Starting phenix.real_space_refine on Fri Sep 19 01:48:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hek_52079/09_2025/9hek_52079.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hek_52079/09_2025/9hek_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_52079/09_2025/9hek_52079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hek_52079/09_2025/9hek_52079.map" model { file = "/net/cci-nas-00/data/ceres_data/9hek_52079/09_2025/9hek_52079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hek_52079/09_2025/9hek_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-2.0-5805/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: 7.07, per 1000 atoms: 0.32 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: 2.02 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.99 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: 4.53 Time building geometry restraints manager: 2.62 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=" 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 bond pdb=" CB CYS A 626 " pdb=" SG CYS A 626 " ideal model delta sigma weight residual 1.808 1.747 0.061 3.30e-02 9.18e+02 3.39e+00 bond pdb=" CB TRP A 436 " pdb=" CG TRP A 436 " ideal model delta sigma weight residual 1.498 1.553 -0.055 3.10e-02 1.04e+03 3.19e+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: 16.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.350 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.810 ------------------------------------------------------------------------------- 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= 0.164 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 aren 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 0.00374 (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 : 0.883 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: 0.1815 time to fit residues: 130.4731 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 : 0.810 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.147009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.124377 restraints weight = 33896.280| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.57 r_work: 0.3486 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 22678 Z= 0.159 Angle : 0.630 9.435 30850 Z= 0.326 Chirality : 0.047 0.236 3281 Planarity : 0.004 0.055 3974 Dihedral : 7.420 86.192 3399 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.62 % Allowed : 18.06 % Favored : 79.32 % 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 aren not related in a simple way. whole: -0.59 (0.15), residues: 2836 helix: 1.30 (0.23), residues: 530 sheet: -0.23 (0.26), residues: 342 loop : -0.95 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 374 TYR 0.011 0.001 TYR F 239 PHE 0.015 0.002 PHE B 638 TRP 0.022 0.002 TRP B 455 HIS 0.008 0.001 HIS B 569 Details of bonding type rmsd covalent geometry : bond 0.00368 (22571) covalent geometry : angle 0.61604 (30623) SS BOND : bond 0.00399 ( 88) SS BOND : angle 1.11342 ( 176) hydrogen bonds : bond 0.04158 ( 738) hydrogen bonds : angle 5.03507 ( 2229) Misc. bond : bond 0.08370 ( 2) link_BETA1-4 : bond 0.00899 ( 6) link_BETA1-4 : angle 2.30906 ( 18) link_NAG-ASN : bond 0.00395 ( 11) link_NAG-ASN : angle 2.98496 ( 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 513 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 452 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.7451 (t80) cc_final: 0.7022 (t80) REVERT: A 348 HIS cc_start: 0.8598 (t-90) cc_final: 0.8334 (t-90) REVERT: A 350 TRP cc_start: 0.8141 (m100) cc_final: 0.7938 (m-10) REVERT: A 408 ASP cc_start: 0.7951 (m-30) cc_final: 0.7682 (m-30) REVERT: A 421 LYS cc_start: 0.8047 (tttt) cc_final: 0.7681 (ttpp) REVERT: A 657 GLN cc_start: 0.8401 (mm-40) cc_final: 0.7722 (mm-40) REVERT: A 786 MET cc_start: 0.8823 (mmm) cc_final: 0.8564 (mmt) REVERT: A 922 TRP cc_start: 0.8639 (m100) cc_final: 0.8331 (m100) REVERT: A 961 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6931 (p0) REVERT: A 994 ASN cc_start: 0.7790 (p0) cc_final: 0.7376 (p0) REVERT: C 392 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8119 (mtt180) REVERT: C 539 GLN cc_start: 0.8218 (mt0) cc_final: 0.7974 (mm-40) REVERT: C 622 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7598 (tp40) REVERT: C 752 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7478 (m-30) REVERT: C 771 SER cc_start: 0.8552 (m) cc_final: 0.8321 (p) REVERT: C 855 MET cc_start: 0.8699 (tpt) cc_final: 0.8074 (tpt) REVERT: C 860 VAL cc_start: 0.8572 (m) cc_final: 0.8348 (t) REVERT: C 983 GLU cc_start: 0.8488 (tp30) cc_final: 0.8155 (tp30) REVERT: B 399 ASP cc_start: 0.8286 (t70) cc_final: 0.7577 (p0) REVERT: B 408 ASP cc_start: 0.7973 (t0) cc_final: 0.7545 (t0) REVERT: B 455 TRP cc_start: 0.8759 (p-90) cc_final: 0.8510 (p-90) REVERT: B 598 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6578 (tt) REVERT: B 610 SER cc_start: 0.8050 (t) cc_final: 0.7825 (p) REVERT: B 723 ASN cc_start: 0.8446 (t160) cc_final: 0.8183 (t0) REVERT: B 789 ASN cc_start: 0.7745 (t0) cc_final: 0.7431 (t0) REVERT: B 791 LYS cc_start: 0.7787 (tttt) cc_final: 0.7517 (mttt) REVERT: B 805 GLN cc_start: 0.7754 (mm110) cc_final: 0.7518 (mm110) REVERT: B 919 GLU cc_start: 0.8520 (tp30) cc_final: 0.8232 (tt0) REVERT: B 922 TRP cc_start: 0.8354 (m100) cc_final: 0.7561 (m100) REVERT: B 995 GLU cc_start: 0.8185 (pm20) cc_final: 0.7593 (pm20) REVERT: D 71 VAL cc_start: 0.8536 (t) cc_final: 0.8277 (p) REVERT: E 106 LEU cc_start: 0.8638 (mt) cc_final: 0.8420 (mp) REVERT: F 339 TRP cc_start: 0.8312 (t60) cc_final: 0.7853 (t60) outliers start: 61 outliers final: 27 residues processed: 491 average time/residue: 0.1774 time to fit residues: 132.4633 Evaluate side-chains 469 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 438 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain F residue 343 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 197 optimal weight: 0.0980 chunk 98 optimal weight: 0.7980 chunk 238 optimal weight: 0.0040 chunk 169 optimal weight: 0.0980 chunk 195 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 217 optimal weight: 0.5980 chunk 167 optimal weight: 5.9990 overall best weight: 0.3192 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.148113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.125565 restraints weight = 33951.060| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.58 r_work: 0.3493 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 22678 Z= 0.117 Angle : 0.576 9.031 30850 Z= 0.297 Chirality : 0.044 0.216 3281 Planarity : 0.004 0.052 3974 Dihedral : 6.739 85.043 3385 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.69 % Allowed : 17.89 % Favored : 78.42 % 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 aren not related in a simple way. whole: -0.41 (0.15), residues: 2836 helix: 1.48 (0.23), residues: 526 sheet: -0.06 (0.26), residues: 357 loop : -0.84 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 517 TYR 0.008 0.001 TYR A 427 PHE 0.012 0.001 PHE F 280 TRP 0.023 0.001 TRP C 295 HIS 0.022 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00273 (22571) covalent geometry : angle 0.56431 (30623) SS BOND : bond 0.00298 ( 88) SS BOND : angle 0.96467 ( 176) hydrogen bonds : bond 0.03628 ( 738) hydrogen bonds : angle 4.66752 ( 2229) Misc. bond : bond 0.09102 ( 2) link_BETA1-4 : bond 0.00800 ( 6) link_BETA1-4 : angle 2.19295 ( 18) link_NAG-ASN : bond 0.00351 ( 11) link_NAG-ASN : angle 2.56366 ( 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 537 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 451 time to evaluate : 1.014 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 280 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6787 (mm-30) REVERT: A 283 PHE cc_start: 0.7400 (t80) cc_final: 0.6795 (t80) REVERT: A 295 TRP cc_start: 0.8231 (t-100) cc_final: 0.7952 (t-100) REVERT: A 348 HIS cc_start: 0.8603 (t-90) cc_final: 0.8307 (t-90) REVERT: A 350 TRP cc_start: 0.8127 (m100) cc_final: 0.7719 (m-10) REVERT: A 408 ASP cc_start: 0.7939 (m-30) cc_final: 0.7600 (m-30) REVERT: A 426 VAL cc_start: 0.7906 (OUTLIER) cc_final: 0.7638 (m) REVERT: A 539 GLN cc_start: 0.7317 (tm-30) cc_final: 0.7045 (tm-30) REVERT: A 656 GLU cc_start: 0.6713 (mp0) cc_final: 0.6363 (mp0) REVERT: A 657 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8032 (mp10) REVERT: A 784 ASP cc_start: 0.7808 (t0) cc_final: 0.7588 (t0) REVERT: A 823 SER cc_start: 0.8604 (t) cc_final: 0.8395 (m) REVERT: A 922 TRP cc_start: 0.8574 (m100) cc_final: 0.8251 (m100) REVERT: A 961 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.6808 (p0) REVERT: A 962 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7508 (m-30) REVERT: A 994 ASN cc_start: 0.7931 (p0) cc_final: 0.7449 (p0) REVERT: C 389 GLU cc_start: 0.7577 (tp30) cc_final: 0.7208 (tt0) REVERT: C 539 GLN cc_start: 0.8185 (mt0) cc_final: 0.7961 (mm-40) REVERT: C 622 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7604 (tp40) REVERT: C 771 SER cc_start: 0.8624 (m) cc_final: 0.8397 (p) REVERT: C 855 MET cc_start: 0.8706 (tpt) cc_final: 0.8032 (tpt) REVERT: C 860 VAL cc_start: 0.8549 (m) cc_final: 0.8335 (t) REVERT: C 983 GLU cc_start: 0.8432 (tp30) cc_final: 0.8097 (tp30) REVERT: C 1012 ARG cc_start: 0.6173 (mmt-90) cc_final: 0.5905 (mmt-90) REVERT: B 399 ASP cc_start: 0.8298 (t70) cc_final: 0.7702 (p0) REVERT: B 408 ASP cc_start: 0.7935 (t0) cc_final: 0.7603 (t0) REVERT: B 455 TRP cc_start: 0.8746 (p-90) cc_final: 0.8463 (p-90) REVERT: B 494 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8477 (tttp) REVERT: B 610 SER cc_start: 0.8121 (t) cc_final: 0.7894 (p) REVERT: B 723 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8075 (t0) REVERT: B 736 HIS cc_start: 0.6683 (OUTLIER) cc_final: 0.6158 (t-90) REVERT: B 791 LYS cc_start: 0.7814 (tttt) cc_final: 0.7545 (mttt) REVERT: B 919 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: B 922 TRP cc_start: 0.8317 (m100) cc_final: 0.7507 (m100) REVERT: E 106 LEU cc_start: 0.8655 (mt) cc_final: 0.8423 (mp) REVERT: F 176 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7557 (ttpp) outliers start: 86 outliers final: 46 residues processed: 504 average time/residue: 0.1759 time to fit residues: 134.7001 Evaluate side-chains 493 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 439 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 386 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 835 CYS 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 995 GLU Chi-restraints excluded: chain A residue 1006 TRP 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 567 CYS Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 872 LYS Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain C residue 1028 CYS 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 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 525 VAL Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 723 ASN Chi-restraints excluded: chain B residue 736 HIS 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 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 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: 0.2980 chunk 0 optimal weight: 6.9990 chunk 242 optimal weight: 0.9980 chunk 229 optimal weight: 0.8980 chunk 148 optimal weight: 0.6980 chunk 262 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 241 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 142 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 HIS E 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.144680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.121605 restraints weight = 33705.730| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.70 r_work: 0.3440 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 22678 Z= 0.172 Angle : 0.602 8.802 30850 Z= 0.311 Chirality : 0.046 0.230 3281 Planarity : 0.004 0.055 3974 Dihedral : 6.687 88.063 3382 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.16 % Allowed : 18.79 % Favored : 77.05 % 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 aren not related in a simple way. whole: -0.45 (0.15), residues: 2836 helix: 1.40 (0.23), residues: 527 sheet: -0.04 (0.25), residues: 392 loop : -0.88 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 517 TYR 0.015 0.001 TYR F 239 PHE 0.024 0.002 PHE F 280 TRP 0.024 0.002 TRP C 295 HIS 0.008 0.001 HIS B 495 Details of bonding type rmsd covalent geometry : bond 0.00403 (22571) covalent geometry : angle 0.58982 (30623) SS BOND : bond 0.00392 ( 88) SS BOND : angle 1.10146 ( 176) hydrogen bonds : bond 0.03786 ( 738) hydrogen bonds : angle 4.71854 ( 2229) Misc. bond : bond 0.09623 ( 2) link_BETA1-4 : bond 0.00899 ( 6) link_BETA1-4 : angle 2.09034 ( 18) link_NAG-ASN : bond 0.00361 ( 11) link_NAG-ASN : angle 2.61266 ( 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 552 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 455 time to evaluate : 0.887 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: 0.8044 (mt0) cc_final: 0.7583 (mt0) REVERT: A 348 HIS cc_start: 0.8445 (t-90) cc_final: 0.8088 (t-90) REVERT: A 353 HIS cc_start: 0.5147 (m90) cc_final: 0.4870 (m170) REVERT: A 408 ASP cc_start: 0.7882 (m-30) cc_final: 0.7597 (m-30) REVERT: A 421 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7734 (ttpp) REVERT: A 539 GLN cc_start: 0.7038 (tm-30) cc_final: 0.6794 (tm-30) REVERT: A 656 GLU cc_start: 0.6619 (mp0) cc_final: 0.6214 (mp0) REVERT: A 657 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7998 (mp10) REVERT: A 823 SER cc_start: 0.8560 (t) cc_final: 0.8313 (m) REVERT: A 961 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6758 (p0) REVERT: A 994 ASN cc_start: 0.7863 (p0) cc_final: 0.7315 (p0) REVERT: C 356 ASN cc_start: 0.7166 (p0) cc_final: 0.6959 (t0) REVERT: C 367 ASP cc_start: 0.7016 (t0) cc_final: 0.6812 (t0) REVERT: C 503 CYS cc_start: 0.7483 (m) cc_final: 0.7247 (m) REVERT: C 539 GLN cc_start: 0.8006 (mt0) cc_final: 0.7690 (mm-40) REVERT: C 619 VAL cc_start: 0.7930 (t) cc_final: 0.7668 (t) REVERT: C 622 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7474 (tp40) REVERT: C 771 SER cc_start: 0.8622 (m) cc_final: 0.8331 (p) REVERT: C 778 THR cc_start: 0.8911 (t) cc_final: 0.8688 (m) REVERT: C 855 MET cc_start: 0.8730 (tpt) cc_final: 0.7985 (tpt) REVERT: C 874 LYS cc_start: 0.8391 (mttt) cc_final: 0.8152 (mttt) REVERT: C 1012 ARG cc_start: 0.6029 (mmt-90) cc_final: 0.5814 (mmt-90) REVERT: B 376 ARG cc_start: 0.7695 (tpp80) cc_final: 0.7419 (tpp80) REVERT: B 399 ASP cc_start: 0.8216 (t70) cc_final: 0.7700 (p0) REVERT: B 408 ASP cc_start: 0.7743 (t0) cc_final: 0.7398 (t0) REVERT: B 494 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8363 (tttp) REVERT: B 598 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6745 (tp) REVERT: B 723 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8095 (t0) REVERT: B 736 HIS cc_start: 0.6706 (OUTLIER) cc_final: 0.6321 (t-90) REVERT: B 742 THR cc_start: 0.8387 (p) cc_final: 0.8174 (p) REVERT: B 789 ASN cc_start: 0.7603 (t0) cc_final: 0.7292 (t0) REVERT: B 791 LYS cc_start: 0.7706 (tttt) cc_final: 0.7459 (mttt) REVERT: B 885 SER cc_start: 0.7661 (t) cc_final: 0.7440 (t) REVERT: B 919 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: B 922 TRP cc_start: 0.8282 (m100) cc_final: 0.7404 (m100) REVERT: B 924 THR cc_start: 0.8467 (t) cc_final: 0.7887 (p) REVERT: D 126 LEU cc_start: 0.8308 (mm) cc_final: 0.8056 (mt) REVERT: F 176 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7628 (ttpp) outliers start: 97 outliers final: 56 residues processed: 512 average time/residue: 0.1804 time to fit residues: 139.7949 Evaluate side-chains 507 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 443 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 363 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 497 ASP 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 952 THR Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 961 ASP 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 333 VAL Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 567 CYS 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 B residue 274 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 344 GLN 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 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 653 THR Chi-restraints excluded: chain B residue 723 ASN 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 841 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 34 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 121 optimal weight: 0.7980 chunk 171 optimal weight: 0.7980 chunk 238 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 chunk 209 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 240 optimal weight: 0.3980 chunk 153 optimal weight: 1.9990 chunk 187 optimal weight: 0.4980 chunk 95 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** C 609 ASN B 445 ASN B 495 HIS B 723 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 = 0.3878 r_free = 0.3878 target = 0.144640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.121637 restraints weight = 33657.288| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.68 r_work: 0.3434 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2380 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= 0.167 Angle : 0.589 8.692 30850 Z= 0.305 Chirality : 0.045 0.235 3281 Planarity : 0.004 0.055 3974 Dihedral : 6.656 84.955 3382 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.86 % Allowed : 19.78 % Favored : 76.36 % 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 aren not related in a simple way. whole: -0.45 (0.15), residues: 2836 helix: 1.42 (0.23), residues: 527 sheet: 0.05 (0.26), residues: 383 loop : -0.91 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 412 TYR 0.011 0.001 TYR F 239 PHE 0.019 0.001 PHE F 280 TRP 0.017 0.001 TRP C1006 HIS 0.006 0.001 HIS B 495 Details of bonding type rmsd covalent geometry : bond 0.00388 (22571) covalent geometry : angle 0.57838 (30623) SS BOND : bond 0.00401 ( 88) SS BOND : angle 1.07224 ( 176) hydrogen bonds : bond 0.03642 ( 738) hydrogen bonds : angle 4.63752 ( 2229) Misc. bond : bond 0.08822 ( 2) link_BETA1-4 : bond 0.00786 ( 6) link_BETA1-4 : angle 2.05353 ( 18) link_NAG-ASN : bond 0.00320 ( 11) link_NAG-ASN : angle 2.35981 ( 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 561 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 471 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 HIS cc_start: 0.8450 (t-90) cc_final: 0.8091 (t-90) REVERT: A 350 TRP cc_start: 0.8081 (m100) cc_final: 0.7568 (m-10) REVERT: A 353 HIS cc_start: 0.5124 (m90) cc_final: 0.4862 (m170) REVERT: A 408 ASP cc_start: 0.7966 (m-30) cc_final: 0.7711 (m-30) REVERT: A 421 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7781 (ttpp) REVERT: A 539 GLN cc_start: 0.7080 (tm-30) cc_final: 0.6863 (tm-30) REVERT: A 657 GLN cc_start: 0.8219 (mm-40) cc_final: 0.8000 (mp10) REVERT: A 722 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8360 (p) REVERT: A 823 SER cc_start: 0.8534 (t) cc_final: 0.8296 (m) REVERT: A 913 ARG cc_start: 0.8370 (ptm160) cc_final: 0.8010 (ptt90) REVERT: A 961 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6710 (p0) REVERT: A 962 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7382 (m-30) REVERT: A 994 ASN cc_start: 0.7897 (p0) cc_final: 0.7331 (p0) REVERT: C 503 CYS cc_start: 0.7491 (m) cc_final: 0.7255 (m) REVERT: C 539 GLN cc_start: 0.8032 (mt0) cc_final: 0.7748 (mm-40) REVERT: C 619 VAL cc_start: 0.7892 (t) cc_final: 0.7645 (t) REVERT: C 622 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7483 (tp40) REVERT: C 720 ARG cc_start: 0.8316 (ptt180) cc_final: 0.8114 (ptt180) REVERT: C 771 SER cc_start: 0.8662 (m) cc_final: 0.8379 (p) REVERT: C 787 LYS cc_start: 0.8423 (tttt) cc_final: 0.8221 (tttt) REVERT: C 805 GLN cc_start: 0.7343 (mm110) cc_final: 0.7122 (tp40) REVERT: C 874 LYS cc_start: 0.8383 (mttt) cc_final: 0.8150 (mttt) REVERT: C 1012 ARG cc_start: 0.5998 (mmt-90) cc_final: 0.5791 (mmt-90) REVERT: B 376 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7430 (tpp80) REVERT: B 399 ASP cc_start: 0.8345 (t70) cc_final: 0.7577 (p0) REVERT: B 408 ASP cc_start: 0.7849 (t0) cc_final: 0.7428 (t0) REVERT: B 412 ARG cc_start: 0.8384 (ttm110) cc_final: 0.8012 (ttm110) REVERT: B 510 GLU cc_start: 0.7757 (mp0) cc_final: 0.7130 (mp0) REVERT: B 569 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7889 (m-70) REVERT: B 598 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6867 (tt) REVERT: B 723 ASN cc_start: 0.8449 (t0) cc_final: 0.8021 (t0) REVERT: B 736 HIS cc_start: 0.6718 (OUTLIER) cc_final: 0.6420 (t-90) REVERT: B 789 ASN cc_start: 0.7643 (t0) cc_final: 0.7353 (t0) REVERT: B 791 LYS cc_start: 0.7732 (tttt) cc_final: 0.7495 (mttt) REVERT: B 876 ASN cc_start: 0.8712 (p0) cc_final: 0.8446 (p0) REVERT: B 885 SER cc_start: 0.7782 (t) cc_final: 0.7564 (t) REVERT: B 919 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7955 (tt0) REVERT: B 924 THR cc_start: 0.8479 (t) cc_final: 0.7855 (p) REVERT: B 977 LYS cc_start: 0.7673 (mttt) cc_final: 0.7383 (mttt) REVERT: D 71 VAL cc_start: 0.8568 (t) cc_final: 0.8333 (p) REVERT: D 118 PHE cc_start: 0.8337 (t80) cc_final: 0.7792 (t80) REVERT: D 126 LEU cc_start: 0.8299 (mm) cc_final: 0.8080 (mt) REVERT: F 176 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7654 (ttpp) outliers start: 90 outliers final: 55 residues processed: 523 average time/residue: 0.1695 time to fit residues: 134.7195 Evaluate side-chains 525 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 460 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 363 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 421 LYS 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 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 919 GLU 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 995 GLU 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 409 VAL Chi-restraints excluded: chain C residue 567 CYS 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 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 344 GLN 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 484 ASP 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 569 HIS 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 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 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 127 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 217 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 268 optimal weight: 0.0970 chunk 56 optimal weight: 0.9980 chunk 57 optimal weight: 0.0980 chunk 180 optimal weight: 0.0980 chunk 78 optimal weight: 1.9990 chunk 134 optimal weight: 0.3980 chunk 251 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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 425 GLN C 609 ASN C 618 HIS B 445 ASN B 754 HIS E 109 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.145596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.122667 restraints weight = 33851.783| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.67 r_work: 0.3453 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 22678 Z= 0.119 Angle : 0.573 10.130 30850 Z= 0.294 Chirality : 0.044 0.250 3281 Planarity : 0.004 0.054 3974 Dihedral : 6.950 82.903 3382 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 3.65 % Allowed : 20.81 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.15), residues: 2836 helix: 1.49 (0.23), residues: 528 sheet: 0.07 (0.26), residues: 387 loop : -0.86 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 517 TYR 0.009 0.001 TYR A 427 PHE 0.012 0.001 PHE F 280 TRP 0.017 0.001 TRP B 922 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00277 (22571) covalent geometry : angle 0.56037 (30623) SS BOND : bond 0.00314 ( 88) SS BOND : angle 0.94796 ( 176) hydrogen bonds : bond 0.03289 ( 738) hydrogen bonds : angle 4.46111 ( 2229) Misc. bond : bond 0.08437 ( 2) link_BETA1-4 : bond 0.00812 ( 6) link_BETA1-4 : angle 2.13814 ( 18) link_NAG-ASN : bond 0.00418 ( 11) link_NAG-ASN : angle 2.93578 ( 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 546 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 461 time to evaluate : 0.628 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 176 PHE cc_start: 0.7050 (t80) cc_final: 0.6840 (t80) REVERT: A 348 HIS cc_start: 0.8408 (t-90) cc_final: 0.8074 (t-90) REVERT: A 350 TRP cc_start: 0.8042 (m100) cc_final: 0.7691 (m-10) REVERT: A 353 HIS cc_start: 0.5061 (m90) cc_final: 0.4823 (m170) REVERT: A 408 ASP cc_start: 0.7974 (m-30) cc_final: 0.7719 (m-30) REVERT: A 421 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7731 (ttpp) REVERT: A 657 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7993 (mp10) REVERT: A 722 VAL cc_start: 0.8605 (m) cc_final: 0.8352 (p) REVERT: A 823 SER cc_start: 0.8509 (t) cc_final: 0.8285 (m) REVERT: A 913 ARG cc_start: 0.8356 (ptm160) cc_final: 0.8002 (ptt90) REVERT: A 961 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6694 (p0) REVERT: A 962 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7352 (m-30) REVERT: A 994 ASN cc_start: 0.7891 (p0) cc_final: 0.7305 (p0) REVERT: C 539 GLN cc_start: 0.7984 (mt0) cc_final: 0.7702 (mm-40) REVERT: C 619 VAL cc_start: 0.7895 (t) cc_final: 0.7631 (t) REVERT: C 622 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7479 (tp40) REVERT: C 720 ARG cc_start: 0.8330 (ptt180) cc_final: 0.8041 (ptt180) REVERT: C 771 SER cc_start: 0.8677 (m) cc_final: 0.8448 (p) REVERT: C 805 GLN cc_start: 0.7280 (mm110) cc_final: 0.7072 (tp40) REVERT: C 874 LYS cc_start: 0.8389 (mttt) cc_final: 0.8158 (mttt) REVERT: C 988 THR cc_start: 0.8743 (t) cc_final: 0.8503 (p) REVERT: B 376 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7405 (tpp80) REVERT: B 399 ASP cc_start: 0.8373 (t70) cc_final: 0.7551 (p0) REVERT: B 408 ASP cc_start: 0.7773 (t0) cc_final: 0.7379 (t0) REVERT: B 412 ARG cc_start: 0.8351 (ttm110) cc_final: 0.8004 (ttm110) REVERT: B 494 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8033 (ttmp) REVERT: B 510 GLU cc_start: 0.7759 (mp0) cc_final: 0.7209 (mp0) REVERT: B 598 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6797 (tp) REVERT: B 723 ASN cc_start: 0.8325 (t0) cc_final: 0.7926 (t0) REVERT: B 752 ASP cc_start: 0.7153 (m-30) cc_final: 0.6884 (m-30) REVERT: B 789 ASN cc_start: 0.7615 (t0) cc_final: 0.7327 (t0) REVERT: B 791 LYS cc_start: 0.7727 (tttt) cc_final: 0.7495 (mttt) REVERT: B 820 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: B 885 SER cc_start: 0.7797 (t) cc_final: 0.7582 (t) REVERT: B 900 ASP cc_start: 0.7689 (t0) cc_final: 0.7421 (t0) REVERT: B 919 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: B 977 LYS cc_start: 0.7700 (mttt) cc_final: 0.7380 (mttt) REVERT: D 71 VAL cc_start: 0.8554 (t) cc_final: 0.8306 (p) REVERT: D 118 PHE cc_start: 0.8271 (t80) cc_final: 0.7740 (t80) REVERT: D 126 LEU cc_start: 0.8287 (mm) cc_final: 0.8080 (mt) REVERT: D 141 TYR cc_start: 0.8436 (t80) cc_final: 0.7711 (t80) REVERT: F 176 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7689 (ttpp) outliers start: 85 outliers final: 51 residues processed: 518 average time/residue: 0.1787 time to fit residues: 140.1040 Evaluate side-chains 511 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 451 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 388 VAL Chi-restraints excluded: chain A residue 421 LYS 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 835 CYS 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 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 409 VAL Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 567 CYS 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 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 484 ASP 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 525 VAL Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 598 LEU 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 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 E residue 79 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 176 LYS 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: 0.3980 chunk 136 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 212 optimal weight: 0.5980 chunk 262 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN C 618 HIS B 445 ASN B 754 HIS B 876 ASN B 964 GLN ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.142027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.119220 restraints weight = 33589.425| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.66 r_work: 0.3392 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 22678 Z= 0.290 Angle : 0.693 9.280 30850 Z= 0.359 Chirality : 0.050 0.238 3281 Planarity : 0.005 0.058 3974 Dihedral : 7.487 88.195 3382 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.38 % Allowed : 20.16 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.73 (0.15), residues: 2836 helix: 1.14 (0.23), residues: 524 sheet: -0.12 (0.26), residues: 369 loop : -1.08 (0.13), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 517 TYR 0.022 0.002 TYR F 239 PHE 0.032 0.002 PHE F 280 TRP 0.022 0.002 TRP C1006 HIS 0.008 0.002 HIS A1020 Details of bonding type rmsd covalent geometry : bond 0.00667 (22571) covalent geometry : angle 0.67930 (30623) SS BOND : bond 0.00605 ( 88) SS BOND : angle 1.42539 ( 176) hydrogen bonds : bond 0.04395 ( 738) hydrogen bonds : angle 4.93365 ( 2229) Misc. bond : bond 0.10150 ( 2) link_BETA1-4 : bond 0.01004 ( 6) link_BETA1-4 : angle 2.26742 ( 18) link_NAG-ASN : bond 0.00510 ( 11) link_NAG-ASN : angle 2.68937 ( 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 581 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 479 time to evaluate : 0.835 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 405 LYS cc_start: 0.8338 (mttt) cc_final: 0.8073 (mttt) REVERT: A 443 ASN cc_start: 0.7660 (t0) cc_final: 0.7425 (t0) REVERT: A 722 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8425 (p) REVERT: A 727 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7121 (ptm160) REVERT: A 758 ARG cc_start: 0.8355 (ttm110) cc_final: 0.8141 (ttm110) REVERT: A 784 ASP cc_start: 0.7870 (t0) cc_final: 0.7611 (t0) REVERT: A 823 SER cc_start: 0.8639 (t) cc_final: 0.8392 (m) REVERT: A 913 ARG cc_start: 0.8319 (ptm160) cc_final: 0.8008 (ptt90) REVERT: A 994 ASN cc_start: 0.7919 (p0) cc_final: 0.7346 (p0) REVERT: C 622 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7460 (tp40) REVERT: C 771 SER cc_start: 0.8709 (m) cc_final: 0.8292 (t) REVERT: C 787 LYS cc_start: 0.8370 (tttt) cc_final: 0.8085 (tptt) REVERT: C 805 GLN cc_start: 0.7413 (mm110) cc_final: 0.7211 (tp40) REVERT: C 874 LYS cc_start: 0.8369 (mttt) cc_final: 0.8143 (mttt) REVERT: C 920 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6700 (mm-30) REVERT: C 988 THR cc_start: 0.8785 (t) cc_final: 0.8530 (p) REVERT: B 372 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7493 (mt-10) REVERT: B 376 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7300 (tpp80) REVERT: B 398 CYS cc_start: 0.7139 (t) cc_final: 0.6877 (t) REVERT: B 408 ASP cc_start: 0.7933 (t0) cc_final: 0.7486 (t0) REVERT: B 494 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.7983 (ttmp) REVERT: B 723 ASN cc_start: 0.8588 (t0) cc_final: 0.8056 (t0) REVERT: B 752 ASP cc_start: 0.7200 (m-30) cc_final: 0.6930 (m-30) REVERT: B 789 ASN cc_start: 0.7679 (t0) cc_final: 0.7411 (t0) REVERT: B 791 LYS cc_start: 0.7728 (tttt) cc_final: 0.7522 (mttt) REVERT: B 812 GLU cc_start: 0.8310 (tt0) cc_final: 0.7194 (mt-10) REVERT: B 820 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: B 885 SER cc_start: 0.7968 (t) cc_final: 0.7755 (t) REVERT: B 900 ASP cc_start: 0.7734 (t0) cc_final: 0.7447 (t0) REVERT: B 968 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7309 (tm-30) REVERT: B 977 LYS cc_start: 0.7853 (mttt) cc_final: 0.7543 (mttt) REVERT: D 71 VAL cc_start: 0.8633 (t) cc_final: 0.8420 (p) REVERT: D 118 PHE cc_start: 0.8462 (t80) cc_final: 0.7900 (t80) REVERT: E 33 LEU cc_start: 0.7804 (mt) cc_final: 0.7494 (mp) REVERT: F 176 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7667 (ttpp) outliers start: 102 outliers final: 63 residues processed: 542 average time/residue: 0.1771 time to fit residues: 145.7035 Evaluate side-chains 535 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 466 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP 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 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 914 LEU Chi-restraints excluded: chain A residue 919 GLU 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 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 409 VAL 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 C residue 1003 SER 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 442 CYS Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 484 ASP 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 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 771 SER Chi-restraints excluded: chain B residue 820 GLU Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 860 VAL 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 18 VAL Chi-restraints excluded: chain D residue 42 THR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 96 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 194 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 251 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 609 ASN C 618 HIS B 445 ASN B 736 HIS B 754 HIS B 964 GLN D 21 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.142970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120130 restraints weight = 33306.973| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.66 r_work: 0.3410 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 22678 Z= 0.201 Angle : 0.637 8.882 30850 Z= 0.329 Chirality : 0.047 0.235 3281 Planarity : 0.005 0.058 3974 Dihedral : 7.318 86.163 3382 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.47 % Allowed : 22.18 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.15), residues: 2836 helix: 1.23 (0.23), residues: 528 sheet: -0.11 (0.26), residues: 359 loop : -1.10 (0.13), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 476 TYR 0.011 0.001 TYR A 427 PHE 0.020 0.002 PHE F 280 TRP 0.019 0.002 TRP C1006 HIS 0.012 0.001 HIS B 495 Details of bonding type rmsd covalent geometry : bond 0.00467 (22571) covalent geometry : angle 0.62417 (30623) SS BOND : bond 0.00471 ( 88) SS BOND : angle 1.26266 ( 176) hydrogen bonds : bond 0.03895 ( 738) hydrogen bonds : angle 4.75893 ( 2229) Misc. bond : bond 0.07965 ( 2) link_BETA1-4 : bond 0.00944 ( 6) link_BETA1-4 : angle 2.13992 ( 18) link_NAG-ASN : bond 0.00324 ( 11) link_NAG-ASN : angle 2.54337 ( 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 554 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 473 time to evaluate : 0.841 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 353 HIS cc_start: 0.5320 (m-70) cc_final: 0.4992 (m90) REVERT: A 405 LYS cc_start: 0.8371 (mttt) cc_final: 0.8055 (mttt) REVERT: A 408 ASP cc_start: 0.8048 (m-30) cc_final: 0.7834 (m-30) REVERT: A 421 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7787 (ttpp) REVERT: A 443 ASN cc_start: 0.7575 (t0) cc_final: 0.7356 (t0) REVERT: A 467 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7011 (mt-10) REVERT: A 722 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8412 (p) REVERT: A 758 ARG cc_start: 0.8333 (ttm110) cc_final: 0.8122 (ttm110) REVERT: A 784 ASP cc_start: 0.7817 (t0) cc_final: 0.7522 (t0) REVERT: A 823 SER cc_start: 0.8597 (t) cc_final: 0.8330 (m) REVERT: A 913 ARG cc_start: 0.8367 (ptm160) cc_final: 0.8031 (ptt90) REVERT: A 994 ASN cc_start: 0.7950 (p0) cc_final: 0.7347 (p0) REVERT: C 539 GLN cc_start: 0.8049 (mt0) cc_final: 0.7786 (mm-40) REVERT: C 622 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7483 (tp40) REVERT: C 771 SER cc_start: 0.8706 (m) cc_final: 0.8391 (p) REVERT: C 787 LYS cc_start: 0.8383 (tttt) cc_final: 0.8090 (tptt) REVERT: C 874 LYS cc_start: 0.8384 (mttt) cc_final: 0.8153 (mttt) REVERT: C 920 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6676 (mm-30) REVERT: C 988 THR cc_start: 0.8770 (t) cc_final: 0.8514 (p) REVERT: B 372 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7477 (mt-10) REVERT: B 398 CYS cc_start: 0.6975 (t) cc_final: 0.6696 (t) REVERT: B 399 ASP cc_start: 0.8481 (t0) cc_final: 0.7814 (p0) REVERT: B 408 ASP cc_start: 0.7928 (t0) cc_final: 0.7454 (t0) REVERT: B 412 ARG cc_start: 0.8476 (ttm110) cc_final: 0.7997 (ttm110) REVERT: B 510 GLU cc_start: 0.7739 (mp0) cc_final: 0.7494 (mp0) REVERT: B 723 ASN cc_start: 0.8490 (t0) cc_final: 0.7897 (t0) REVERT: B 752 ASP cc_start: 0.7152 (m-30) cc_final: 0.6910 (m-30) REVERT: B 789 ASN cc_start: 0.7665 (t0) cc_final: 0.7390 (t0) REVERT: B 791 LYS cc_start: 0.7738 (tttt) cc_final: 0.7521 (mttt) REVERT: B 820 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: B 885 SER cc_start: 0.7999 (t) cc_final: 0.7781 (t) REVERT: B 900 ASP cc_start: 0.7727 (t0) cc_final: 0.7442 (t0) REVERT: B 919 GLU cc_start: 0.8284 (tp30) cc_final: 0.8010 (tt0) REVERT: B 968 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7287 (tm-30) REVERT: B 977 LYS cc_start: 0.7870 (mttt) cc_final: 0.7558 (mttt) REVERT: D 71 VAL cc_start: 0.8596 (t) cc_final: 0.8338 (p) REVERT: D 118 PHE cc_start: 0.8416 (t80) cc_final: 0.7854 (t80) REVERT: F 176 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7652 (ttpp) outliers start: 81 outliers final: 66 residues processed: 526 average time/residue: 0.1839 time to fit residues: 147.7733 Evaluate side-chains 541 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 470 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 CYS 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 421 LYS 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 734 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 919 GLU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 970 LEU 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 409 VAL 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 962 ASP Chi-restraints excluded: chain C residue 1003 SER 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 430 ILE Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 484 ASP 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 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 860 VAL 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 176 LYS Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 207 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 166 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 75 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 214 optimal weight: 0.2980 chunk 161 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.143288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.120441 restraints weight = 33724.370| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.69 r_work: 0.3409 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 22678 Z= 0.169 Angle : 0.621 9.764 30850 Z= 0.321 Chirality : 0.046 0.227 3281 Planarity : 0.005 0.058 3974 Dihedral : 7.225 84.447 3382 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.56 % Allowed : 22.65 % Favored : 73.79 % 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 aren not related in a simple way. whole: -0.66 (0.15), residues: 2836 helix: 1.36 (0.23), residues: 524 sheet: -0.05 (0.27), residues: 349 loop : -1.08 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 476 TYR 0.012 0.001 TYR A 427 PHE 0.017 0.001 PHE F 280 TRP 0.022 0.002 TRP E 16 HIS 0.004 0.001 HIS A1020 Details of bonding type rmsd covalent geometry : bond 0.00395 (22571) covalent geometry : angle 0.60970 (30623) SS BOND : bond 0.00408 ( 88) SS BOND : angle 1.19429 ( 176) hydrogen bonds : bond 0.03698 ( 738) hydrogen bonds : angle 4.64560 ( 2229) Misc. bond : bond 0.08182 ( 2) link_BETA1-4 : bond 0.00816 ( 6) link_BETA1-4 : angle 2.03927 ( 18) link_NAG-ASN : bond 0.00309 ( 11) link_NAG-ASN : angle 2.47489 ( 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 556 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 473 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8243 (mm110) cc_final: 0.7973 (mp10) REVERT: A 350 TRP cc_start: 0.8152 (m100) cc_final: 0.7636 (m-10) REVERT: A 358 ASN cc_start: 0.7333 (m-40) cc_final: 0.7083 (m-40) REVERT: A 405 LYS cc_start: 0.8384 (mttt) cc_final: 0.8047 (mttt) REVERT: A 408 ASP cc_start: 0.8062 (m-30) cc_final: 0.7845 (m-30) REVERT: A 421 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7779 (ttpp) REVERT: A 443 ASN cc_start: 0.7559 (t0) cc_final: 0.7337 (t0) REVERT: A 467 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6986 (mt-10) REVERT: A 722 VAL cc_start: 0.8648 (m) cc_final: 0.8415 (p) REVERT: A 727 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7102 (ptm160) REVERT: A 758 ARG cc_start: 0.8306 (ttm110) cc_final: 0.8095 (ttm110) REVERT: A 784 ASP cc_start: 0.7797 (t0) cc_final: 0.7486 (t0) REVERT: A 823 SER cc_start: 0.8560 (t) cc_final: 0.8299 (m) REVERT: A 913 ARG cc_start: 0.8357 (ptm160) cc_final: 0.8020 (ptt90) REVERT: A 994 ASN cc_start: 0.7935 (p0) cc_final: 0.7332 (p0) REVERT: C 539 GLN cc_start: 0.8034 (mt0) cc_final: 0.7774 (mm-40) REVERT: C 622 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7482 (tp40) REVERT: C 771 SER cc_start: 0.8705 (m) cc_final: 0.8449 (p) REVERT: C 787 LYS cc_start: 0.8368 (tttt) cc_final: 0.8065 (tptt) REVERT: C 874 LYS cc_start: 0.8379 (mttt) cc_final: 0.8131 (mttt) REVERT: C 920 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6727 (mm-30) REVERT: C 988 THR cc_start: 0.8764 (t) cc_final: 0.8511 (p) REVERT: B 372 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7353 (mt-10) REVERT: B 399 ASP cc_start: 0.8511 (t0) cc_final: 0.7660 (p0) REVERT: B 408 ASP cc_start: 0.7914 (t0) cc_final: 0.7483 (t0) REVERT: B 412 ARG cc_start: 0.8482 (ttm110) cc_final: 0.7999 (ttm110) REVERT: B 510 GLU cc_start: 0.7777 (mp0) cc_final: 0.7557 (mp0) REVERT: B 723 ASN cc_start: 0.8415 (t0) cc_final: 0.7838 (t0) REVERT: B 752 ASP cc_start: 0.7140 (m-30) cc_final: 0.6913 (m-30) REVERT: B 758 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.8066 (ttm110) REVERT: B 789 ASN cc_start: 0.7683 (t0) cc_final: 0.7416 (t0) REVERT: B 791 LYS cc_start: 0.7738 (tttt) cc_final: 0.7527 (mttt) REVERT: B 820 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: B 885 SER cc_start: 0.8020 (t) cc_final: 0.7808 (t) REVERT: B 900 ASP cc_start: 0.7729 (t0) cc_final: 0.7460 (t0) REVERT: B 919 GLU cc_start: 0.8311 (tp30) cc_final: 0.7959 (tt0) REVERT: B 968 GLN cc_start: 0.7670 (tm-30) cc_final: 0.7249 (tm-30) REVERT: B 977 LYS cc_start: 0.7860 (mttt) cc_final: 0.7530 (mttt) REVERT: D 118 PHE cc_start: 0.8395 (t80) cc_final: 0.7856 (t80) REVERT: F 176 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7653 (ttpp) outliers start: 83 outliers final: 66 residues processed: 530 average time/residue: 0.1828 time to fit residues: 146.0611 Evaluate side-chains 545 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 474 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 CYS 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 421 LYS Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 586 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 835 CYS Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 919 GLU 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 353 HIS Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 409 VAL 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 962 ASP 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 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 445 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 484 ASP 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 585 LEU Chi-restraints excluded: chain B residue 598 LEU 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 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 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: 0.5980 chunk 128 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 242 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 72 optimal weight: 0.0670 chunk 191 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 ASN 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.143417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120516 restraints weight = 33661.497| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.69 r_work: 0.3408 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 22678 Z= 0.179 Angle : 0.636 19.738 30850 Z= 0.325 Chirality : 0.047 0.230 3281 Planarity : 0.005 0.074 3974 Dihedral : 7.197 82.061 3382 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.35 % Allowed : 22.87 % Favored : 73.79 % 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 aren not related in a simple way. whole: -0.67 (0.15), residues: 2836 helix: 1.34 (0.23), residues: 524 sheet: -0.04 (0.26), residues: 358 loop : -1.08 (0.13), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 476 TYR 0.012 0.001 TYR A 427 PHE 0.018 0.002 PHE F 280 TRP 0.050 0.002 TRP E 16 HIS 0.004 0.001 HIS F 253 Details of bonding type rmsd covalent geometry : bond 0.00419 (22571) covalent geometry : angle 0.62414 (30623) SS BOND : bond 0.00425 ( 88) SS BOND : angle 1.22971 ( 176) hydrogen bonds : bond 0.03737 ( 738) hydrogen bonds : angle 4.66875 ( 2229) Misc. bond : bond 0.08568 ( 2) link_BETA1-4 : bond 0.00842 ( 6) link_BETA1-4 : angle 2.01516 ( 18) link_NAG-ASN : bond 0.00306 ( 11) link_NAG-ASN : angle 2.50053 ( 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 562 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 484 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8232 (mm110) cc_final: 0.7966 (mp10) REVERT: A 350 TRP cc_start: 0.8141 (m100) cc_final: 0.7685 (m-10) REVERT: A 358 ASN cc_start: 0.7323 (m-40) cc_final: 0.7067 (m-40) REVERT: A 405 LYS cc_start: 0.8406 (mttt) cc_final: 0.8057 (mttt) REVERT: A 408 ASP cc_start: 0.8076 (m-30) cc_final: 0.7861 (m-30) REVERT: A 421 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7790 (ttpp) REVERT: A 443 ASN cc_start: 0.7540 (t0) cc_final: 0.7308 (t0) REVERT: A 477 GLU cc_start: 0.7475 (tt0) cc_final: 0.7218 (tt0) REVERT: A 523 THR cc_start: 0.8176 (m) cc_final: 0.7780 (p) REVERT: A 722 VAL cc_start: 0.8656 (m) cc_final: 0.8423 (p) REVERT: A 727 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7112 (ptm160) REVERT: A 758 ARG cc_start: 0.8307 (ttm110) cc_final: 0.8097 (ttm110) REVERT: A 784 ASP cc_start: 0.7812 (t0) cc_final: 0.7496 (t0) REVERT: A 823 SER cc_start: 0.8569 (t) cc_final: 0.8310 (m) REVERT: A 913 ARG cc_start: 0.8356 (ptm160) cc_final: 0.8025 (ptt90) REVERT: A 994 ASN cc_start: 0.7942 (p0) cc_final: 0.7333 (p0) REVERT: C 539 GLN cc_start: 0.8020 (mt0) cc_final: 0.7767 (mm-40) REVERT: C 622 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7458 (tp40) REVERT: C 771 SER cc_start: 0.8686 (m) cc_final: 0.8374 (p) REVERT: C 787 LYS cc_start: 0.8370 (tttt) cc_final: 0.8058 (tptt) REVERT: C 874 LYS cc_start: 0.8389 (mttt) cc_final: 0.8144 (mttt) REVERT: C 920 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6816 (mm-30) REVERT: C 988 THR cc_start: 0.8764 (t) cc_final: 0.8511 (p) REVERT: B 372 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7354 (mt-10) REVERT: B 408 ASP cc_start: 0.7910 (t0) cc_final: 0.7608 (t0) REVERT: B 412 ARG cc_start: 0.8487 (ttm110) cc_final: 0.8180 (ttm110) REVERT: B 510 GLU cc_start: 0.7792 (mp0) cc_final: 0.7563 (mp0) REVERT: B 723 ASN cc_start: 0.8399 (t0) cc_final: 0.7816 (t0) REVERT: B 758 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.7990 (ttm110) REVERT: B 789 ASN cc_start: 0.7692 (t0) cc_final: 0.7428 (t0) REVERT: B 791 LYS cc_start: 0.7743 (tttt) cc_final: 0.7533 (mttt) REVERT: B 820 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: B 885 SER cc_start: 0.8038 (t) cc_final: 0.7829 (t) REVERT: B 900 ASP cc_start: 0.7741 (t0) cc_final: 0.7470 (t0) REVERT: B 919 GLU cc_start: 0.8319 (tp30) cc_final: 0.8007 (tt0) REVERT: B 968 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7238 (tm-30) REVERT: B 977 LYS cc_start: 0.7883 (mttt) cc_final: 0.7550 (mttt) REVERT: D 118 PHE cc_start: 0.8407 (t80) cc_final: 0.7853 (t80) REVERT: F 176 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7672 (ttpp) outliers start: 78 outliers final: 68 residues processed: 536 average time/residue: 0.1845 time to fit residues: 148.3565 Evaluate side-chains 547 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 475 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 CYS 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 421 LYS Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 586 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 835 CYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 919 GLU 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 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 962 ASP 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 416 CYS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 442 CYS 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 484 ASP 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 585 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 628 VAL 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 860 VAL Chi-restraints excluded: chain B residue 890 VAL 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 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: 0.0770 chunk 66 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 275 optimal weight: 0.4980 chunk 250 optimal weight: 0.9990 chunk 262 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 272 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 618 HIS ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.143917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121132 restraints weight = 33515.976| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.68 r_work: 0.3424 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 22678 Z= 0.150 Angle : 0.617 17.388 30850 Z= 0.317 Chirality : 0.046 0.231 3281 Planarity : 0.005 0.057 3974 Dihedral : 7.113 79.945 3382 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.35 % Allowed : 22.99 % Favored : 73.66 % 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 aren not related in a simple way. whole: -0.63 (0.15), residues: 2836 helix: 1.37 (0.23), residues: 523 sheet: -0.05 (0.26), residues: 360 loop : -1.05 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 476 TYR 0.012 0.001 TYR A 427 PHE 0.015 0.001 PHE F 280 TRP 0.061 0.002 TRP E 16 HIS 0.004 0.001 HIS B 754 Details of bonding type rmsd covalent geometry : bond 0.00353 (22571) covalent geometry : angle 0.60653 (30623) SS BOND : bond 0.00363 ( 88) SS BOND : angle 1.10951 ( 176) hydrogen bonds : bond 0.03541 ( 738) hydrogen bonds : angle 4.61397 ( 2229) Misc. bond : bond 0.08733 ( 2) link_BETA1-4 : bond 0.00773 ( 6) link_BETA1-4 : angle 1.91539 ( 18) link_NAG-ASN : bond 0.00290 ( 11) link_NAG-ASN : angle 2.45896 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6196.36 seconds wall clock time: 106 minutes 48.01 seconds (6408.01 seconds total)