9, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 19 Unusual residues: {' CA': 5, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 33 Unusual residues: {' CA': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.05, per 1000 atoms: 0.23 Number of scatterers: 22064 At special positions: 0 Unit cell: (138.112, 148.096, 158.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 Ca 19 19.99 S 209 16.00 O 4264 8.00 N 3927 7.00 C 13643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=88, symmetry=0 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 258 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 238 " distance=2.03 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 416 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 462 " distance=2.03 Simple disulfide: pdb=" SG CYS A 411 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 442 " - pdb=" SG CYS A 452 " distance=2.02 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 577 " distance=2.04 Simple disulfide: pdb=" SG CYS A 547 " - pdb=" SG CYS A 557 " distance=2.03 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 626 " distance=2.02 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 682 " distance=2.02 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 728 " - pdb=" SG CYS A 762 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 808 " distance=2.03 Simple disulfide: pdb=" SG CYS A 757 " - pdb=" SG CYS A 818 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS A 835 " - pdb=" SG CYS A 869 " distance=2.02 Simple disulfide: pdb=" SG CYS A 864 " - pdb=" SG CYS A 925 " distance=2.04 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS A 905 " distance=2.03 Simple disulfide: pdb=" SG CYS A 938 " - pdb=" SG CYS A 972 " distance=2.03 Simple disulfide: pdb=" SG CYS A 954 " - pdb=" SG CYS A1018 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A1028 " distance=2.03 Simple disulfide: pdb=" SG CYS A 998 " - pdb=" SG CYS A1008 " distance=2.03 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C 309 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 355 " distance=2.03 Simple disulfide: pdb=" SG CYS C 304 " - pdb=" SG CYS C 365 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 416 " distance=2.02 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 462 " distance=2.03 Simple disulfide: pdb=" SG CYS C 411 " - pdb=" SG CYS C 472 " distance=2.03 Simple disulfide: pdb=" SG CYS C 442 " - pdb=" SG CYS C 452 " distance=2.04 Simple disulfide: pdb=" SG CYS C 487 " - pdb=" SG CYS C 521 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 516 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 547 " - pdb=" SG CYS C 557 " distance=2.03 Simple disulfide: pdb=" SG CYS C 592 " - pdb=" SG CYS C 626 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 621 " - pdb=" SG CYS C 682 " distance=2.03 Simple disulfide: pdb=" SG CYS C 652 " - pdb=" SG CYS C 662 " distance=2.03 Simple disulfide: pdb=" SG CYS C 728 " - pdb=" SG CYS C 762 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 808 " distance=2.03 Simple disulfide: pdb=" SG CYS C 757 " - pdb=" SG CYS C 818 " distance=2.03 Simple disulfide: pdb=" SG CYS C 788 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 835 " - pdb=" SG CYS C 869 " distance=2.03 Simple disulfide: pdb=" SG CYS C 864 " - pdb=" SG CYS C 925 " distance=2.03 Simple disulfide: pdb=" SG CYS C 895 " - pdb=" SG CYS C 905 " distance=2.03 Simple disulfide: pdb=" SG CYS C 938 " - pdb=" SG CYS C 972 " distance=2.03 Simple disulfide: pdb=" SG CYS C 954 " - pdb=" SG CYS C1018 " distance=2.03 Simple disulfide: pdb=" SG CYS C 967 " - pdb=" SG CYS C1028 " distance=2.03 Simple disulfide: pdb=" SG CYS C 998 " - pdb=" SG CYS C1008 " distance=2.03 Simple disulfide: pdb=" SG CYS B 275 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 355 " distance=2.03 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 462 " distance=2.03 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 442 " - pdb=" SG CYS B 452 " distance=2.03 Simple disulfide: pdb=" SG CYS B 487 " - pdb=" SG CYS B 521 " distance=2.02 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 516 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 547 " - pdb=" SG CYS B 557 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 621 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS B 652 " - pdb=" SG CYS B 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 728 " - pdb=" SG CYS B 762 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 808 " distance=2.03 Simple disulfide: pdb=" SG CYS B 757 " - pdb=" SG CYS B 818 " distance=2.02 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 835 " - pdb=" SG CYS B 869 " distance=2.03 Simple disulfide: pdb=" SG CYS B 864 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B 895 " - pdb=" SG CYS B 905 " distance=2.03 Simple disulfide: pdb=" SG CYS B 938 " - pdb=" SG CYS B 972 " distance=2.03 Simple disulfide: pdb=" SG CYS B 954 " - pdb=" SG CYS B1018 " distance=2.03 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS B1028 " distance=2.02 Simple disulfide: pdb=" SG CYS B 998 " - pdb=" SG CYS B1008 " distance=2.03 Simple disulfide: pdb=" SG CYS F 90 " - pdb=" SG CYS F 207 " distance=2.04 Simple disulfide: pdb=" SG CYS F 250 " - pdb=" SG CYS F 281 " distance=2.03 Simple disulfide: pdb=" SG CYS F 292 " - pdb=" SG CYS F 322 " 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=2, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1201 " - " ASN A1027 " " NAG A1202 " - " ASN A 445 " " NAG B1201 " - " ASN B 320 " " NAG B1202 " - " ASN B1027 " " NAG C1201 " - " ASN C1027 " " NAG F 401 " - " ASN F 182 " " NAG G 1 " - " ASN A 767 " " NAG H 1 " - " ASN A 320 " " NAG I 1 " - " ASN C 767 " " NAG J 1 " - " ASN C 320 " " NAG K 1 " - " ASN B 767 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 1.1 seconds 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5066 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 50 sheets defined 25.0% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 189 through 200 removed outlier: 3.730A pdb=" N GLN A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 200 " --> pdb=" O ILE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.527A pdb=" N CYS A 238 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.892A pdb=" N ASP A 253 " --> pdb=" O HIS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.661A pdb=" N CYS A 345 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.869A pdb=" N ASP A 360 " --> pdb=" O HIS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 415 removed outlier: 3.795A pdb=" N VAL A 409 " --> pdb=" O LYS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 613 through 624 Processing helix chain 'A' and resid 658 through 662 Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'A' and resid 856 through 868 Processing helix chain 'A' and resid 901 through 905 removed outlier: 3.661A pdb=" N GLN A 904 " --> pdb=" O THR A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.041A pdb=" N VAL A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'A' and resid 1019 through 1023 removed outlier: 3.609A pdb=" N ASP A1023 " --> pdb=" O HIS A1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 307 Processing helix chain 'C' and resid 341 through 345 Processing helix chain 'C' and resid 403 through 414 removed outlier: 3.936A pdb=" N VAL C 409 " --> pdb=" O LYS C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 452 Processing helix chain 'C' and resid 474 through 476 No H-bonds generated for 'chain 'C' and resid 474 through 476' Processing helix chain 'C' and resid 504 through 507 removed outlier: 3.839A pdb=" N PHE C 507 " --> pdb=" O ASP C 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 504 through 507' Processing helix chain 'C' and resid 508 through 519 Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.770A pdb=" N ASP C 572 " --> pdb=" O HIS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 624 removed outlier: 3.573A pdb=" N VAL C 619 " --> pdb=" O GLU C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.796A pdb=" N ARG C 637 " --> pdb=" O GLY C 634 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE C 638 " --> pdb=" O GLY C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 662 Processing helix chain 'C' and resid 749 through 760 removed outlier: 3.778A pdb=" N VAL C 755 " --> pdb=" O SER C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 798 Processing helix chain 'C' and resid 809 through 813 removed outlier: 3.620A pdb=" N ASP C 813 " --> pdb=" O HIS C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 868 Processing helix chain 'C' and resid 901 through 905 Processing helix chain 'C' and resid 916 through 920 Processing helix chain 'C' and resid 959 through 971 removed outlier: 3.550A pdb=" N VAL C 965 " --> pdb=" O ASP C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1023 removed outlier: 3.786A pdb=" N ASP C1023 " --> pdb=" O HIS C1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 307 Processing helix chain 'B' and resid 356 through 360 removed outlier: 3.937A pdb=" N ASP B 360 " --> pdb=" O HIS B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 415 removed outlier: 4.675A pdb=" N VAL B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N CYS B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 568 through 572 Processing helix chain 'B' and resid 613 through 624 Processing helix chain 'B' and resid 658 through 662 Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 794 through 798 removed outlier: 3.629A pdb=" N GLN B 797 " --> pdb=" O ARG B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 813 removed outlier: 3.754A pdb=" N ASP B 813 " --> pdb=" O HIS B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 868 removed outlier: 3.836A pdb=" N VAL B 860 " --> pdb=" O SER B 856 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY B 861 " --> pdb=" O GLU B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 905 Processing helix chain 'B' and resid 916 through 920 Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.696A pdb=" N VAL B 965 " --> pdb=" O ASP B 961 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 970 " --> pdb=" O VAL B 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 19 removed outlier: 3.996A pdb=" N GLY D 19 " --> pdb=" O TRP D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 37 Processing helix chain 'D' and resid 38 through 44 removed outlier: 3.605A pdb=" N THR D 42 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR D 43 " --> pdb=" O THR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 73 Processing helix chain 'D' and resid 76 through 81 Processing helix chain 'D' and resid 81 through 90 Processing helix chain 'D' and resid 95 through 114 removed outlier: 4.065A pdb=" N PHE D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 100 " --> pdb=" O PRO D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 139 Processing helix chain 'E' and resid 5 through 17 Processing helix chain 'E' and resid 20 through 36 removed outlier: 3.870A pdb=" N VAL E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLY E 26 " --> pdb=" O ASP E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 42 removed outlier: 3.778A pdb=" N ARG E 41 " --> pdb=" O TRP E 38 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE E 42 " --> pdb=" O THR E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 47 Processing helix chain 'E' and resid 51 through 57 Processing helix chain 'E' and resid 58 through 78 Processing helix chain 'E' and resid 81 through 86 Processing helix chain 'E' and resid 86 through 96 Processing helix chain 'E' and resid 100 through 120 removed outlier: 4.114A pdb=" N PHE E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG E 105 " --> pdb=" O PRO E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 123 No H-bonds generated for 'chain 'E' and resid 121 through 123' Processing helix chain 'E' and resid 124 through 144 removed outlier: 3.549A pdb=" N ALA E 130 " --> pdb=" O PRO E 126 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N HIS E 144 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 145 No H-bonds generated for 'chain 'F' and resid 143 through 145' Processing helix chain 'F' and resid 154 through 159 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 246 through 256 Processing helix chain 'F' and resid 259 through 263 Processing helix chain 'F' and resid 336 through 347 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 162 removed outlier: 3.951A pdb=" N GLU A 158 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 162 removed outlier: 3.951A pdb=" N GLU A 158 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 269 removed outlier: 3.672A pdb=" N SER A 265 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 269 removed outlier: 3.672A pdb=" N SER A 265 " --> pdb=" O ARG A 282 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU A 279 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE A 290 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N HIS A 327 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 376 removed outlier: 6.740A pdb=" N THR A 471 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 376 removed outlier: 6.816A pdb=" N VAL A 386 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 397 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A 394 " --> pdb=" O THR A 435 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU A 437 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS A 396 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 476 through 482 Processing sheet with id=AA8, first strand: chain 'A' and resid 476 through 482 removed outlier: 6.447A pdb=" N GLY A 574 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ILE A 527 " --> pdb=" O GLY A 574 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A 576 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 582 through 586 removed outlier: 4.638A pdb=" N GLU A 582 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE A 681 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 582 through 586 removed outlier: 4.638A pdb=" N GLU A 582 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 596 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N TRP A 604 " --> pdb=" O GLN A 644 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TRP A 646 " --> pdb=" O TRP A 604 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N SER A 606 " --> pdb=" O TRP A 646 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 649 through 650 Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 726 removed outlier: 3.941A pdb=" N GLN A 718 " --> pdb=" O TYR A 735 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 724 " --> pdb=" O ALA A 729 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ALA A 729 " --> pdb=" O GLY A 724 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 726 removed outlier: 3.941A pdb=" N GLN A 718 " --> pdb=" O TYR A 735 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 724 " --> pdb=" O ALA A 729 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ALA A 729 " --> pdb=" O GLY A 724 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A 732 " --> pdb=" O ILE A 743 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE A 743 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TRP A 782 " --> pdb=" O TRP A 740 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N THR A 742 " --> pdb=" O TRP A 782 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 831 through 832 Processing sheet with id=AB6, first strand: chain 'A' and resid 831 through 832 removed outlier: 6.658A pdb=" N LEU A 839 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 850 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP A 889 " --> pdb=" O TRP A 847 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N THR A 849 " --> pdb=" O TRP A 889 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 929 through 933 removed outlier: 6.900A pdb=" N ASN A1027 " --> pdb=" O LEU A 976 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 929 through 933 removed outlier: 6.660A pdb=" N VAL A 942 " --> pdb=" O VAL A 953 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 953 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N TRP A 992 " --> pdb=" O TRP A 950 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N THR A 952 " --> pdb=" O TRP A 992 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 267 through 269 Processing sheet with id=AC1, first strand: chain 'C' and resid 267 through 269 Processing sheet with id=AC2, first strand: chain 'C' and resid 371 through 380 removed outlier: 7.009A pdb=" N ALA C 383 " --> pdb=" O GLY C 378 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR C 471 " --> pdb=" O LEU C 420 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 437 through 438 Processing sheet with id=AC4, first strand: chain 'C' and resid 477 through 482 Processing sheet with id=AC5, first strand: chain 'C' and resid 477 through 482 removed outlier: 6.579A pdb=" N VAL C 491 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE C 502 " --> pdb=" O VAL C 491 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN C 539 " --> pdb=" O TRP C 499 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 544 through 545 Processing sheet with id=AC7, first strand: chain 'C' and resid 583 through 585 Processing sheet with id=AC8, first strand: chain 'C' and resid 583 through 585 removed outlier: 7.375A pdb=" N ILE C 681 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 649 through 650 Processing sheet with id=AD1, first strand: chain 'C' and resid 719 through 723 removed outlier: 6.341A pdb=" N GLY C 815 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA C 768 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE C 817 " --> pdb=" O ILE C 766 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 719 through 723 removed outlier: 6.938A pdb=" N VAL C 732 " --> pdb=" O ILE C 743 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE C 743 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N TRP C 782 " --> pdb=" O TRP C 740 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N THR C 742 " --> pdb=" O TRP C 782 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 823 through 827 removed outlier: 3.597A pdb=" N SER C 823 " --> pdb=" O PHE C 842 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 823 through 827 removed outlier: 3.597A pdb=" N SER C 823 " --> pdb=" O PHE C 842 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU C 839 " --> pdb=" O VAL C 850 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL C 850 " --> pdb=" O LEU C 839 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP C 889 " --> pdb=" O TRP C 847 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR C 849 " --> pdb=" O TRP C 889 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 929 through 932 removed outlier: 3.963A pdb=" N ALA C1025 " --> pdb=" O PHE C 979 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 929 through 932 removed outlier: 6.774A pdb=" N VAL C 942 " --> pdb=" O VAL C 953 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL C 953 " --> pdb=" O VAL C 942 " (cutoff:3.500A) removed outlier: 10.429A pdb=" N TRP C 950 " --> pdb=" O ILE C 991 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N LEU C 993 " --> pdb=" O TRP C 950 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR C 952 " --> pdb=" O LEU C 993 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N GLU C 995 " --> pdb=" O THR C 952 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN C 994 " --> pdb=" O ARG C1012 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG C1012 " --> pdb=" O ASN C 994 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL C 996 " --> pdb=" O ALA C1010 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA C1010 " --> pdb=" O VAL C 996 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 265 through 269 removed outlier: 3.658A pdb=" N SER B 265 " --> pdb=" O ARG B 282 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 265 through 269 removed outlier: 3.658A pdb=" N SER B 265 " --> pdb=" O ARG B 282 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU B 279 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE B 290 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP B 287 " --> pdb=" O HIS B 327 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TRP B 329 " --> pdb=" O TRP B 287 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR B 289 " --> pdb=" O TRP B 329 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 371 through 376 removed outlier: 6.932A pdb=" N THR B 471 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 371 through 376 removed outlier: 7.320A pdb=" N VAL B 386 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL B 397 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N LEU B 437 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS B 396 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 476 through 480 Processing sheet with id=AE3, first strand: chain 'B' and resid 476 through 480 Processing sheet with id=AE4, first strand: chain 'B' and resid 582 through 586 removed outlier: 4.542A pdb=" N GLU B 582 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE B 681 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 582 through 586 removed outlier: 4.542A pdb=" N GLU B 582 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 596 " --> pdb=" O LEU B 607 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN B 644 " --> pdb=" O TRP B 604 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 649 through 650 Processing sheet with id=AE7, first strand: chain 'B' and resid 719 through 722 Processing sheet with id=AE8, first strand: chain 'B' and resid 719 through 722 removed outlier: 6.713A pdb=" N VAL B 732 " --> pdb=" O ILE B 743 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE B 743 " --> pdb=" O VAL B 732 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TRP B 782 " --> pdb=" O TRP B 740 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR B 742 " --> pdb=" O TRP B 782 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 831 through 834 removed outlier: 4.603A pdb=" N ARG B 832 " --> pdb=" O SER B 828 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER B 828 " --> pdb=" O ARG B 832 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU B 826 " --> pdb=" O ALA B 834 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 831 through 834 removed outlier: 4.603A pdb=" N ARG B 832 " --> pdb=" O SER B 828 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER B 828 " --> pdb=" O ARG B 832 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU B 826 " --> pdb=" O ALA B 834 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 929 through 932 removed outlier: 6.813A pdb=" N ASN B1027 " --> pdb=" O LEU B 976 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 929 through 932 removed outlier: 15.159A pdb=" N GLY B 940 " --> pdb=" O ASP B 955 " (cutoff:3.500A) removed outlier: 11.715A pdb=" N ASP B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL B 942 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 953 " --> pdb=" O VAL B 942 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 991 " --> pdb=" O TRP B 950 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR B 952 " --> pdb=" O ILE B 991 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 993 " --> pdb=" O THR B 952 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLU B 995 " --> pdb=" O CYS B 954 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASP B 956 " --> pdb=" O GLU B 995 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 108 through 109 removed outlier: 3.539A pdb=" N LEU F 108 " --> pdb=" O TYR F 239 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS F 281 " --> pdb=" O ALA F 245 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL F 329 " --> pdb=" O SER F 317 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE F 300 " --> pdb=" O THR F 313 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA F 299 " --> pdb=" O SER F 223 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N SER F 223 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N HIS F 303 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL F 219 " --> pdb=" O HIS F 303 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS F 238 " --> pdb=" O GLY F 224 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 170 through 172 removed outlier: 4.011A pdb=" N LEU F 164 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N GLY F 129 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N THR F 141 " --> pdb=" O GLY F 129 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE F 191 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE F 188 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU F 179 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU F 190 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL F 177 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LYS F 192 " --> pdb=" O GLU F 175 " (cutoff:3.500A) 842 hydrogen bonds defined for protein. 2229 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.14 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 8261 1.38 - 1.55: 13988 1.55 - 1.72: 75 1.72 - 1.88: 239 1.88 - 2.05: 8 Bond restraints: 22571 Sorted by residual: bond pdb=" O1 OXY D 202 " pdb=" O2 OXY D 202 " ideal model delta sigma weight residual 1.109 1.208 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" O1 OXY E 202 " pdb=" O2 OXY E 202 " ideal model delta sigma weight residual 1.109 1.207 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" N VAL B 397 " pdb=" CA VAL B 397 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.18e-02 7.18e+03 1.31e+01 bond pdb=" N CYS B 398 " pdb=" CA CYS B 398 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.24e-02 6.50e+03 6.83e+00 bond pdb=" N ASP B 399 " pdb=" CA ASP B 399 " ideal model delta sigma weight residual 1.461 1.486 -0.025 1.30e-02 5.92e+03 3.61e+00 ... (remaining 22566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 30047 2.36 - 4.71: 500 4.71 - 7.07: 58 7.07 - 9.42: 15 9.42 - 11.78: 3 Bond angle restraints: 30623 Sorted by residual: angle pdb=" C SER A 211 " pdb=" CA SER A 211 " pdb=" CB SER A 211 " ideal model delta sigma weight residual 116.54 110.00 6.54 1.15e+00 7.56e-01 3.24e+01 angle pdb=" CA GLU B1017 " pdb=" CB GLU B1017 " pdb=" CG GLU B1017 " ideal model delta sigma weight residual 114.10 123.16 -9.06 2.00e+00 2.50e-01 2.05e+01 angle pdb=" N LYS F 92 " pdb=" CA LYS F 92 " pdb=" C LYS F 92 " ideal model delta sigma weight residual 108.66 117.63 -8.97 2.16e+00 2.14e-01 1.72e+01 angle pdb=" CA GLU B 389 " pdb=" CB GLU B 389 " pdb=" CG GLU B 389 " ideal model delta sigma weight residual 114.10 121.85 -7.75 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA VAL B 397 " pdb=" C VAL B 397 " pdb=" O VAL B 397 " ideal model delta sigma weight residual 121.67 117.59 4.08 1.06e+00 8.90e-01 1.48e+01 ... (remaining 30618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 11947 18.00 - 36.00: 1200 36.00 - 53.99: 315 53.99 - 71.99: 69 71.99 - 89.99: 37 Dihedral angle restraints: 13568 sinusoidal: 5616 harmonic: 7952 Sorted by residual: dihedral pdb=" CB CYS A 592 " pdb=" SG CYS A 592 " pdb=" SG CYS A 626 " pdb=" CB CYS A 626 " ideal model delta sinusoidal sigma weight residual 93.00 179.64 -86.64 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYS B 304 " pdb=" SG CYS B 304 " pdb=" SG CYS B 365 " pdb=" CB CYS B 365 " ideal model delta sinusoidal sigma weight residual 93.00 165.80 -72.80 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CB CYS B 487 " pdb=" SG CYS B 487 " pdb=" SG CYS B 521 " pdb=" CB CYS B 521 " ideal model delta sinusoidal sigma weight residual -86.00 -155.85 69.85 1 1.00e+01 1.00e-02 6.29e+01 ... (remaining 13565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2443 0.052 - 0.104: 667 0.104 - 0.157: 156 0.157 - 0.209: 11 0.209 - 0.261: 4 Chirality restraints: 3281 Sorted by residual: chirality pdb=" CB THR B 498 " pdb=" CA THR B 498 " pdb=" OG1 THR B 498 " pdb=" CG2 THR B 498 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C1 NAG A1201 " pdb=" ND2 ASN A1027 " pdb=" C2 NAG A1201 " pdb=" O5 NAG A1201 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE C 316 " pdb=" N ILE C 316 " pdb=" C ILE C 316 " pdb=" CB ILE C 316 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3278 not shown) Planarity restraints: 3985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 320 " -0.011 2.00e-02 2.50e+03 3.52e-02 1.54e+01 pdb=" CG ASN C 320 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN C 320 " -0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN C 320 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 320 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.72e+00 pdb=" CG ASN C 320 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN C 320 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN C 320 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 466 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.63e+00 pdb=" C GLU A 466 " -0.048 2.00e-02 2.50e+03 pdb=" O GLU A 466 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU A 467 " 0.016 2.00e-02 2.50e+03 ... (remaining 3982 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 379 2.66 - 3.22: 20279 3.22 - 3.78: 32506 3.78 - 4.34: 45212 4.34 - 4.90: 74532 Nonbonded interactions: 172908 Sorted by model distance: nonbonded pdb=" OE1 GLU A 857 " pdb=" NZ LYS A 872 " model vdw 2.101 3.120 nonbonded pdb=" OD1 ASN C 356 " pdb=" N HIS C 357 " model vdw 2.150 3.120 nonbonded pdb=" N GLU C 446 " pdb=" OE1 GLU C 446 " model vdw 2.150 3.120 nonbonded pdb=" O ASN E 81 " pdb=" OG1 THR E 85 " model vdw 2.154 3.040 nonbonded pdb=" OE1 GLU C 933 " pdb=" NH1 ARG C 941 " model vdw 2.192 3.120 ... (remaining 172903 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 266 through 686 or resid 719 through 1201 or resid 1203 th \ rough 1206)) selection = (chain 'B' and (resid 266 through 1201 or resid 1203 through 1206)) selection = (chain 'C' and (resid 266 through 686 or resid 719 through 1201 or resid 1203 th \ rough 1206)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' } 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: 12.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.940 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 22678 Z= 0.170 Angle : 0.772 15.565 30850 Z= 0.403 Chirality : 0.050 0.261 3281 Planarity : 0.005 0.060 3974 Dihedral : 15.987 89.988 8238 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.56 % Allowed : 19.91 % Favored : 79.54 % 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: -0.85 (0.15), residues: 2836 helix: 1.02 (0.24), residues: 502 sheet: -0.51 (0.25), residues: 354 loop : -1.04 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 913 TYR 0.015 0.001 TYR C 424 PHE 0.017 0.001 PHE A 638 TRP 0.038 0.002 TRP B 402 HIS 0.008 0.001 HIS F 180 Details of bonding type rmsd covalent geometry : bond 0.00385 (22571) covalent geometry : angle 0.75418 (30623) SS BOND : bond 0.00369 ( 88) SS BOND : angle 1.54634 ( 176) hydrogen bonds : bond 0.14932 ( 738) hydrogen bonds : angle 6.37104 ( 2229) Misc. bond : bond 0.07012 ( 2) link_BETA1-4 : bond 0.01010 ( 6) link_BETA1-4 : angle 2.06746 ( 18) link_NAG-ASN : bond 0.00457 ( 11) link_NAG-ASN : angle 3.82269 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 469 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 TRP cc_start: 0.8182 (t-100) cc_final: 0.7967 (t-100) REVERT: A 922 TRP cc_start: 0.8576 (m100) cc_final: 0.8242 (m100) REVERT: A 979 PHE cc_start: 0.8446 (m-80) cc_final: 0.8189 (m-80) REVERT: C 295 TRP cc_start: 0.7392 (t-100) cc_final: 0.7182 (t-100) REVERT: C 329 TRP cc_start: 0.8387 (m100) cc_final: 0.7499 (m100) REVERT: C 855 MET cc_start: 0.8622 (tpt) cc_final: 0.7898 (tpt) REVERT: C 983 GLU cc_start: 0.8441 (tp30) cc_final: 0.8084 (tp30) REVERT: B 789 ASN cc_start: 0.7824 (t0) cc_final: 0.7484 (t0) REVERT: B 791 LYS cc_start: 0.7747 (tttt) cc_final: 0.7498 (mttt) REVERT: B 805 GLN cc_start: 0.7796 (mm110) cc_final: 0.7567 (mm110) REVERT: B 919 GLU cc_start: 0.8500 (tp30) cc_final: 0.8191 (tt0) REVERT: D 141 TYR cc_start: 0.8538 (t80) cc_final: 0.8015 (t80) REVERT: F 190 LEU cc_start: 0.6991 (mp) cc_final: 0.6666 (mp) REVERT: F 339 TRP cc_start: 0.7980 (t60) cc_final: 0.7457 (t60) outliers start: 13 outliers final: 6 residues processed: 475 average time/residue: 0.1618 time to fit residues: 116.1828 Evaluate side-chains 447 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 441 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 977 LYS Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 894 GLN Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 494 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 197 optimal weight: 0.0060 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 GLN C 348 HIS C 609 ASN C 964 GLN B 413 GLN B 445 ASN B 723 ASN B 736 HIS B 754 HIS B 797 GLN B 866 GLN B 894 GLN E 109 ASN F 230 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.146940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124405 restraints weight = 33882.165| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.56 r_work: 0.3486 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 22678 Z= 0.159 Angle : 0.629 9.864 30850 Z= 0.326 Chirality : 0.046 0.236 3281 Planarity : 0.004 0.055 3974 Dihedral : 7.371 86.707 3399 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.75 % Allowed : 18.19 % Favored : 79.06 % 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: -0.59 (0.15), residues: 2836 helix: 1.30 (0.23), residues: 530 sheet: -0.22 (0.26), residues: 341 loop : -0.95 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 376 TYR 0.010 0.001 TYR F 239 PHE 0.016 0.001 PHE B 638 TRP 0.020 0.002 TRP B 455 HIS 0.006 0.001 HIS B 569 Details of bonding type rmsd covalent geometry : bond 0.00369 (22571) covalent geometry : angle 0.61523 (30623) SS BOND : bond 0.00387 ( 88) SS BOND : angle 1.11680 ( 176) hydrogen bonds : bond 0.04279 ( 738) hydrogen bonds : angle 5.00720 ( 2229) Misc. bond : bond 0.08496 ( 2) link_BETA1-4 : bond 0.00790 ( 6) link_BETA1-4 : angle 2.43822 ( 18) link_NAG-ASN : bond 0.00391 ( 11) link_NAG-ASN : angle 3.01074 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 448 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.7438 (t80) cc_final: 0.6765 (t80) REVERT: A 348 HIS cc_start: 0.8597 (t-90) cc_final: 0.8344 (t-90) REVERT: A 350 TRP cc_start: 0.8143 (m100) cc_final: 0.7784 (m-10) REVERT: A 408 ASP cc_start: 0.7943 (m-30) cc_final: 0.7702 (m-30) REVERT: A 421 LYS cc_start: 0.8042 (tttt) cc_final: 0.7673 (ttpp) REVERT: A 539 GLN cc_start: 0.7216 (tm-30) cc_final: 0.6877 (tm-30) REVERT: A 657 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7721 (mm-40) REVERT: A 922 TRP cc_start: 0.8643 (m100) cc_final: 0.8328 (m100) REVERT: A 961 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6911 (p0) REVERT: A 994 ASN cc_start: 0.7790 (p0) cc_final: 0.7371 (p0) REVERT: C 392 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8133 (mtt180) REVERT: C 539 GLN cc_start: 0.8224 (mt0) cc_final: 0.7984 (mm-40) REVERT: C 622 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7611 (tp40) REVERT: C 752 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: C 771 SER cc_start: 0.8564 (m) cc_final: 0.8338 (p) REVERT: C 855 MET cc_start: 0.8703 (tpt) cc_final: 0.8080 (tpt) REVERT: C 860 VAL cc_start: 0.8575 (m) cc_final: 0.8351 (t) REVERT: C 983 GLU cc_start: 0.8472 (tp30) cc_final: 0.8143 (tp30) REVERT: B 399 ASP cc_start: 0.8297 (t70) cc_final: 0.7589 (p0) REVERT: B 408 ASP cc_start: 0.7978 (t0) cc_final: 0.7551 (t0) REVERT: B 455 TRP cc_start: 0.8762 (p-90) cc_final: 0.8514 (p-90) REVERT: B 598 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6581 (tt) REVERT: B 610 SER cc_start: 0.8055 (t) cc_final: 0.7833 (p) REVERT: B 723 ASN cc_start: 0.8472 (t160) cc_final: 0.8213 (t0) REVERT: B 789 ASN cc_start: 0.7752 (t0) cc_final: 0.7446 (t0) REVERT: B 791 LYS cc_start: 0.7787 (tttt) cc_final: 0.7497 (mttt) REVERT: B 805 GLN cc_start: 0.7746 (mm110) cc_final: 0.7511 (mm110) REVERT: B 919 GLU cc_start: 0.8527 (tp30) cc_final: 0.8243 (tt0) REVERT: B 922 TRP cc_start: 0.8359 (m100) cc_final: 0.7575 (m100) REVERT: B 995 GLU cc_start: 0.8199 (pm20) cc_final: 0.7576 (pm20) REVERT: D 71 VAL cc_start: 0.8535 (t) cc_final: 0.8280 (p) REVERT: E 106 LEU cc_start: 0.8647 (mt) cc_final: 0.8371 (mp) REVERT: F 339 TRP cc_start: 0.8319 (t60) cc_final: 0.7879 (t60) outliers start: 64 outliers final: 29 residues processed: 489 average time/residue: 0.1575 time to fit residues: 117.5326 Evaluate side-chains 473 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 440 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 889 TRP Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 752 ASP Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 317 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 197 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 238 optimal weight: 0.0770 chunk 169 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 270 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 GLN A 797 GLN C 609 ASN B 445 ASN B 754 HIS B 797 GLN B 866 GLN F 230 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.145014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.122451 restraints weight = 33723.884| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.55 r_work: 0.3436 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 22678 Z= 0.209 Angle : 0.643 9.960 30850 Z= 0.332 Chirality : 0.047 0.216 3281 Planarity : 0.005 0.054 3974 Dihedral : 6.966 88.925 3385 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.73 % Allowed : 18.28 % Favored : 77.99 % 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 (0.15), residues: 2836 helix: 1.23 (0.23), residues: 527 sheet: -0.24 (0.26), residues: 367 loop : -0.98 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 517 TYR 0.015 0.002 TYR F 239 PHE 0.023 0.002 PHE F 280 TRP 0.017 0.002 TRP C 295 HIS 0.034 0.002 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00483 (22571) covalent geometry : angle 0.62917 (30623) SS BOND : bond 0.00602 ( 88) SS BOND : angle 1.27769 ( 176) hydrogen bonds : bond 0.04282 ( 738) hydrogen bonds : angle 4.93252 ( 2229) Misc. bond : bond 0.09245 ( 2) link_BETA1-4 : bond 0.00933 ( 6) link_BETA1-4 : angle 2.22275 ( 18) link_NAG-ASN : bond 0.00352 ( 11) link_NAG-ASN : angle 2.78151 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 462 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 GLN cc_start: 0.8106 (mt0) cc_final: 0.7894 (mp10) REVERT: A 295 TRP cc_start: 0.8387 (t-100) cc_final: 0.8180 (t-100) REVERT: A 348 HIS cc_start: 0.8648 (t-90) cc_final: 0.8329 (t-90) REVERT: A 408 ASP cc_start: 0.8074 (m-30) cc_final: 0.7807 (m-30) REVERT: A 421 LYS cc_start: 0.8203 (tttt) cc_final: 0.7973 (ttpp) REVERT: A 539 GLN cc_start: 0.7366 (tm-30) cc_final: 0.7009 (tm-30) REVERT: A 657 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8158 (mp10) REVERT: A 778 THR cc_start: 0.8737 (t) cc_final: 0.8510 (m) REVERT: A 913 ARG cc_start: 0.8573 (ptm160) cc_final: 0.8347 (ptt90) REVERT: A 961 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6976 (p0) REVERT: A 994 ASN cc_start: 0.8013 (p0) cc_final: 0.7486 (p0) REVERT: C 356 ASN cc_start: 0.7313 (p0) cc_final: 0.7005 (t0) REVERT: C 367 ASP cc_start: 0.7166 (t0) cc_final: 0.6938 (t0) REVERT: C 389 GLU cc_start: 0.7691 (tp30) cc_final: 0.7451 (tt0) REVERT: C 409 VAL cc_start: 0.8654 (p) cc_final: 0.8432 (m) REVERT: C 539 GLN cc_start: 0.8230 (mt0) cc_final: 0.7930 (mm-40) REVERT: C 619 VAL cc_start: 0.8036 (t) cc_final: 0.7786 (t) REVERT: C 622 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7735 (tp40) REVERT: C 771 SER cc_start: 0.8730 (m) cc_final: 0.8447 (p) REVERT: C 874 LYS cc_start: 0.8539 (mttt) cc_final: 0.8311 (mttt) REVERT: B 399 ASP cc_start: 0.8400 (t70) cc_final: 0.7792 (p0) REVERT: B 408 ASP cc_start: 0.8096 (t0) cc_final: 0.7677 (t0) REVERT: B 455 TRP cc_start: 0.8797 (p-90) cc_final: 0.8564 (p-90) REVERT: B 494 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8502 (tttp) REVERT: B 598 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6830 (tp) REVERT: B 723 ASN cc_start: 0.8619 (t160) cc_final: 0.8234 (t0) REVERT: B 736 HIS cc_start: 0.6829 (OUTLIER) cc_final: 0.6272 (t-90) REVERT: B 789 ASN cc_start: 0.7810 (t0) cc_final: 0.7515 (t0) REVERT: B 791 LYS cc_start: 0.7856 (tttt) cc_final: 0.7603 (mttt) REVERT: B 805 GLN cc_start: 0.7809 (mm110) cc_final: 0.7560 (mm-40) REVERT: B 885 SER cc_start: 0.7688 (t) cc_final: 0.7461 (t) REVERT: B 919 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: B 922 TRP cc_start: 0.8410 (m100) cc_final: 0.7523 (m100) REVERT: B 924 THR cc_start: 0.8588 (t) cc_final: 0.8023 (p) REVERT: B 993 LEU cc_start: 0.8793 (mt) cc_final: 0.8556 (mt) REVERT: D 71 VAL cc_start: 0.8594 (t) cc_final: 0.8334 (p) REVERT: D 126 LEU cc_start: 0.8511 (mm) cc_final: 0.8294 (mt) REVERT: D 141 TYR cc_start: 0.8525 (t80) cc_final: 0.8048 (t80) REVERT: E 106 LEU cc_start: 0.8712 (mt) cc_final: 0.8452 (mp) REVERT: F 176 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7561 (ttpp) outliers start: 87 outliers final: 48 residues processed: 515 average time/residue: 0.1590 time to fit residues: 124.7502 Evaluate side-chains 499 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 445 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 889 TRP Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 872 LYS Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 494 LYS Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 569 HIS Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 835 CYS Chi-restraints excluded: chain B residue 919 GLU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 1026 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 317 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 258 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 242 optimal weight: 0.0770 chunk 229 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 262 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 241 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 142 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS C 609 ASN B 445 ASN B 495 HIS B 723 ASN B 754 HIS E 103 ASN E 109 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.144779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.121835 restraints weight = 33690.369| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.68 r_work: 0.3429 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 22678 Z= 0.165 Angle : 0.600 8.727 30850 Z= 0.311 Chirality : 0.046 0.226 3281 Planarity : 0.004 0.056 3974 Dihedral : 6.805 85.977 3385 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.99 % Allowed : 19.43 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 2836 helix: 1.32 (0.23), residues: 527 sheet: 0.01 (0.25), residues: 382 loop : -0.94 (0.13), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 517 TYR 0.015 0.001 TYR B 580 PHE 0.018 0.001 PHE F 280 TRP 0.019 0.001 TRP C 295 HIS 0.006 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00384 (22571) covalent geometry : angle 0.58863 (30623) SS BOND : bond 0.00414 ( 88) SS BOND : angle 1.11440 ( 176) hydrogen bonds : bond 0.03787 ( 738) hydrogen bonds : angle 4.75050 ( 2229) Misc. bond : bond 0.08676 ( 2) link_BETA1-4 : bond 0.00806 ( 6) link_BETA1-4 : angle 2.15911 ( 18) link_NAG-ASN : bond 0.00319 ( 11) link_NAG-ASN : angle 2.39823 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 470 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 TRP cc_start: 0.8299 (t-100) cc_final: 0.7996 (t-100) REVERT: A 348 HIS cc_start: 0.8442 (t-90) cc_final: 0.8095 (t-90) REVERT: A 350 TRP cc_start: 0.8114 (m100) cc_final: 0.7579 (m-10) REVERT: A 408 ASP cc_start: 0.7941 (m-30) cc_final: 0.7705 (m-30) REVERT: A 421 LYS cc_start: 0.8163 (tttt) cc_final: 0.7777 (ttpp) REVERT: A 539 GLN cc_start: 0.7084 (tm-30) cc_final: 0.6839 (tm-30) REVERT: A 657 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7998 (mp10) REVERT: A 758 ARG cc_start: 0.8295 (ttm110) cc_final: 0.8081 (ttm110) REVERT: A 778 THR cc_start: 0.8666 (t) cc_final: 0.8464 (m) REVERT: A 961 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6734 (p0) REVERT: A 962 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7382 (m-30) REVERT: A 994 ASN cc_start: 0.7920 (p0) cc_final: 0.7363 (p0) REVERT: C 409 VAL cc_start: 0.8554 (p) cc_final: 0.8330 (m) REVERT: C 619 VAL cc_start: 0.7908 (t) cc_final: 0.7653 (t) REVERT: C 622 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7470 (tp40) REVERT: C 771 SER cc_start: 0.8655 (m) cc_final: 0.8378 (p) REVERT: C 778 THR cc_start: 0.8947 (t) cc_final: 0.8747 (m) REVERT: C 874 LYS cc_start: 0.8375 (mttt) cc_final: 0.8143 (mttt) REVERT: C 1012 ARG cc_start: 0.6015 (mmt-90) cc_final: 0.5810 (mmt-90) REVERT: B 372 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7373 (mt-10) REVERT: B 376 ARG cc_start: 0.7694 (tpp80) cc_final: 0.7431 (tpp80) REVERT: B 399 ASP cc_start: 0.8214 (t70) cc_final: 0.7725 (p0) REVERT: B 408 ASP cc_start: 0.7907 (t0) cc_final: 0.7529 (t0) REVERT: B 510 GLU cc_start: 0.7767 (mp0) cc_final: 0.7124 (mp0) REVERT: B 598 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6866 (tt) REVERT: B 723 ASN cc_start: 0.8475 (t0) cc_final: 0.8053 (t0) REVERT: B 736 HIS cc_start: 0.6729 (OUTLIER) cc_final: 0.6387 (t-90) REVERT: B 791 LYS cc_start: 0.7723 (tttt) cc_final: 0.7475 (mttt) REVERT: B 885 SER cc_start: 0.7750 (t) cc_final: 0.7526 (t) REVERT: B 919 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: B 922 TRP cc_start: 0.8297 (m100) cc_final: 0.7394 (m100) REVERT: B 993 LEU cc_start: 0.8673 (mt) cc_final: 0.8462 (mt) REVERT: D 118 PHE cc_start: 0.8363 (t80) cc_final: 0.7866 (t80) REVERT: D 126 LEU cc_start: 0.8309 (mm) cc_final: 0.8083 (mt) REVERT: D 141 TYR cc_start: 0.8462 (t80) cc_final: 0.7867 (t80) REVERT: F 176 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7615 (ttpp) outliers start: 93 outliers final: 58 residues processed: 526 average time/residue: 0.1658 time to fit residues: 132.5120 Evaluate side-chains 525 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 461 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 889 TRP Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 872 LYS Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 835 CYS Chi-restraints excluded: chain B residue 919 GLU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain B residue 1026 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 317 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 121 optimal weight: 0.0070 chunk 171 optimal weight: 1.9990 chunk 238 optimal weight: 0.0980 chunk 166 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 240 optimal weight: 0.2980 chunk 153 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN C 609 ASN C 618 HIS B 445 ASN B 754 HIS E 132 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.145244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122431 restraints weight = 33732.715| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.65 r_work: 0.3447 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 22678 Z= 0.132 Angle : 0.582 8.966 30850 Z= 0.300 Chirality : 0.045 0.270 3281 Planarity : 0.004 0.055 3974 Dihedral : 7.127 86.448 3382 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 3.78 % Allowed : 20.38 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.15), residues: 2836 helix: 1.44 (0.23), residues: 528 sheet: 0.06 (0.26), residues: 379 loop : -0.90 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 517 TYR 0.013 0.001 TYR B 580 PHE 0.014 0.001 PHE F 280 TRP 0.018 0.001 TRP A 612 HIS 0.006 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00306 (22571) covalent geometry : angle 0.56931 (30623) SS BOND : bond 0.00340 ( 88) SS BOND : angle 1.02081 ( 176) hydrogen bonds : bond 0.03435 ( 738) hydrogen bonds : angle 4.54931 ( 2229) Misc. bond : bond 0.08395 ( 2) link_BETA1-4 : bond 0.00854 ( 6) link_BETA1-4 : angle 2.27607 ( 18) link_NAG-ASN : bond 0.00301 ( 11) link_NAG-ASN : angle 2.70484 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 467 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 HIS cc_start: 0.8407 (t-90) cc_final: 0.8060 (t-90) REVERT: A 350 TRP cc_start: 0.8109 (m100) cc_final: 0.7682 (m-10) REVERT: A 408 ASP cc_start: 0.7947 (m-30) cc_final: 0.7703 (m-30) REVERT: A 421 LYS cc_start: 0.8149 (tttt) cc_final: 0.7752 (ttpp) REVERT: A 539 GLN cc_start: 0.7074 (tm-30) cc_final: 0.6843 (tm-30) REVERT: A 657 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7993 (mp10) REVERT: A 722 VAL cc_start: 0.8630 (m) cc_final: 0.8368 (p) REVERT: A 758 ARG cc_start: 0.8254 (ttm110) cc_final: 0.8040 (ttm110) REVERT: A 784 ASP cc_start: 0.7792 (t0) cc_final: 0.7539 (t0) REVERT: A 797 GLN cc_start: 0.8300 (mp10) cc_final: 0.8020 (mp10) REVERT: A 913 ARG cc_start: 0.8343 (ptm160) cc_final: 0.7963 (ptt90) REVERT: A 961 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6711 (p0) REVERT: A 962 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7347 (m-30) REVERT: A 994 ASN cc_start: 0.7901 (p0) cc_final: 0.7335 (p0) REVERT: C 409 VAL cc_start: 0.8524 (p) cc_final: 0.8278 (m) REVERT: C 518 GLU cc_start: 0.7914 (tt0) cc_final: 0.7651 (tt0) REVERT: C 539 GLN cc_start: 0.7986 (mt0) cc_final: 0.7704 (mm-40) REVERT: C 619 VAL cc_start: 0.7891 (t) cc_final: 0.7643 (t) REVERT: C 622 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7473 (tp40) REVERT: C 771 SER cc_start: 0.8657 (m) cc_final: 0.8389 (p) REVERT: C 805 GLN cc_start: 0.7299 (mm110) cc_final: 0.7083 (tp40) REVERT: C 874 LYS cc_start: 0.8356 (mttt) cc_final: 0.8121 (mttt) REVERT: C 988 THR cc_start: 0.8730 (t) cc_final: 0.8443 (p) REVERT: B 372 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7378 (mt-10) REVERT: B 376 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7308 (tpp80) REVERT: B 399 ASP cc_start: 0.8326 (t70) cc_final: 0.7563 (p0) REVERT: B 408 ASP cc_start: 0.7852 (t0) cc_final: 0.7479 (t0) REVERT: B 494 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8071 (ttmp) REVERT: B 510 GLU cc_start: 0.7764 (mp0) cc_final: 0.7238 (mp0) REVERT: B 598 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6838 (tp) REVERT: B 723 ASN cc_start: 0.8432 (t0) cc_final: 0.8013 (t0) REVERT: B 736 HIS cc_start: 0.6754 (OUTLIER) cc_final: 0.6473 (t-90) REVERT: B 789 ASN cc_start: 0.7609 (t0) cc_final: 0.7268 (t0) REVERT: B 791 LYS cc_start: 0.7734 (tttt) cc_final: 0.7470 (mttt) REVERT: B 885 SER cc_start: 0.7806 (t) cc_final: 0.7584 (t) REVERT: B 900 ASP cc_start: 0.7691 (t0) cc_final: 0.7406 (t0) REVERT: B 919 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: B 977 LYS cc_start: 0.7673 (mttt) cc_final: 0.7395 (mttt) REVERT: D 118 PHE cc_start: 0.8285 (t80) cc_final: 0.7772 (t80) REVERT: D 126 LEU cc_start: 0.8283 (mm) cc_final: 0.8082 (mt) REVERT: D 141 TYR cc_start: 0.8433 (t80) cc_final: 0.7747 (t80) REVERT: F 176 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7637 (ttpp) outliers start: 88 outliers final: 52 residues processed: 521 average time/residue: 0.1691 time to fit residues: 133.4455 Evaluate side-chains 514 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 454 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 889 TRP Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 568 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 872 LYS Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain C residue 916 SER Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 494 LYS Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 569 HIS Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 919 GLU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain B residue 1026 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 207 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 217 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 251 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN C 618 HIS B 445 ASN B 754 HIS B 964 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.143064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120118 restraints weight = 33746.421| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.68 r_work: 0.3412 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 22678 Z= 0.206 Angle : 0.629 8.524 30850 Z= 0.325 Chirality : 0.047 0.230 3281 Planarity : 0.005 0.056 3974 Dihedral : 7.284 86.073 3382 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.16 % Allowed : 20.38 % Favored : 75.46 % 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: -0.61 (0.15), residues: 2836 helix: 1.27 (0.23), residues: 528 sheet: -0.13 (0.26), residues: 375 loop : -0.99 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 476 TYR 0.015 0.002 TYR F 239 PHE 0.024 0.002 PHE F 280 TRP 0.019 0.002 TRP C1006 HIS 0.013 0.001 HIS B 495 Details of bonding type rmsd covalent geometry : bond 0.00476 (22571) covalent geometry : angle 0.61696 (30623) SS BOND : bond 0.00524 ( 88) SS BOND : angle 1.23521 ( 176) hydrogen bonds : bond 0.03893 ( 738) hydrogen bonds : angle 4.71596 ( 2229) Misc. bond : bond 0.08973 ( 2) link_BETA1-4 : bond 0.00862 ( 6) link_BETA1-4 : angle 2.16065 ( 18) link_NAG-ASN : bond 0.00380 ( 11) link_NAG-ASN : angle 2.53452 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 466 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6908 (mm-30) REVERT: A 348 HIS cc_start: 0.8422 (t-90) cc_final: 0.8056 (t-90) REVERT: A 408 ASP cc_start: 0.8057 (m-30) cc_final: 0.7836 (m-30) REVERT: A 421 LYS cc_start: 0.8182 (tttt) cc_final: 0.7716 (ttpp) REVERT: A 443 ASN cc_start: 0.7602 (t0) cc_final: 0.7362 (t0) REVERT: A 539 GLN cc_start: 0.7059 (tm-30) cc_final: 0.6825 (tm-30) REVERT: A 722 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8406 (p) REVERT: A 727 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7139 (ptm160) REVERT: A 758 ARG cc_start: 0.8310 (ttm110) cc_final: 0.8098 (ttm110) REVERT: A 913 ARG cc_start: 0.8335 (ptm160) cc_final: 0.7980 (ptt90) REVERT: A 994 ASN cc_start: 0.7915 (p0) cc_final: 0.7312 (p0) REVERT: C 409 VAL cc_start: 0.8606 (p) cc_final: 0.8364 (m) REVERT: C 622 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7544 (tp40) REVERT: C 771 SER cc_start: 0.8695 (m) cc_final: 0.8393 (p) REVERT: C 805 GLN cc_start: 0.7393 (mm110) cc_final: 0.7191 (tp40) REVERT: C 874 LYS cc_start: 0.8367 (mttt) cc_final: 0.8138 (mttt) REVERT: C 988 THR cc_start: 0.8763 (t) cc_final: 0.8505 (p) REVERT: B 372 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7449 (mt-10) REVERT: B 398 CYS cc_start: 0.7070 (t) cc_final: 0.6802 (t) REVERT: B 399 ASP cc_start: 0.8365 (t70) cc_final: 0.7571 (p0) REVERT: B 408 ASP cc_start: 0.7927 (t0) cc_final: 0.7443 (t0) REVERT: B 598 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7009 (tt) REVERT: B 723 ASN cc_start: 0.8544 (t0) cc_final: 0.8022 (t0) REVERT: B 736 HIS cc_start: 0.6876 (OUTLIER) cc_final: 0.6601 (t-90) REVERT: B 752 ASP cc_start: 0.7180 (m-30) cc_final: 0.6922 (m-30) REVERT: B 789 ASN cc_start: 0.7659 (t0) cc_final: 0.7346 (t0) REVERT: B 791 LYS cc_start: 0.7737 (tttt) cc_final: 0.7516 (mttt) REVERT: B 820 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: B 885 SER cc_start: 0.7940 (t) cc_final: 0.7722 (t) REVERT: B 900 ASP cc_start: 0.7752 (t0) cc_final: 0.7457 (t0) REVERT: B 919 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: B 977 LYS cc_start: 0.7807 (mttt) cc_final: 0.7495 (mttt) REVERT: B 1017 GLU cc_start: 0.7667 (tp30) cc_final: 0.7441 (tp30) REVERT: D 118 PHE cc_start: 0.8399 (t80) cc_final: 0.7879 (t80) REVERT: F 176 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7651 (ttpp) outliers start: 97 outliers final: 64 residues processed: 530 average time/residue: 0.1727 time to fit residues: 138.3945 Evaluate side-chains 531 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 460 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 568 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 872 LYS Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain C residue 916 SER Chi-restraints excluded: chain C residue 968 GLN Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 820 GLU Chi-restraints excluded: chain B residue 835 CYS Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 919 GLU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain B residue 1026 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 207 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 220 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 259 optimal weight: 0.9980 chunk 263 optimal weight: 0.9990 chunk 212 optimal weight: 0.8980 chunk 262 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 176 optimal weight: 0.9990 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 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 HIS B 445 ASN B 754 HIS B 964 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.143010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120178 restraints weight = 33584.450| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.67 r_work: 0.3410 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 22678 Z= 0.205 Angle : 0.624 8.663 30850 Z= 0.323 Chirality : 0.047 0.234 3281 Planarity : 0.005 0.056 3974 Dihedral : 7.244 82.222 3382 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.90 % Allowed : 21.54 % Favored : 74.56 % 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 (0.15), residues: 2836 helix: 1.32 (0.23), residues: 524 sheet: -0.05 (0.26), residues: 371 loop : -1.05 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 517 TYR 0.013 0.002 TYR F 239 PHE 0.021 0.002 PHE A 176 TRP 0.023 0.002 TRP A 950 HIS 0.006 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00475 (22571) covalent geometry : angle 0.61169 (30623) SS BOND : bond 0.00475 ( 88) SS BOND : angle 1.25542 ( 176) hydrogen bonds : bond 0.03853 ( 738) hydrogen bonds : angle 4.69377 ( 2229) Misc. bond : bond 0.08419 ( 2) link_BETA1-4 : bond 0.00817 ( 6) link_BETA1-4 : angle 2.12949 ( 18) link_NAG-ASN : bond 0.00347 ( 11) link_NAG-ASN : angle 2.53714 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 481 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6991 (mm-30) REVERT: A 348 HIS cc_start: 0.8405 (t-90) cc_final: 0.8045 (t-90) REVERT: A 350 TRP cc_start: 0.8175 (m100) cc_final: 0.7540 (m-10) REVERT: A 358 ASN cc_start: 0.7284 (m-40) cc_final: 0.7038 (m-40) REVERT: A 374 ARG cc_start: 0.7636 (mtm-85) cc_final: 0.7309 (mtt-85) REVERT: A 405 LYS cc_start: 0.8317 (mttt) cc_final: 0.8038 (mttt) REVERT: A 443 ASN cc_start: 0.7564 (t0) cc_final: 0.7321 (t0) REVERT: A 467 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7128 (mt-10) REVERT: A 539 GLN cc_start: 0.7056 (tm-30) cc_final: 0.6842 (tm-30) REVERT: A 722 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8419 (p) REVERT: A 727 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7137 (ptm160) REVERT: A 758 ARG cc_start: 0.8319 (ttm110) cc_final: 0.8116 (ttm110) REVERT: A 784 ASP cc_start: 0.7850 (t0) cc_final: 0.7542 (t0) REVERT: A 913 ARG cc_start: 0.8348 (ptm160) cc_final: 0.8001 (ptt90) REVERT: A 994 ASN cc_start: 0.7922 (p0) cc_final: 0.7313 (p0) REVERT: C 405 LYS cc_start: 0.8317 (tttm) cc_final: 0.8105 (ttpm) REVERT: C 409 VAL cc_start: 0.8584 (p) cc_final: 0.8331 (m) REVERT: C 622 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7438 (tp40) REVERT: C 771 SER cc_start: 0.8697 (m) cc_final: 0.8401 (p) REVERT: C 805 GLN cc_start: 0.7401 (mm110) cc_final: 0.7197 (tp40) REVERT: C 874 LYS cc_start: 0.8366 (mttt) cc_final: 0.8138 (mttt) REVERT: C 988 THR cc_start: 0.8764 (t) cc_final: 0.8510 (p) REVERT: B 372 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7452 (mt-10) REVERT: B 398 CYS cc_start: 0.7070 (t) cc_final: 0.6844 (t) REVERT: B 408 ASP cc_start: 0.7938 (t0) cc_final: 0.7640 (t0) REVERT: B 510 GLU cc_start: 0.7737 (mp0) cc_final: 0.7164 (mp0) REVERT: B 723 ASN cc_start: 0.8517 (t0) cc_final: 0.7935 (t0) REVERT: B 727 ARG cc_start: 0.8046 (ttt-90) cc_final: 0.7809 (ttt-90) REVERT: B 752 ASP cc_start: 0.7185 (m-30) cc_final: 0.6933 (m-30) REVERT: B 758 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.8048 (ttm110) REVERT: B 789 ASN cc_start: 0.7680 (t0) cc_final: 0.7379 (t0) REVERT: B 791 LYS cc_start: 0.7740 (tttt) cc_final: 0.7518 (mttt) REVERT: B 820 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: B 885 SER cc_start: 0.7973 (t) cc_final: 0.7754 (t) REVERT: B 900 ASP cc_start: 0.7750 (t0) cc_final: 0.7470 (t0) REVERT: B 919 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: B 977 LYS cc_start: 0.7816 (mttt) cc_final: 0.7507 (mttt) REVERT: D 71 VAL cc_start: 0.8581 (t) cc_final: 0.8344 (p) REVERT: D 118 PHE cc_start: 0.8395 (t80) cc_final: 0.7843 (t80) REVERT: F 176 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7648 (ttpp) outliers start: 91 outliers final: 71 residues processed: 537 average time/residue: 0.1711 time to fit residues: 138.2798 Evaluate side-chains 541 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 464 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 872 LYS Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain C residue 916 SER Chi-restraints excluded: chain C residue 968 GLN Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 820 GLU Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 919 GLU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain B residue 1026 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 207 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 96 optimal weight: 0.7980 chunk 233 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 ASN C 550 HIS C 618 HIS B 445 ASN B 754 HIS B 964 GLN D 21 HIS ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.119007 restraints weight = 33409.947| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.62 r_work: 0.3392 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 22678 Z= 0.271 Angle : 0.691 20.252 30850 Z= 0.354 Chirality : 0.049 0.238 3281 Planarity : 0.005 0.057 3974 Dihedral : 7.435 81.971 3382 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.29 % Allowed : 21.71 % Favored : 74.00 % 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: -0.84 (0.15), residues: 2836 helix: 1.08 (0.23), residues: 528 sheet: -0.23 (0.25), residues: 403 loop : -1.16 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 517 TYR 0.019 0.002 TYR F 239 PHE 0.027 0.002 PHE F 280 TRP 0.028 0.002 TRP A 950 HIS 0.008 0.001 HIS A1020 Details of bonding type rmsd covalent geometry : bond 0.00624 (22571) covalent geometry : angle 0.67746 (30623) SS BOND : bond 0.00583 ( 88) SS BOND : angle 1.44978 ( 176) hydrogen bonds : bond 0.04259 ( 738) hydrogen bonds : angle 4.87713 ( 2229) Misc. bond : bond 0.10420 ( 2) link_BETA1-4 : bond 0.00930 ( 6) link_BETA1-4 : angle 2.15835 ( 18) link_NAG-ASN : bond 0.00418 ( 11) link_NAG-ASN : angle 2.67701 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 477 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7227 (mm-30) REVERT: A 329 TRP cc_start: 0.8327 (m100) cc_final: 0.7810 (m100) REVERT: A 348 HIS cc_start: 0.8624 (t-90) cc_final: 0.8252 (t-90) REVERT: A 374 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7499 (mtt-85) REVERT: A 443 ASN cc_start: 0.7737 (t0) cc_final: 0.7474 (t0) REVERT: A 467 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: A 523 THR cc_start: 0.8289 (m) cc_final: 0.7902 (p) REVERT: A 545 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.5982 (t80) REVERT: A 722 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8512 (p) REVERT: A 727 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7224 (ptm160) REVERT: A 784 ASP cc_start: 0.8043 (t0) cc_final: 0.7771 (t0) REVERT: A 913 ARG cc_start: 0.8529 (ptm160) cc_final: 0.8178 (ptt90) REVERT: A 994 ASN cc_start: 0.8040 (p0) cc_final: 0.7432 (p0) REVERT: C 360 ASP cc_start: 0.7699 (m-30) cc_final: 0.7487 (m-30) REVERT: C 371 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8284 (mt) REVERT: C 376 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8110 (ttm-80) REVERT: C 409 VAL cc_start: 0.8692 (p) cc_final: 0.8465 (m) REVERT: C 622 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7725 (tp40) REVERT: C 638 PHE cc_start: 0.8508 (m-80) cc_final: 0.8258 (m-80) REVERT: C 676 GLN cc_start: 0.7845 (mp10) cc_final: 0.7625 (mp10) REVERT: C 771 SER cc_start: 0.8804 (m) cc_final: 0.8387 (t) REVERT: C 977 LYS cc_start: 0.8302 (mttt) cc_final: 0.8056 (mttt) REVERT: C 988 THR cc_start: 0.8828 (t) cc_final: 0.8551 (p) REVERT: B 372 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7770 (mt-10) REVERT: B 398 CYS cc_start: 0.7748 (t) cc_final: 0.7464 (t) REVERT: B 399 ASP cc_start: 0.8617 (t0) cc_final: 0.7928 (p0) REVERT: B 408 ASP cc_start: 0.8244 (t0) cc_final: 0.7847 (t0) REVERT: B 723 ASN cc_start: 0.8750 (t0) cc_final: 0.8172 (t0) REVERT: B 752 ASP cc_start: 0.7550 (m-30) cc_final: 0.7342 (m-30) REVERT: B 758 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.8182 (ttm110) REVERT: B 789 ASN cc_start: 0.7875 (t0) cc_final: 0.7604 (t0) REVERT: B 791 LYS cc_start: 0.7907 (tttt) cc_final: 0.7698 (mttt) REVERT: B 820 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: B 900 ASP cc_start: 0.7953 (t0) cc_final: 0.7689 (t0) REVERT: B 919 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: B 968 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7375 (tm-30) REVERT: B 977 LYS cc_start: 0.8063 (mttt) cc_final: 0.7723 (mttt) REVERT: D 71 VAL cc_start: 0.8669 (t) cc_final: 0.8421 (p) REVERT: D 97 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8396 (t) REVERT: D 118 PHE cc_start: 0.8547 (t80) cc_final: 0.8036 (t80) REVERT: F 176 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7633 (ttpp) outliers start: 100 outliers final: 77 residues processed: 537 average time/residue: 0.1724 time to fit residues: 139.0628 Evaluate side-chains 554 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 468 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 872 LYS Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain C residue 916 SER Chi-restraints excluded: chain C residue 968 GLN Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 820 GLU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 919 GLU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain B residue 1022 GLU Chi-restraints excluded: chain B residue 1026 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 258 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 166 optimal weight: 0.5980 chunk 188 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 119 optimal weight: 0.6980 chunk 214 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 609 ASN C 618 HIS B 445 ASN B 754 HIS B 964 GLN D 21 HIS ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.142647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.120107 restraints weight = 33854.696| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.65 r_work: 0.3410 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 22678 Z= 0.177 Angle : 0.639 16.653 30850 Z= 0.329 Chirality : 0.046 0.232 3281 Planarity : 0.005 0.055 3974 Dihedral : 7.284 77.240 3382 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.90 % Allowed : 22.48 % Favored : 73.62 % 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: -0.74 (0.15), residues: 2836 helix: 1.28 (0.23), residues: 524 sheet: -0.19 (0.26), residues: 361 loop : -1.11 (0.13), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 517 TYR 0.012 0.001 TYR A 427 PHE 0.030 0.002 PHE A 176 TRP 0.052 0.002 TRP E 16 HIS 0.006 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00415 (22571) covalent geometry : angle 0.62771 (30623) SS BOND : bond 0.00426 ( 88) SS BOND : angle 1.22049 ( 176) hydrogen bonds : bond 0.03785 ( 738) hydrogen bonds : angle 4.72497 ( 2229) Misc. bond : bond 0.08829 ( 2) link_BETA1-4 : bond 0.00747 ( 6) link_BETA1-4 : angle 2.01660 ( 18) link_NAG-ASN : bond 0.00299 ( 11) link_NAG-ASN : angle 2.54930 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 478 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7014 (mm-30) REVERT: A 344 GLN cc_start: 0.8241 (mm110) cc_final: 0.7974 (mp10) REVERT: A 348 HIS cc_start: 0.8417 (t-90) cc_final: 0.8077 (t-90) REVERT: A 350 TRP cc_start: 0.8187 (m100) cc_final: 0.7711 (m-10) REVERT: A 421 LYS cc_start: 0.8196 (tttt) cc_final: 0.7817 (ttpp) REVERT: A 443 ASN cc_start: 0.7445 (t0) cc_final: 0.7217 (t0) REVERT: A 467 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6998 (mt-10) REVERT: A 523 THR cc_start: 0.8184 (m) cc_final: 0.7799 (p) REVERT: A 722 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8422 (p) REVERT: A 727 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7102 (ptm160) REVERT: A 784 ASP cc_start: 0.7852 (t0) cc_final: 0.7538 (t0) REVERT: A 797 GLN cc_start: 0.8279 (mp10) cc_final: 0.8063 (mp10) REVERT: A 913 ARG cc_start: 0.8339 (ptm160) cc_final: 0.7988 (ptt90) REVERT: A 994 ASN cc_start: 0.7913 (p0) cc_final: 0.7291 (p0) REVERT: C 359 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6752 (mt-10) REVERT: C 360 ASP cc_start: 0.7466 (m-30) cc_final: 0.7250 (m-30) REVERT: C 409 VAL cc_start: 0.8536 (p) cc_final: 0.8299 (m) REVERT: C 622 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7472 (tp40) REVERT: C 638 PHE cc_start: 0.8424 (m-80) cc_final: 0.8202 (m-80) REVERT: C 771 SER cc_start: 0.8698 (m) cc_final: 0.8397 (p) REVERT: C 977 LYS cc_start: 0.8115 (mttt) cc_final: 0.7871 (mttt) REVERT: C 988 THR cc_start: 0.8767 (t) cc_final: 0.8510 (p) REVERT: B 292 ASP cc_start: 0.8421 (p0) cc_final: 0.8190 (p0) REVERT: B 372 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7327 (mt-10) REVERT: B 398 CYS cc_start: 0.7049 (t) cc_final: 0.6793 (t) REVERT: B 399 ASP cc_start: 0.8449 (t0) cc_final: 0.7755 (p0) REVERT: B 408 ASP cc_start: 0.7962 (t0) cc_final: 0.7695 (t0) REVERT: B 723 ASN cc_start: 0.8494 (t0) cc_final: 0.7913 (t0) REVERT: B 758 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.8045 (ttm110) REVERT: B 789 ASN cc_start: 0.7707 (t0) cc_final: 0.7471 (t0) REVERT: B 791 LYS cc_start: 0.7747 (tttt) cc_final: 0.7535 (mttt) REVERT: B 820 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: B 840 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7266 (mt-10) REVERT: B 919 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: B 968 GLN cc_start: 0.7644 (tm-30) cc_final: 0.7203 (tm-30) REVERT: B 977 LYS cc_start: 0.7850 (mttt) cc_final: 0.7521 (mttt) REVERT: D 71 VAL cc_start: 0.8574 (t) cc_final: 0.8330 (p) REVERT: D 118 PHE cc_start: 0.8397 (t80) cc_final: 0.7865 (t80) REVERT: F 176 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7655 (ttpp) outliers start: 91 outliers final: 71 residues processed: 537 average time/residue: 0.1693 time to fit residues: 136.8688 Evaluate side-chains 545 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 467 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 872 LYS Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain C residue 916 SER Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1022 GLU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 820 GLU Chi-restraints excluded: chain B residue 835 CYS Chi-restraints excluded: chain B residue 840 GLU Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 919 GLU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain B residue 1026 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 207 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 30 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 242 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 72 optimal weight: 0.0570 chunk 191 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 618 HIS B 445 ASN B 736 HIS B 754 HIS B 964 GLN D 21 HIS ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.142751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120032 restraints weight = 33642.260| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.67 r_work: 0.3409 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 22678 Z= 0.187 Angle : 0.646 16.337 30850 Z= 0.332 Chirality : 0.047 0.235 3281 Planarity : 0.005 0.056 3974 Dihedral : 7.252 76.510 3382 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.60 % Allowed : 23.12 % Favored : 73.27 % 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: -0.73 (0.15), residues: 2836 helix: 1.28 (0.23), residues: 523 sheet: -0.22 (0.26), residues: 361 loop : -1.10 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 476 TYR 0.014 0.001 TYR A 427 PHE 0.029 0.002 PHE A 176 TRP 0.061 0.002 TRP E 16 HIS 0.007 0.001 HIS B 495 Details of bonding type rmsd covalent geometry : bond 0.00438 (22571) covalent geometry : angle 0.63406 (30623) SS BOND : bond 0.00438 ( 88) SS BOND : angle 1.23694 ( 176) hydrogen bonds : bond 0.03824 ( 738) hydrogen bonds : angle 4.72683 ( 2229) Misc. bond : bond 0.09111 ( 2) link_BETA1-4 : bond 0.00796 ( 6) link_BETA1-4 : angle 1.97700 ( 18) link_NAG-ASN : bond 0.00306 ( 11) link_NAG-ASN : angle 2.57854 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 476 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6883 (mm-30) REVERT: A 348 HIS cc_start: 0.8422 (t-90) cc_final: 0.8092 (t-90) REVERT: A 350 TRP cc_start: 0.8197 (m100) cc_final: 0.7730 (m-10) REVERT: A 443 ASN cc_start: 0.7432 (t0) cc_final: 0.7210 (t0) REVERT: A 523 THR cc_start: 0.8189 (m) cc_final: 0.7800 (p) REVERT: A 722 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8424 (p) REVERT: A 727 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7068 (ptm160) REVERT: A 784 ASP cc_start: 0.7848 (t0) cc_final: 0.7535 (t0) REVERT: A 811 LYS cc_start: 0.8747 (pttp) cc_final: 0.8496 (pttp) REVERT: A 913 ARG cc_start: 0.8341 (ptm160) cc_final: 0.7991 (ptt90) REVERT: A 994 ASN cc_start: 0.7919 (p0) cc_final: 0.7314 (p0) REVERT: C 359 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6763 (mt-10) REVERT: C 360 ASP cc_start: 0.7457 (m-30) cc_final: 0.7248 (m-30) REVERT: C 409 VAL cc_start: 0.8520 (p) cc_final: 0.8286 (m) REVERT: C 622 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7483 (tp40) REVERT: C 638 PHE cc_start: 0.8439 (m-80) cc_final: 0.8204 (m-80) REVERT: C 771 SER cc_start: 0.8691 (m) cc_final: 0.8386 (p) REVERT: C 977 LYS cc_start: 0.8124 (mttt) cc_final: 0.7880 (mttt) REVERT: C 988 THR cc_start: 0.8758 (t) cc_final: 0.8504 (p) REVERT: B 292 ASP cc_start: 0.8440 (p0) cc_final: 0.8209 (p0) REVERT: B 372 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7327 (mt-10) REVERT: B 398 CYS cc_start: 0.7046 (t) cc_final: 0.6778 (t) REVERT: B 399 ASP cc_start: 0.8415 (t0) cc_final: 0.7704 (p0) REVERT: B 408 ASP cc_start: 0.7971 (t0) cc_final: 0.7653 (t0) REVERT: B 485 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7941 (mm) REVERT: B 723 ASN cc_start: 0.8468 (t0) cc_final: 0.7900 (t0) REVERT: B 752 ASP cc_start: 0.7194 (m-30) cc_final: 0.6912 (m-30) REVERT: B 758 ARG cc_start: 0.8355 (ttm-80) cc_final: 0.8038 (ttm110) REVERT: B 789 ASN cc_start: 0.7716 (t0) cc_final: 0.7462 (t0) REVERT: B 820 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: B 840 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7257 (mt-10) REVERT: B 876 ASN cc_start: 0.8769 (p0) cc_final: 0.8527 (p0) REVERT: B 919 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: B 968 GLN cc_start: 0.7642 (tm-30) cc_final: 0.7197 (tm-30) REVERT: B 977 LYS cc_start: 0.7885 (mttt) cc_final: 0.7539 (mttt) REVERT: D 71 VAL cc_start: 0.8561 (t) cc_final: 0.8327 (p) REVERT: D 118 PHE cc_start: 0.8407 (t80) cc_final: 0.7861 (t80) REVERT: F 176 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7668 (ttpp) outliers start: 84 outliers final: 73 residues processed: 530 average time/residue: 0.1769 time to fit residues: 140.8017 Evaluate side-chains 549 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 469 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1006 TRP Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 872 LYS Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain C residue 916 SER Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1022 GLU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 820 GLU Chi-restraints excluded: chain B residue 835 CYS Chi-restraints excluded: chain B residue 840 GLU Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 919 GLU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain B residue 1026 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 207 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 18 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 275 optimal weight: 0.6980 chunk 250 optimal weight: 0.7980 chunk 262 optimal weight: 3.9990 chunk 251 optimal weight: 0.9990 chunk 272 optimal weight: 0.8980 chunk 137 optimal weight: 0.0030 chunk 64 optimal weight: 0.1980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 618 HIS B 445 ASN B 736 HIS B 754 HIS B 964 GLN D 21 HIS ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.142813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.120602 restraints weight = 33616.113| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.54 r_work: 0.3434 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 22678 Z= 0.152 Angle : 0.630 15.954 30850 Z= 0.324 Chirality : 0.046 0.232 3281 Planarity : 0.005 0.055 3974 Dihedral : 7.152 76.805 3382 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.43 % Allowed : 23.55 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 2836 helix: 1.38 (0.23), residues: 522 sheet: -0.08 (0.27), residues: 348 loop : -1.08 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 476 TYR 0.013 0.001 TYR A 427 PHE 0.029 0.001 PHE A 176 TRP 0.056 0.002 TRP E 16 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00356 (22571) covalent geometry : angle 0.61918 (30623) SS BOND : bond 0.00379 ( 88) SS BOND : angle 1.11519 ( 176) hydrogen bonds : bond 0.03606 ( 738) hydrogen bonds : angle 4.63385 ( 2229) Misc. bond : bond 0.08724 ( 2) link_BETA1-4 : bond 0.00772 ( 6) link_BETA1-4 : angle 1.90179 ( 18) link_NAG-ASN : bond 0.00293 ( 11) link_NAG-ASN : angle 2.51172 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6093.22 seconds wall clock time: 104 minutes 55.37 seconds (6295.37 seconds total)