Starting phenix.real_space_refine on Mon May 4 20:43:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nb6_49218/05_2026/9nb6_49218.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nb6_49218/05_2026/9nb6_49218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nb6_49218/05_2026/9nb6_49218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nb6_49218/05_2026/9nb6_49218.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nb6_49218/05_2026/9nb6_49218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nb6_49218/05_2026/9nb6_49218.map" } resolution = 3.3 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= 0.014 sd= 0.070 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 23 9.91 5 Fe 2 7.16 5 S 231 5.16 5 C 14846 2.51 5 N 4280 2.21 5 O 4621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24003 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 860, 6504 Classifications: {'peptide': 860} Link IDs: {'PTRANS': 24, 'TRANS': 835} Chain breaks: 1 Chain: "B" Number of atoms: 6494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6494 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 24, 'TRANS': 833} Chain breaks: 1 Chain: "C" Number of atoms: 5684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5684 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 23, 'TRANS': 727} Chain breaks: 1 Chain: "D" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1068 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "E" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1122 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "F" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2437 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 16, 'TRANS': 293} Chain breaks: 1 Chain: "G" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 455 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 51 Unusual residues: {' CA': 9, 'NAG': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 50 Unusual residues: {' CA': 8, 'NAG': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 48 Unusual residues: {' CA': 6, 'NAG': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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} Time building chain proxies: 5.85, per 1000 atoms: 0.24 Number of scatterers: 24003 At special positions: 0 Unit cell: (139.86, 140.97, 195.36, 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 23 19.99 S 231 16.00 O 4621 8.00 N 4280 7.00 C 14846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=98, 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=2.04 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 693 " - pdb=" SG CYS A 713 " 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=2.03 Simple disulfide: pdb=" SG CYS A 864 " - pdb=" SG CYS A 925 " distance=2.03 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 B 168 " - pdb=" SG CYS B 202 " distance=2.02 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 258 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 238 " 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=2.03 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 693 " - pdb=" SG CYS B 713 " 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 998 " - pdb=" SG CYS B1008 " 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=2.03 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=2.03 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=2.03 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 693 " - pdb=" SG CYS C 713 " 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 F 33 " - pdb=" SG CYS G 33 " distance=2.03 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 86 " distance=2.03 Simple disulfide: pdb=" SG CYS F 90 " - pdb=" SG CYS F 207 " distance=2.03 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 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 86 " 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 NAG-ASN " NAG A1101 " - " ASN A 320 " " NAG A1102 " - " ASN A 445 " " NAG A1103 " - " ASN A 767 " " NAG B1101 " - " ASN B 320 " " NAG B1102 " - " ASN B 445 " " NAG B1103 " - " ASN B 767 " " NAG C1101 " - " ASN C 320 " " NAG C1102 " - " ASN C 445 " " NAG C1103 " - " ASN C 767 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.2 seconds 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5544 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 60 sheets defined 21.4% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 189 through 200 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.673A pdb=" N ASP A 360 " --> pdb=" O HIS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 414 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 568 through 572 removed outlier: 3.509A pdb=" N ASP A 572 " --> pdb=" O HIS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 624 removed outlier: 3.624A pdb=" N VAL A 619 " --> pdb=" O GLU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 removed outlier: 4.458A pdb=" N VAL A 755 " --> pdb=" O SER A 751 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL A 756 " --> pdb=" O ASP A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 798 removed outlier: 3.549A pdb=" N GLN A 797 " --> pdb=" O ARG A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 867 removed outlier: 3.556A pdb=" N VAL A 860 " --> pdb=" O SER A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 905 Processing helix chain 'A' and resid 959 through 971 Processing helix chain 'B' and resid 189 through 200 Processing helix chain 'B' and resid 296 through 308 Processing helix chain 'B' and resid 403 through 414 removed outlier: 4.310A pdb=" N VAL B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 Processing helix chain 'B' and resid 474 through 476 No H-bonds generated for 'chain 'B' and resid 474 through 476' Processing helix chain 'B' and resid 504 through 507 Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 568 through 572 removed outlier: 3.732A pdb=" N ARG B 571 " --> pdb=" O SER B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 624 Processing helix chain 'B' and resid 749 through 761 Processing helix chain 'B' and resid 794 through 798 Processing helix chain 'B' and resid 856 through 868 Processing helix chain 'B' and resid 901 through 905 Processing helix chain 'B' and resid 959 through 971 removed outlier: 3.501A pdb=" N ALA B 963 " --> pdb=" O ASP B 959 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 965 " --> pdb=" O ASP B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1023 removed outlier: 4.102A pdb=" N ASP B1023 " --> pdb=" O HIS B1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 308 Processing helix chain 'C' and resid 403 through 415 removed outlier: 4.143A pdb=" N VAL C 409 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 410 " --> pdb=" O GLU C 406 " (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 Processing helix chain 'C' and resid 508 through 519 removed outlier: 3.584A pdb=" N LEU C 519 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 613 through 625 removed outlier: 3.627A pdb=" N GLN C 623 " --> pdb=" O VAL C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 760 removed outlier: 4.221A pdb=" N VAL C 755 " --> pdb=" O SER C 751 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL C 756 " --> pdb=" O ASP C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 798 Processing helix chain 'C' and resid 856 through 867 removed outlier: 3.512A pdb=" N LEU C 867 " --> pdb=" O VAL C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 905 removed outlier: 3.702A pdb=" N GLN C 904 " --> pdb=" O THR C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 970 removed outlier: 3.725A pdb=" N VAL C 965 " --> pdb=" O ASP C 961 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 966 " --> pdb=" O ASP C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1023 Processing helix chain 'D' and resid 4 through 19 removed outlier: 3.610A pdb=" N ASN D 10 " --> pdb=" O ALA D 6 " (cutoff:3.500A) removed outlier: 3.575A 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 Processing helix chain 'D' and resid 53 through 73 Processing helix chain 'D' and resid 76 through 81 removed outlier: 3.935A pdb=" N ALA D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 91 Processing helix chain 'D' and resid 95 through 114 removed outlier: 4.177A pdb=" N PHE D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS D 100 " --> pdb=" O PRO D 96 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 139 Processing helix chain 'E' and resid 5 through 19 removed outlier: 3.623A pdb=" N GLY E 17 " --> pdb=" O THR E 13 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL E 19 " --> pdb=" O LEU E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 36 removed outlier: 3.632A pdb=" N GLY E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY E 26 " --> pdb=" O ASP E 22 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 42 removed outlier: 3.837A pdb=" N ARG E 41 " --> pdb=" O TRP E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 47 removed outlier: 3.612A pdb=" N GLY E 47 " --> pdb=" O GLU E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 58 Processing helix chain 'E' and resid 58 through 76 removed outlier: 3.569A pdb=" N LYS E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 78 No H-bonds generated for 'chain 'E' and resid 77 through 78' Processing helix chain 'E' and resid 79 through 80 No H-bonds generated for 'chain 'E' and resid 79 through 80' Processing helix chain 'E' and resid 81 through 86 Processing helix chain 'E' and resid 86 through 96 removed outlier: 3.818A pdb=" N LEU E 92 " --> pdb=" O THR E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 120 removed outlier: 3.899A pdb=" N PHE E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 144 Processing helix chain 'F' and resid 141 through 146 Processing helix chain 'F' and resid 154 through 159 removed outlier: 3.869A pdb=" N ILE F 158 " --> pdb=" O THR F 154 " (cutoff:3.500A) 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 248 through 256 Processing helix chain 'F' and resid 259 through 263 Processing helix chain 'F' and resid 333 through 346 removed outlier: 4.527A pdb=" N ASP F 338 " --> pdb=" O THR F 334 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TRP F 339 " --> pdb=" O SER F 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 166 removed outlier: 3.544A pdb=" N GLU A 158 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 164 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N SER A 169 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 166 removed outlier: 3.544A pdb=" N GLU A 158 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 164 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N SER A 169 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 273 removed outlier: 4.162A pdb=" N GLY A 271 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER A 276 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 273 removed outlier: 4.162A pdb=" N GLY A 271 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER A 276 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU A 279 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE A 290 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N TRP A 329 " --> pdb=" O TRP A 287 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR A 289 " --> pdb=" O TRP A 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 376 removed outlier: 3.561A pdb=" N ILE A 470 " --> pdb=" O GLY A 384 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR A 471 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 372 through 376 removed outlier: 6.582A pdb=" N VAL A 386 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL A 397 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU A 437 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS A 396 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU A 439 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 477 through 481 removed outlier: 3.587A pdb=" N GLU A 477 " --> pdb=" O LYS A 494 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 477 through 481 removed outlier: 3.587A pdb=" N GLU A 477 " --> pdb=" O LYS A 494 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 544 through 545 removed outlier: 3.713A pdb=" N ALA A 560 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 582 through 586 removed outlier: 4.720A pdb=" N GLU A 582 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 594 " --> pdb=" O VAL A 680 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 680 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER A 631 " --> pdb=" O ILE A 681 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 582 through 586 removed outlier: 4.720A pdb=" N GLU A 582 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL A 596 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TRP A 604 " --> pdb=" O GLN A 644 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TRP A 646 " --> pdb=" O TRP A 604 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER A 606 " --> pdb=" O TRP A 646 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 649 through 650 removed outlier: 3.594A pdb=" N MET A 649 " --> pdb=" O THR A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 720 through 722 Processing sheet with id=AB5, first strand: chain 'A' and resid 720 through 722 removed outlier: 7.085A pdb=" N VAL A 732 " --> pdb=" O ILE A 743 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE A 743 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TRP A 782 " --> pdb=" O TRP A 740 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N THR A 742 " --> pdb=" O TRP A 782 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 823 through 827 removed outlier: 3.656A pdb=" N SER A 823 " --> pdb=" O PHE A 842 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 823 through 827 removed outlier: 3.656A pdb=" N SER A 823 " --> pdb=" O PHE A 842 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TRP A 922 " --> pdb=" O ASN A 876 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 929 through 932 removed outlier: 4.133A pdb=" N ALA A1025 " --> pdb=" O PHE A 979 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A1027 " --> pdb=" O LYS A 977 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS A 977 " --> pdb=" O ASN A1027 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 929 through 932 removed outlier: 6.496A pdb=" N VAL A 942 " --> pdb=" O VAL A 953 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 953 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 949 " --> pdb=" O HIS A 946 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TRP A 992 " --> pdb=" O TRP A 950 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR A 952 " --> pdb=" O TRP A 992 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.537A pdb=" N GLU B 158 " --> pdb=" O LYS B 175 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 170 through 171 removed outlier: 7.653A pdb=" N GLY B 255 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE B 208 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N ILE B 257 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.904A pdb=" N ASP B 224 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY B 242 " --> pdb=" O ASP B 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 266 through 269 Processing sheet with id=AC5, first strand: chain 'B' and resid 266 through 269 removed outlier: 3.608A pdb=" N GLY B 277 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 372 through 376 removed outlier: 6.899A pdb=" N THR B 471 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 372 through 376 removed outlier: 6.695A pdb=" N VAL B 386 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 397 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU B 394 " --> pdb=" O THR B 435 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N LEU B 437 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS B 396 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 477 through 481 removed outlier: 6.431A pdb=" N GLY B 574 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE B 527 " --> pdb=" O GLY B 574 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL B 576 " --> pdb=" O VAL B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 477 through 481 removed outlier: 6.523A pdb=" N VAL B 491 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE B 502 " --> pdb=" O VAL B 491 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N TRP B 541 " --> pdb=" O TRP B 499 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER B 501 " --> pdb=" O TRP B 541 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AD2, first strand: chain 'B' and resid 582 through 586 removed outlier: 4.665A pdb=" N GLU B 582 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER B 631 " --> pdb=" O ILE B 681 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 582 through 586 removed outlier: 4.665A pdb=" N GLU B 582 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL B 596 " --> pdb=" O LEU B 607 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLN B 644 " --> pdb=" O TRP B 604 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 649 through 650 Processing sheet with id=AD5, first strand: chain 'B' and resid 691 through 692 removed outlier: 7.337A pdb=" N SER B 691 " --> pdb=" O ILE B 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 719 through 726 removed outlier: 3.681A pdb=" N ARG B 720 " --> pdb=" O GLU B 733 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 724 " --> pdb=" O ALA B 729 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ALA B 729 " --> pdb=" O GLY B 724 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 719 through 726 removed outlier: 3.681A pdb=" N ARG B 720 " --> pdb=" O GLU B 733 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 724 " --> pdb=" O ALA B 729 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ALA B 729 " --> pdb=" O GLY B 724 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 824 through 827 Processing sheet with id=AD9, first strand: chain 'B' and resid 824 through 827 Processing sheet with id=AE1, first strand: chain 'B' and resid 929 through 932 removed outlier: 3.912A pdb=" N ASN B1027 " --> pdb=" O LYS B 977 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS B 977 " --> pdb=" O ASN B1027 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 929 through 932 removed outlier: 6.781A pdb=" N VAL B 942 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL B 953 " --> pdb=" O VAL B 942 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N TRP B 992 " --> pdb=" O TRP B 950 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N THR B 952 " --> pdb=" O TRP B 992 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 265 through 273 removed outlier: 3.581A pdb=" N SER C 265 " --> pdb=" O ARG C 282 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY C 271 " --> pdb=" O SER C 276 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N SER C 276 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 265 through 273 removed outlier: 3.581A pdb=" N SER C 265 " --> pdb=" O ARG C 282 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY C 271 " --> pdb=" O SER C 276 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N SER C 276 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 372 through 376 removed outlier: 3.688A pdb=" N LYS C 421 " --> pdb=" O THR C 471 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 372 through 376 removed outlier: 6.666A pdb=" N VAL C 386 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL C 397 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU C 437 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS C 396 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N LEU C 439 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 477 through 481 removed outlier: 3.525A pdb=" N GLY C 489 " --> pdb=" O VAL C 575 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 526 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 477 through 481 removed outlier: 6.468A pdb=" N VAL C 491 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE C 502 " --> pdb=" O VAL C 491 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N TRP C 541 " --> pdb=" O TRP C 499 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N SER C 501 " --> pdb=" O TRP C 541 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 544 through 545 removed outlier: 3.580A pdb=" N GLU C 544 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 583 through 586 Processing sheet with id=AF2, first strand: chain 'C' and resid 583 through 586 removed outlier: 3.617A pdb=" N VAL C 680 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 649 through 650 Processing sheet with id=AF4, first strand: chain 'C' and resid 719 through 722 Processing sheet with id=AF5, first strand: chain 'C' and resid 719 through 722 removed outlier: 3.523A pdb=" N VAL C 816 " --> pdb=" O GLY C 730 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 824 through 827 Processing sheet with id=AF7, first strand: chain 'C' and resid 824 through 827 removed outlier: 6.643A pdb=" N LEU C 839 " --> pdb=" O VAL C 850 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL C 850 " --> pdb=" O LEU C 839 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP C 889 " --> pdb=" O TRP C 847 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR C 849 " --> pdb=" O TRP C 889 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 929 through 932 Processing sheet with id=AF9, first strand: chain 'C' and resid 929 through 932 removed outlier: 6.337A pdb=" N VAL C 942 " --> pdb=" O VAL C 953 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL C 953 " --> pdb=" O VAL C 942 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N TRP C 950 " --> pdb=" O ILE C 991 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N LEU C 993 " --> pdb=" O TRP C 950 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR C 952 " --> pdb=" O LEU C 993 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 66 through 67 Processing sheet with id=AG2, first strand: chain 'F' and resid 66 through 67 removed outlier: 4.095A pdb=" N SER G 47 " --> pdb=" O SER F 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 56 through 59 Processing sheet with id=AG4, first strand: chain 'F' and resid 107 through 108 removed outlier: 3.684A pdb=" N LYS F 238 " --> pdb=" O GLY F 224 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N VAL F 219 " --> pdb=" O HIS F 303 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N HIS F 303 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER F 223 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA F 299 " --> pdb=" O SER F 223 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY F 314 " --> pdb=" O PHE F 300 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL F 302 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ALA F 312 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP F 304 " --> pdb=" O TRP F 310 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TRP F 310 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL F 329 " --> pdb=" O SER F 317 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 163 through 166 removed outlier: 4.151A pdb=" N LYS F 119 " --> pdb=" O TYR F 165 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 57 through 58 845 hydrogen bonds defined for protein. 2244 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.46 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 8845 1.37 - 1.55: 15424 1.55 - 1.72: 11 1.72 - 1.89: 263 1.89 - 2.07: 8 Bond restraints: 24551 Sorted by residual: bond pdb=" O1 OXY D 202 " pdb=" O2 OXY D 202 " ideal model delta sigma weight residual 1.109 1.207 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" O1 OXY E 202 " pdb=" O2 OXY E 202 " ideal model delta sigma weight residual 1.109 1.207 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" CA LYS B 469 " pdb=" C LYS B 469 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.24e-02 6.50e+03 1.62e+01 bond pdb=" C CYS F 207 " pdb=" N LEU F 208 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.47e-02 4.63e+03 8.54e+00 bond pdb=" CA GLN C 425 " pdb=" C GLN C 425 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.30e-02 5.92e+03 6.25e+00 ... (remaining 24546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 33193 3.30 - 6.60: 95 6.60 - 9.90: 8 9.90 - 13.20: 1 13.20 - 16.50: 1 Bond angle restraints: 33298 Sorted by residual: angle pdb=" C CYS F 207 " pdb=" N LEU F 208 " pdb=" CA LEU F 208 " ideal model delta sigma weight residual 120.68 137.18 -16.50 1.52e+00 4.33e-01 1.18e+02 angle pdb=" CB LYS C 453 " pdb=" CG LYS C 453 " pdb=" CD LYS C 453 " ideal model delta sigma weight residual 111.30 121.22 -9.92 2.30e+00 1.89e-01 1.86e+01 angle pdb=" N ILE C 766 " pdb=" CA ILE C 766 " pdb=" C ILE C 766 " ideal model delta sigma weight residual 112.96 109.08 3.88 1.00e+00 1.00e+00 1.50e+01 angle pdb=" N GLY A 898 " pdb=" CA GLY A 898 " pdb=" C GLY A 898 " ideal model delta sigma weight residual 112.34 119.85 -7.51 2.04e+00 2.40e-01 1.36e+01 angle pdb=" C LYS A 352 " pdb=" N HIS A 353 " pdb=" CA HIS A 353 " ideal model delta sigma weight residual 121.54 128.35 -6.81 1.91e+00 2.74e-01 1.27e+01 ... (remaining 33293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 12364 18.00 - 35.99: 1671 35.99 - 53.99: 509 53.99 - 71.99: 85 71.99 - 89.99: 40 Dihedral angle restraints: 14669 sinusoidal: 5963 harmonic: 8706 Sorted by residual: dihedral pdb=" CB CYS B 197 " pdb=" SG CYS B 197 " pdb=" SG CYS B 258 " pdb=" CB CYS B 258 " ideal model delta sinusoidal sigma weight residual 93.00 179.33 -86.33 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS B 184 " pdb=" SG CYS B 184 " pdb=" SG CYS B 248 " pdb=" CB CYS B 248 " ideal model delta sinusoidal sigma weight residual -86.00 -2.48 -83.52 1 1.00e+01 1.00e-02 8.52e+01 dihedral pdb=" CB CYS A 547 " pdb=" SG CYS A 547 " pdb=" SG CYS A 557 " pdb=" CB CYS A 557 " ideal model delta sinusoidal sigma weight residual 93.00 13.33 79.67 1 1.00e+01 1.00e-02 7.88e+01 ... (remaining 14666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3229 0.073 - 0.146: 300 0.146 - 0.219: 3 0.219 - 0.293: 2 0.293 - 0.366: 1 Chirality restraints: 3535 Sorted by residual: chirality pdb=" C1 NAG C1102 " pdb=" ND2 ASN C 445 " pdb=" C2 NAG C1102 " pdb=" O5 NAG C1102 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C1 NAG B1101 " pdb=" ND2 ASN B 320 " pdb=" C2 NAG B1101 " pdb=" O5 NAG B1101 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C1 NAG A1101 " pdb=" ND2 ASN A 320 " pdb=" C2 NAG A1101 " pdb=" O5 NAG A1101 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 3532 not shown) Planarity restraints: 4348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 124 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO E 125 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 125 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 125 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 81 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" C ASN E 81 " -0.033 2.00e-02 2.50e+03 pdb=" O ASN E 81 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU E 82 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 465 " 0.015 2.00e-02 2.50e+03 1.33e-02 3.51e+00 pdb=" CG TYR C 465 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR C 465 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR C 465 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 465 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 465 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR C 465 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 465 " -0.000 2.00e-02 2.50e+03 ... (remaining 4345 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4629 2.77 - 3.30: 22436 3.30 - 3.84: 39462 3.84 - 4.37: 45397 4.37 - 4.90: 78964 Nonbonded interactions: 190888 Sorted by model distance: nonbonded pdb=" OH TYR B 354 " pdb=" O HIS E 144 " model vdw 2.241 3.040 nonbonded pdb=" O LYS B 352 " pdb=" ND1 HIS B 353 " model vdw 2.244 3.120 nonbonded pdb=" O SER A 332 " pdb=" OG SER A 332 " model vdw 2.247 3.040 nonbonded pdb=" OG SER C 853 " pdb=" OD1 ASP C 891 " model vdw 2.249 3.040 nonbonded pdb=" OG1 THR E 51 " pdb=" OD1 ASP E 53 " model vdw 2.253 3.040 ... (remaining 190883 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 263 through 1109) selection = (chain 'B' and resid 263 through 1109) selection = chain 'C' } 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: 6.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.200 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 : 0.003 0.195 24660 Z= 0.123 Angle : 0.546 16.501 33521 Z= 0.290 Chirality : 0.041 0.366 3535 Planarity : 0.003 0.048 4339 Dihedral : 17.730 89.987 8831 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.64 % Allowed : 30.45 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.14), residues: 3100 helix: 1.07 (0.22), residues: 531 sheet: -0.58 (0.29), residues: 326 loop : -0.51 (0.12), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 584 TYR 0.032 0.001 TYR C 465 PHE 0.011 0.001 PHE B 842 TRP 0.026 0.001 TRP B 541 HIS 0.009 0.001 HIS C 773 Details of bonding type rmsd covalent geometry : bond 0.00237 (24551) covalent geometry : angle 0.53510 (33298) SS BOND : bond 0.00199 ( 98) SS BOND : angle 0.77439 ( 196) hydrogen bonds : bond 0.24929 ( 738) hydrogen bonds : angle 8.34105 ( 2244) Misc. bond : bond 0.17824 ( 2) link_NAG-ASN : bond 0.00607 ( 9) link_NAG-ASN : angle 3.63588 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 190 time to evaluate : 0.893 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 507 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.6930 (m-80) REVERT: A 589 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8332 (pttm) REVERT: A 810 HIS cc_start: 0.7653 (m90) cc_final: 0.6957 (m90) REVERT: A 886 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7621 (pt) REVERT: A 888 MET cc_start: 0.7734 (ptp) cc_final: 0.7331 (ptp) REVERT: A 927 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7719 (t0) REVERT: B 243 TRP cc_start: 0.2928 (OUTLIER) cc_final: 0.2725 (m100) REVERT: B 327 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.6718 (t70) REVERT: B 357 HIS cc_start: 0.7544 (OUTLIER) cc_final: 0.6958 (t70) REVERT: B 507 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7341 (t80) REVERT: B 880 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.5884 (mt) REVERT: C 283 PHE cc_start: 0.5758 (OUTLIER) cc_final: 0.4848 (p90) REVERT: C 390 ILE cc_start: 0.9397 (mt) cc_final: 0.9126 (mm) REVERT: C 569 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7147 (t-90) REVERT: C 626 CYS cc_start: 0.5536 (OUTLIER) cc_final: 0.5028 (m) REVERT: C 657 GLN cc_start: 0.7860 (tp-100) cc_final: 0.7474 (tp40) REVERT: C 737 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: C 850 VAL cc_start: 0.8491 (t) cc_final: 0.8188 (m) REVERT: C 872 LYS cc_start: 0.8563 (mmtm) cc_final: 0.8350 (mmtm) REVERT: C 884 MET cc_start: 0.7707 (tpt) cc_final: 0.7396 (mmm) REVERT: C 891 ASP cc_start: 0.7886 (t70) cc_final: 0.7514 (t70) REVERT: C 900 ASP cc_start: 0.8435 (p0) cc_final: 0.8193 (p0) REVERT: C 988 THR cc_start: 0.8449 (p) cc_final: 0.8138 (p) REVERT: D 24 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7531 (tm-30) REVERT: D 33 MET cc_start: 0.7915 (ttp) cc_final: 0.7608 (ttp) REVERT: D 57 LYS cc_start: 0.8117 (tppt) cc_final: 0.7651 (mttt) REVERT: E 64 HIS cc_start: 0.7784 (t70) cc_final: 0.7068 (t-170) REVERT: G 46 HIS cc_start: 0.4857 (OUTLIER) cc_final: 0.4016 (t-90) REVERT: G 74 TRP cc_start: 0.4369 (m100) cc_final: 0.4096 (m100) outliers start: 93 outliers final: 66 residues processed: 269 average time/residue: 0.1550 time to fit residues: 67.4616 Evaluate side-chains 264 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 184 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 343 TRP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1020 HIS Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 808 CYS Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain C residue 626 CYS Chi-restraints excluded: chain C residue 638 PHE Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 774 PHE Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 808 CYS Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1020 HIS Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain G residue 46 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0570 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 0.0670 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 306 GLN C 336 GLN D 90 HIS E 64 HIS E 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.129191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.099382 restraints weight = 58236.522| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.05 r_work: 0.3220 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.180 24660 Z= 0.118 Angle : 0.547 9.714 33521 Z= 0.284 Chirality : 0.043 0.372 3535 Planarity : 0.004 0.053 4339 Dihedral : 7.679 67.726 3644 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 6.30 % Allowed : 26.85 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3100 helix: 1.65 (0.23), residues: 547 sheet: -0.65 (0.28), residues: 350 loop : -0.56 (0.12), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 758 TYR 0.032 0.001 TYR C 465 PHE 0.015 0.001 PHE F 280 TRP 0.013 0.001 TRP A 236 HIS 0.007 0.001 HIS C 773 Details of bonding type rmsd covalent geometry : bond 0.00264 (24551) covalent geometry : angle 0.53446 (33298) SS BOND : bond 0.00244 ( 98) SS BOND : angle 0.85821 ( 196) hydrogen bonds : bond 0.04132 ( 738) hydrogen bonds : angle 5.56928 ( 2244) Misc. bond : bond 0.17889 ( 2) link_NAG-ASN : bond 0.00629 ( 9) link_NAG-ASN : angle 3.75687 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 186 time to evaluate : 0.855 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 179 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7933 (mpp80) REVERT: A 292 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8262 (p0) REVERT: A 618 HIS cc_start: 0.8503 (m170) cc_final: 0.8295 (m90) REVERT: A 785 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: A 872 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8036 (ttpm) REVERT: A 888 MET cc_start: 0.7818 (ptp) cc_final: 0.7176 (ptp) REVERT: B 327 HIS cc_start: 0.7357 (OUTLIER) cc_final: 0.6825 (t70) REVERT: B 357 HIS cc_start: 0.7573 (OUTLIER) cc_final: 0.7005 (t70) REVERT: B 548 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: B 615 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6256 (pt0) REVERT: B 809 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7973 (ttm170) REVERT: B 880 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.5853 (mt) REVERT: B 908 SER cc_start: 0.7263 (OUTLIER) cc_final: 0.6799 (p) REVERT: C 283 PHE cc_start: 0.5614 (OUTLIER) cc_final: 0.4699 (p90) REVERT: C 319 VAL cc_start: 0.7235 (OUTLIER) cc_final: 0.7028 (m) REVERT: C 390 ILE cc_start: 0.9256 (mt) cc_final: 0.8815 (mm) REVERT: C 391 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7775 (mp10) REVERT: C 396 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8198 (mttp) REVERT: C 535 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: C 569 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.6867 (t-90) REVERT: C 626 CYS cc_start: 0.5390 (OUTLIER) cc_final: 0.4923 (m) REVERT: C 657 GLN cc_start: 0.7937 (tp-100) cc_final: 0.7440 (tp40) REVERT: C 850 VAL cc_start: 0.8508 (t) cc_final: 0.8237 (m) REVERT: C 900 ASP cc_start: 0.8486 (p0) cc_final: 0.8233 (p0) REVERT: C 988 THR cc_start: 0.8396 (p) cc_final: 0.8094 (p) REVERT: D 57 LYS cc_start: 0.7935 (tppt) cc_final: 0.7531 (mttt) REVERT: E 64 HIS cc_start: 0.7701 (t-170) cc_final: 0.7257 (t-170) outliers start: 161 outliers final: 99 residues processed: 327 average time/residue: 0.1593 time to fit residues: 83.2431 Evaluate side-chains 294 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 177 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 343 TRP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 457 TRP Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 506 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 808 CYS Chi-restraints excluded: chain B residue 809 ARG Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain C residue 267 ARG Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 626 CYS Chi-restraints excluded: chain C residue 638 PHE Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 808 CYS Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain C residue 1020 HIS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain G residue 79 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 105 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 126 optimal weight: 0.0980 chunk 91 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 177 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 190 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 ASN B 347 HIS ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 ASN ** F 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.109693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.079909 restraints weight = 58786.164| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.02 r_work: 0.3167 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.272 24660 Z= 0.193 Angle : 0.587 11.281 33521 Z= 0.302 Chirality : 0.044 0.399 3535 Planarity : 0.004 0.050 4339 Dihedral : 7.185 67.887 3584 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 7.75 % Allowed : 26.18 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3100 helix: 1.55 (0.23), residues: 547 sheet: -0.75 (0.28), residues: 333 loop : -0.71 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 562 TYR 0.019 0.002 TYR C 424 PHE 0.028 0.002 PHE F 280 TRP 0.031 0.001 TRP G 74 HIS 0.007 0.001 HIS F 253 Details of bonding type rmsd covalent geometry : bond 0.00455 (24551) covalent geometry : angle 0.57109 (33298) SS BOND : bond 0.00362 ( 98) SS BOND : angle 1.12079 ( 196) hydrogen bonds : bond 0.04100 ( 738) hydrogen bonds : angle 5.23413 ( 2244) Misc. bond : bond 0.25579 ( 2) link_NAG-ASN : bond 0.00595 ( 9) link_NAG-ASN : angle 3.99429 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 180 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7938 (mpp80) REVERT: A 292 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8531 (p0) REVERT: A 582 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8104 (pt0) REVERT: A 587 ASN cc_start: 0.6505 (OUTLIER) cc_final: 0.6168 (t0) REVERT: A 785 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6325 (mp0) REVERT: A 787 LYS cc_start: 0.9303 (tttp) cc_final: 0.9016 (mmtm) REVERT: A 872 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8135 (ttpm) REVERT: A 888 MET cc_start: 0.7761 (ptp) cc_final: 0.7218 (ptp) REVERT: A 927 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7743 (t0) REVERT: A 1013 TRP cc_start: 0.8387 (m100) cc_final: 0.7532 (m100) REVERT: B 327 HIS cc_start: 0.7445 (OUTLIER) cc_final: 0.6899 (t70) REVERT: B 357 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.6928 (t70) REVERT: B 548 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: B 615 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6201 (pt0) REVERT: B 785 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: B 809 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8157 (ttm170) REVERT: B 880 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.5840 (mt) REVERT: B 908 SER cc_start: 0.7337 (OUTLIER) cc_final: 0.6929 (p) REVERT: C 267 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.5000 (ptp-170) REVERT: C 283 PHE cc_start: 0.5564 (OUTLIER) cc_final: 0.4661 (p90) REVERT: C 319 VAL cc_start: 0.7438 (OUTLIER) cc_final: 0.7217 (m) REVERT: C 390 ILE cc_start: 0.9256 (mt) cc_final: 0.8839 (mm) REVERT: C 391 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.7810 (mp10) REVERT: C 535 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: C 569 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.6997 (t-90) REVERT: C 626 CYS cc_start: 0.5626 (OUTLIER) cc_final: 0.5210 (m) REVERT: C 657 GLN cc_start: 0.7701 (tp-100) cc_final: 0.7356 (tp40) REVERT: C 850 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8322 (t) REVERT: C 891 ASP cc_start: 0.8137 (t70) cc_final: 0.7792 (t0) REVERT: C 900 ASP cc_start: 0.8532 (p0) cc_final: 0.8281 (p0) REVERT: C 988 THR cc_start: 0.8447 (p) cc_final: 0.8158 (p) REVERT: D 57 LYS cc_start: 0.8010 (tppt) cc_final: 0.7565 (mttt) REVERT: E 64 HIS cc_start: 0.7890 (t-170) cc_final: 0.7533 (t-170) REVERT: F 61 GLU cc_start: 0.3961 (OUTLIER) cc_final: 0.3066 (pp20) REVERT: G 74 TRP cc_start: 0.5122 (m100) cc_final: 0.4734 (m100) outliers start: 198 outliers final: 132 residues processed: 351 average time/residue: 0.1594 time to fit residues: 89.2663 Evaluate side-chains 333 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 177 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 343 TRP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 457 TRP Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 506 ASP Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 611 HIS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 808 CYS Chi-restraints excluded: chain B residue 809 ARG Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain C residue 267 ARG Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 298 TYR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 626 CYS Chi-restraints excluded: chain C residue 638 PHE Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 808 CYS Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 853 SER Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain C residue 1007 ASP Chi-restraints excluded: chain C residue 1018 CYS Chi-restraints excluded: chain C residue 1020 HIS Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain G residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 297 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 308 optimal weight: 20.0000 chunk 115 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 807 ASN B 805 GLN C 754 HIS ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.127740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.097795 restraints weight = 58409.686| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.02 r_work: 0.3172 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.252 24660 Z= 0.160 Angle : 0.561 11.154 33521 Z= 0.287 Chirality : 0.044 0.396 3535 Planarity : 0.004 0.057 4339 Dihedral : 7.131 68.092 3584 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 7.59 % Allowed : 26.14 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3100 helix: 1.64 (0.23), residues: 546 sheet: -0.83 (0.29), residues: 319 loop : -0.73 (0.12), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 376 TYR 0.023 0.001 TYR C 465 PHE 0.020 0.001 PHE F 280 TRP 0.014 0.001 TRP B 541 HIS 0.008 0.001 HIS F 46 Details of bonding type rmsd covalent geometry : bond 0.00377 (24551) covalent geometry : angle 0.54633 (33298) SS BOND : bond 0.00306 ( 98) SS BOND : angle 0.98157 ( 196) hydrogen bonds : bond 0.03559 ( 738) hydrogen bonds : angle 5.04605 ( 2244) Misc. bond : bond 0.23890 ( 2) link_NAG-ASN : bond 0.00587 ( 9) link_NAG-ASN : angle 4.00398 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 182 time to evaluate : 0.955 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 179 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7943 (mpp80) REVERT: A 582 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8074 (pt0) REVERT: A 787 LYS cc_start: 0.9312 (tttp) cc_final: 0.9014 (mmtm) REVERT: A 872 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8139 (ttpm) REVERT: A 876 ASN cc_start: 0.8820 (t0) cc_final: 0.8497 (t0) REVERT: A 888 MET cc_start: 0.7677 (ptp) cc_final: 0.7270 (ptp) REVERT: A 927 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7744 (t0) REVERT: A 1013 TRP cc_start: 0.8451 (m100) cc_final: 0.7700 (m100) REVERT: B 327 HIS cc_start: 0.7534 (OUTLIER) cc_final: 0.7031 (t70) REVERT: B 343 TRP cc_start: 0.8013 (OUTLIER) cc_final: 0.7355 (m100) REVERT: B 357 HIS cc_start: 0.7706 (OUTLIER) cc_final: 0.6733 (t-90) REVERT: B 548 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: B 615 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6201 (pt0) REVERT: B 785 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: B 809 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8186 (ttm170) REVERT: B 880 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.5815 (mt) REVERT: B 908 SER cc_start: 0.7311 (OUTLIER) cc_final: 0.6935 (p) REVERT: C 267 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.4987 (ptp-170) REVERT: C 283 PHE cc_start: 0.5514 (OUTLIER) cc_final: 0.4825 (p90) REVERT: C 299 ASP cc_start: 0.8050 (t0) cc_final: 0.7842 (t0) REVERT: C 319 VAL cc_start: 0.7488 (OUTLIER) cc_final: 0.7269 (m) REVERT: C 390 ILE cc_start: 0.9245 (mt) cc_final: 0.8816 (mm) REVERT: C 391 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7855 (mp10) REVERT: C 535 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: C 569 HIS cc_start: 0.7980 (OUTLIER) cc_final: 0.7123 (t-90) REVERT: C 626 CYS cc_start: 0.5584 (OUTLIER) cc_final: 0.5173 (m) REVERT: C 657 GLN cc_start: 0.7768 (tp-100) cc_final: 0.7422 (tp40) REVERT: C 891 ASP cc_start: 0.8102 (t70) cc_final: 0.7764 (t0) REVERT: C 900 ASP cc_start: 0.8522 (p0) cc_final: 0.8271 (p0) REVERT: C 988 THR cc_start: 0.8437 (p) cc_final: 0.8137 (p) REVERT: D 57 LYS cc_start: 0.7984 (tppt) cc_final: 0.7556 (mttt) REVERT: E 16 TRP cc_start: 0.8526 (OUTLIER) cc_final: 0.7833 (t-100) REVERT: E 64 HIS cc_start: 0.7782 (t-170) cc_final: 0.7370 (t-170) REVERT: F 61 GLU cc_start: 0.4028 (OUTLIER) cc_final: 0.3131 (pp20) REVERT: F 90 CYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6557 (t) REVERT: G 46 HIS cc_start: 0.5338 (OUTLIER) cc_final: 0.3931 (t70) outliers start: 194 outliers final: 144 residues processed: 352 average time/residue: 0.1555 time to fit residues: 87.8525 Evaluate side-chains 340 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 172 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 343 TRP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 457 TRP Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 506 ASP Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 611 HIS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 957 SER Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 343 TRP Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 808 CYS Chi-restraints excluded: chain B residue 809 ARG Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain C residue 267 ARG Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 626 CYS Chi-restraints excluded: chain C residue 638 PHE Chi-restraints excluded: chain C residue 640 LYS Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 808 CYS Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 853 SER Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 964 GLN Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain C residue 1018 CYS Chi-restraints excluded: chain C residue 1020 HIS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain E residue 16 TRP Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain G residue 46 HIS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 206 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 308 optimal weight: 20.0000 chunk 272 optimal weight: 6.9990 chunk 303 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS ** G 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.108254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.078452 restraints weight = 58463.202| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.00 r_work: 0.3138 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.318 24660 Z= 0.241 Angle : 0.629 13.080 33521 Z= 0.321 Chirality : 0.046 0.420 3535 Planarity : 0.004 0.054 4339 Dihedral : 7.303 68.764 3578 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 8.65 % Allowed : 25.40 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3100 helix: 1.42 (0.23), residues: 544 sheet: -1.00 (0.27), residues: 338 loop : -0.91 (0.12), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 376 TYR 0.022 0.002 TYR C 424 PHE 0.029 0.002 PHE F 280 TRP 0.040 0.002 TRP B 541 HIS 0.019 0.001 HIS F 46 Details of bonding type rmsd covalent geometry : bond 0.00572 (24551) covalent geometry : angle 0.61309 (33298) SS BOND : bond 0.00441 ( 98) SS BOND : angle 1.15057 ( 196) hydrogen bonds : bond 0.03973 ( 738) hydrogen bonds : angle 5.16253 ( 2244) Misc. bond : bond 0.30773 ( 2) link_NAG-ASN : bond 0.00611 ( 9) link_NAG-ASN : angle 4.19115 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 177 time to evaluate : 0.866 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 163 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8303 (mtp85) REVERT: A 179 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8010 (mpp80) REVERT: A 343 TRP cc_start: 0.8653 (OUTLIER) cc_final: 0.8370 (p90) REVERT: A 582 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8144 (pt0) REVERT: A 872 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8183 (ttpm) REVERT: A 888 MET cc_start: 0.7732 (ptp) cc_final: 0.7204 (ptp) REVERT: A 927 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7767 (t0) REVERT: A 1013 TRP cc_start: 0.8546 (m100) cc_final: 0.7955 (m100) REVERT: B 327 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.7121 (t70) REVERT: B 343 TRP cc_start: 0.8223 (OUTLIER) cc_final: 0.7620 (m100) REVERT: B 357 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.6659 (t-90) REVERT: B 548 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: B 615 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6252 (pt0) REVERT: B 785 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: B 854 SER cc_start: 0.8654 (OUTLIER) cc_final: 0.8349 (p) REVERT: B 880 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.5901 (mt) REVERT: B 908 SER cc_start: 0.7395 (OUTLIER) cc_final: 0.7055 (p) REVERT: C 267 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.5120 (ptp-170) REVERT: C 283 PHE cc_start: 0.5739 (OUTLIER) cc_final: 0.4984 (p90) REVERT: C 319 VAL cc_start: 0.7527 (OUTLIER) cc_final: 0.7302 (m) REVERT: C 390 ILE cc_start: 0.9234 (mt) cc_final: 0.8780 (mm) REVERT: C 391 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: C 535 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: C 569 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7139 (t-90) REVERT: C 737 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7589 (mt-10) REVERT: C 850 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8355 (t) REVERT: C 855 MET cc_start: 0.8376 (tpt) cc_final: 0.7849 (tpt) REVERT: C 884 MET cc_start: 0.7781 (tpt) cc_final: 0.7529 (mmm) REVERT: C 891 ASP cc_start: 0.8158 (t70) cc_final: 0.7842 (t0) REVERT: C 900 ASP cc_start: 0.8504 (p0) cc_final: 0.8246 (p0) REVERT: C 988 THR cc_start: 0.8495 (p) cc_final: 0.8209 (p) REVERT: C 1013 TRP cc_start: 0.8045 (m100) cc_final: 0.7719 (m100) REVERT: D 57 LYS cc_start: 0.8048 (tppt) cc_final: 0.7585 (mttt) REVERT: E 64 HIS cc_start: 0.7758 (t-170) cc_final: 0.7385 (t-170) REVERT: F 90 CYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6676 (t) REVERT: G 46 HIS cc_start: 0.5176 (OUTLIER) cc_final: 0.3986 (t70) outliers start: 221 outliers final: 163 residues processed: 364 average time/residue: 0.1631 time to fit residues: 93.5985 Evaluate side-chains 353 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 165 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 343 TRP Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 457 TRP Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 506 ASP Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 611 HIS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 957 SER Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 343 TRP Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 808 CYS Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain C residue 267 ARG Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 638 PHE Chi-restraints excluded: chain C residue 640 LYS Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 791 LYS Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 808 CYS Chi-restraints excluded: chain C residue 822 MET Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 853 SER Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 964 GLN Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain C residue 1007 ASP Chi-restraints excluded: chain C residue 1018 CYS Chi-restraints excluded: chain C residue 1020 HIS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 92 LYS Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain G residue 46 HIS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 210 optimal weight: 0.0370 chunk 168 optimal weight: 0.7980 chunk 41 optimal weight: 0.0670 chunk 72 optimal weight: 0.4980 chunk 288 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 238 optimal weight: 0.0770 chunk 167 optimal weight: 2.9990 chunk 231 optimal weight: 0.0170 chunk 203 optimal weight: 6.9990 chunk 304 optimal weight: 0.7980 overall best weight: 0.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.129629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.099935 restraints weight = 58396.273| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.04 r_work: 0.3218 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.185 24660 Z= 0.095 Angle : 0.531 10.158 33521 Z= 0.272 Chirality : 0.042 0.373 3535 Planarity : 0.003 0.055 4339 Dihedral : 6.703 69.106 3575 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.95 % Allowed : 27.51 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.14), residues: 3100 helix: 1.84 (0.23), residues: 545 sheet: -0.94 (0.29), residues: 326 loop : -0.71 (0.12), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 930 TYR 0.020 0.001 TYR C 424 PHE 0.012 0.001 PHE F 300 TRP 0.021 0.001 TRP G 74 HIS 0.010 0.001 HIS F 46 Details of bonding type rmsd covalent geometry : bond 0.00206 (24551) covalent geometry : angle 0.51756 (33298) SS BOND : bond 0.00197 ( 98) SS BOND : angle 0.81500 ( 196) hydrogen bonds : bond 0.02840 ( 738) hydrogen bonds : angle 4.66138 ( 2244) Misc. bond : bond 0.17095 ( 2) link_NAG-ASN : bond 0.00642 ( 9) link_NAG-ASN : angle 3.93541 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 196 time to evaluate : 0.923 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 163 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8214 (mtp85) REVERT: A 179 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7940 (mpp80) REVERT: A 343 TRP cc_start: 0.8467 (OUTLIER) cc_final: 0.8237 (p90) REVERT: A 396 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8561 (mmtp) REVERT: A 485 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7969 (pt) REVERT: A 582 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: A 810 HIS cc_start: 0.7890 (m90) cc_final: 0.7020 (m90) REVERT: A 872 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8084 (mtmm) REVERT: A 886 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7783 (pt) REVERT: A 888 MET cc_start: 0.7573 (ptp) cc_final: 0.7244 (ptp) REVERT: A 927 ASN cc_start: 0.8094 (OUTLIER) cc_final: 0.7727 (t0) REVERT: A 1013 TRP cc_start: 0.8400 (m100) cc_final: 0.7619 (m100) REVERT: B 327 HIS cc_start: 0.7502 (OUTLIER) cc_final: 0.6964 (t70) REVERT: B 343 TRP cc_start: 0.7861 (OUTLIER) cc_final: 0.7182 (m100) REVERT: B 357 HIS cc_start: 0.7539 (OUTLIER) cc_final: 0.6531 (t-90) REVERT: B 548 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: B 615 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6131 (pt0) REVERT: B 649 MET cc_start: 0.7479 (mtm) cc_final: 0.7147 (mtt) REVERT: B 785 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: B 880 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.5660 (mt) REVERT: B 908 SER cc_start: 0.7216 (OUTLIER) cc_final: 0.6874 (p) REVERT: C 283 PHE cc_start: 0.5557 (OUTLIER) cc_final: 0.4937 (p90) REVERT: C 299 ASP cc_start: 0.8005 (t0) cc_final: 0.7782 (t0) REVERT: C 319 VAL cc_start: 0.7457 (OUTLIER) cc_final: 0.7234 (m) REVERT: C 390 ILE cc_start: 0.9218 (mt) cc_final: 0.8785 (mm) REVERT: C 391 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.7867 (mp10) REVERT: C 569 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7103 (t-90) REVERT: C 855 MET cc_start: 0.8076 (tpt) cc_final: 0.7651 (tpt) REVERT: C 884 MET cc_start: 0.7726 (tpt) cc_final: 0.7499 (mmm) REVERT: C 891 ASP cc_start: 0.7997 (t70) cc_final: 0.7674 (t0) REVERT: C 900 ASP cc_start: 0.8504 (p0) cc_final: 0.8241 (p0) REVERT: C 988 THR cc_start: 0.8455 (p) cc_final: 0.8070 (p) REVERT: C 1020 HIS cc_start: 0.7669 (OUTLIER) cc_final: 0.7107 (m-70) REVERT: D 57 LYS cc_start: 0.8100 (tppt) cc_final: 0.7681 (mmtt) REVERT: E 44 GLU cc_start: 0.7302 (tp30) cc_final: 0.6925 (tp30) REVERT: E 64 HIS cc_start: 0.7655 (t-170) cc_final: 0.7242 (t-170) REVERT: E 118 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7356 (t-90) REVERT: F 61 GLU cc_start: 0.4016 (OUTLIER) cc_final: 0.3181 (pp20) REVERT: F 90 CYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6397 (t) REVERT: G 46 HIS cc_start: 0.4911 (OUTLIER) cc_final: 0.3503 (t-170) outliers start: 152 outliers final: 96 residues processed: 327 average time/residue: 0.1722 time to fit residues: 87.9645 Evaluate side-chains 295 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 173 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 343 TRP Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 457 TRP Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1015 HIS Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 343 TRP Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 808 CYS Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain C residue 267 ARG Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 640 LYS Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 796 TRP Chi-restraints excluded: chain C residue 808 CYS Chi-restraints excluded: chain C residue 853 SER Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 964 GLN Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1020 HIS Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain G residue 46 HIS Chi-restraints excluded: chain G residue 48 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 202 optimal weight: 0.9990 chunk 272 optimal weight: 4.9990 chunk 104 optimal weight: 0.0770 chunk 66 optimal weight: 5.9990 chunk 229 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 179 optimal weight: 0.7980 chunk 75 optimal weight: 0.3980 chunk 200 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 ASN ** F 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.128686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.098801 restraints weight = 58439.917| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.04 r_work: 0.3199 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.230 24660 Z= 0.116 Angle : 0.552 10.410 33521 Z= 0.279 Chirality : 0.043 0.379 3535 Planarity : 0.004 0.053 4339 Dihedral : 6.603 67.957 3569 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.87 % Allowed : 27.44 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.14), residues: 3100 helix: 1.87 (0.23), residues: 544 sheet: -0.92 (0.28), residues: 351 loop : -0.69 (0.12), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 562 TYR 0.026 0.001 TYR C 465 PHE 0.014 0.001 PHE F 280 TRP 0.044 0.001 TRP B 541 HIS 0.009 0.001 HIS F 46 Details of bonding type rmsd covalent geometry : bond 0.00269 (24551) covalent geometry : angle 0.53533 (33298) SS BOND : bond 0.00230 ( 98) SS BOND : angle 1.16402 ( 196) hydrogen bonds : bond 0.02977 ( 738) hydrogen bonds : angle 4.65789 ( 2244) Misc. bond : bond 0.19507 ( 2) link_NAG-ASN : bond 0.00639 ( 9) link_NAG-ASN : angle 3.92527 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 178 time to evaluate : 0.913 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 163 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8224 (mtp85) REVERT: A 179 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7964 (mpp80) REVERT: A 485 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7988 (pt) REVERT: A 582 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8082 (pt0) REVERT: A 587 ASN cc_start: 0.6479 (OUTLIER) cc_final: 0.6255 (t0) REVERT: A 810 HIS cc_start: 0.7896 (m90) cc_final: 0.7022 (m90) REVERT: A 872 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8105 (mtmm) REVERT: A 886 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7767 (pt) REVERT: A 888 MET cc_start: 0.7624 (ptp) cc_final: 0.7217 (ptp) REVERT: A 927 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7723 (t0) REVERT: A 1013 TRP cc_start: 0.8394 (m100) cc_final: 0.7757 (m100) REVERT: B 327 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.7045 (t70) REVERT: B 357 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.6535 (t-90) REVERT: B 467 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7547 (pt0) REVERT: B 548 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: B 615 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6162 (pt0) REVERT: B 630 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8204 (mt) REVERT: B 649 MET cc_start: 0.7580 (mtm) cc_final: 0.7195 (mtt) REVERT: B 785 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: B 809 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7942 (ttm170) REVERT: B 880 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.5655 (mt) REVERT: B 908 SER cc_start: 0.7272 (OUTLIER) cc_final: 0.6909 (p) REVERT: C 267 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.4962 (ptp-170) REVERT: C 283 PHE cc_start: 0.5570 (OUTLIER) cc_final: 0.5249 (p90) REVERT: C 319 VAL cc_start: 0.7478 (OUTLIER) cc_final: 0.7252 (m) REVERT: C 390 ILE cc_start: 0.9275 (mt) cc_final: 0.8768 (mm) REVERT: C 391 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.7824 (mp10) REVERT: C 569 HIS cc_start: 0.7980 (OUTLIER) cc_final: 0.7138 (t-90) REVERT: C 778 THR cc_start: 0.8513 (m) cc_final: 0.8284 (t) REVERT: C 900 ASP cc_start: 0.8517 (p0) cc_final: 0.8251 (p0) REVERT: C 988 THR cc_start: 0.8468 (p) cc_final: 0.8106 (p) REVERT: C 1013 TRP cc_start: 0.8130 (m100) cc_final: 0.7864 (m100) REVERT: C 1020 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.7201 (m-70) REVERT: D 57 LYS cc_start: 0.7956 (tppt) cc_final: 0.7521 (mmtt) REVERT: E 44 GLU cc_start: 0.7352 (tp30) cc_final: 0.6964 (tp30) REVERT: E 64 HIS cc_start: 0.7666 (t-170) cc_final: 0.7253 (t-170) REVERT: E 118 HIS cc_start: 0.7697 (OUTLIER) cc_final: 0.7354 (t-90) REVERT: F 90 CYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6417 (t) REVERT: G 46 HIS cc_start: 0.4586 (OUTLIER) cc_final: 0.3406 (t-170) outliers start: 150 outliers final: 108 residues processed: 308 average time/residue: 0.1643 time to fit residues: 79.5131 Evaluate side-chains 304 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 169 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 457 TRP Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1015 HIS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 808 CYS Chi-restraints excluded: chain B residue 809 ARG Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain C residue 267 ARG Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 640 LYS Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 808 CYS Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 853 SER Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 964 GLN Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain C residue 1018 CYS Chi-restraints excluded: chain C residue 1020 HIS Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain G residue 46 HIS Chi-restraints excluded: chain G residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 210 optimal weight: 1.9990 chunk 263 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 252 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 275 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 HIS G 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.110862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.081213 restraints weight = 58520.626| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.02 r_work: 0.3193 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.248 24660 Z= 0.124 Angle : 0.550 10.587 33521 Z= 0.278 Chirality : 0.043 0.381 3535 Planarity : 0.004 0.052 4339 Dihedral : 6.530 67.918 3565 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.95 % Allowed : 27.36 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.15), residues: 3100 helix: 1.91 (0.23), residues: 543 sheet: -0.92 (0.27), residues: 358 loop : -0.68 (0.12), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 562 TYR 0.021 0.001 TYR C 424 PHE 0.016 0.001 PHE F 280 TRP 0.040 0.001 TRP B 541 HIS 0.008 0.001 HIS F 46 Details of bonding type rmsd covalent geometry : bond 0.00290 (24551) covalent geometry : angle 0.53500 (33298) SS BOND : bond 0.00234 ( 98) SS BOND : angle 1.02863 ( 196) hydrogen bonds : bond 0.03026 ( 738) hydrogen bonds : angle 4.62386 ( 2244) Misc. bond : bond 0.21102 ( 2) link_NAG-ASN : bond 0.00625 ( 9) link_NAG-ASN : angle 3.94200 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 177 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8212 (mtp85) REVERT: A 179 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7999 (mpp80) REVERT: A 485 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.8001 (pt) REVERT: A 582 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8085 (pt0) REVERT: A 638 PHE cc_start: 0.2787 (m-80) cc_final: 0.2506 (m-80) REVERT: A 809 ARG cc_start: 0.6181 (OUTLIER) cc_final: 0.5728 (ttm170) REVERT: A 810 HIS cc_start: 0.7883 (m90) cc_final: 0.7030 (m90) REVERT: A 872 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8128 (mtmm) REVERT: A 888 MET cc_start: 0.7636 (ptp) cc_final: 0.7210 (ptp) REVERT: A 927 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7728 (t0) REVERT: A 1013 TRP cc_start: 0.8409 (m100) cc_final: 0.7757 (m100) REVERT: B 197 CYS cc_start: 0.1611 (OUTLIER) cc_final: 0.1217 (m) REVERT: B 327 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.7024 (t70) REVERT: B 357 HIS cc_start: 0.7576 (OUTLIER) cc_final: 0.6550 (t-90) REVERT: B 467 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: B 548 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: B 615 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6172 (pt0) REVERT: B 630 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8240 (mt) REVERT: B 785 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: B 809 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7910 (ttm170) REVERT: B 880 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.5639 (mt) REVERT: B 908 SER cc_start: 0.7286 (OUTLIER) cc_final: 0.6922 (p) REVERT: C 267 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.5109 (ptp-170) REVERT: C 283 PHE cc_start: 0.5573 (OUTLIER) cc_final: 0.5222 (p90) REVERT: C 319 VAL cc_start: 0.7488 (OUTLIER) cc_final: 0.7261 (m) REVERT: C 390 ILE cc_start: 0.9278 (mt) cc_final: 0.8771 (mm) REVERT: C 391 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: C 569 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.7143 (t-90) REVERT: C 778 THR cc_start: 0.8525 (m) cc_final: 0.8304 (t) REVERT: C 900 ASP cc_start: 0.8519 (p0) cc_final: 0.8258 (p0) REVERT: C 988 THR cc_start: 0.8465 (p) cc_final: 0.8113 (p) REVERT: C 1013 TRP cc_start: 0.8138 (m100) cc_final: 0.7907 (m100) REVERT: C 1020 HIS cc_start: 0.7676 (OUTLIER) cc_final: 0.7260 (m-70) REVERT: D 57 LYS cc_start: 0.7999 (tppt) cc_final: 0.7539 (mmtt) REVERT: E 44 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7073 (tp30) REVERT: E 64 HIS cc_start: 0.7661 (t-170) cc_final: 0.7248 (t-170) REVERT: E 118 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.7409 (t-90) REVERT: F 90 CYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6464 (t) REVERT: G 46 HIS cc_start: 0.4613 (OUTLIER) cc_final: 0.3603 (t-170) outliers start: 152 outliers final: 115 residues processed: 305 average time/residue: 0.1689 time to fit residues: 80.3554 Evaluate side-chains 313 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 170 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 457 TRP Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 809 ARG Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1015 HIS Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 808 CYS Chi-restraints excluded: chain B residue 809 ARG Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain C residue 267 ARG Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 640 LYS Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 808 CYS Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 853 SER Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 964 GLN Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain C residue 1020 HIS Chi-restraints excluded: chain C residue 1028 CYS Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain G residue 46 HIS Chi-restraints excluded: chain G residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 262 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 171 optimal weight: 0.6980 chunk 221 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 273 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 187 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 HIS C 336 GLN ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.110932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.081290 restraints weight = 58692.690| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.03 r_work: 0.3192 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.244 24660 Z= 0.119 Angle : 0.549 10.510 33521 Z= 0.276 Chirality : 0.043 0.379 3535 Planarity : 0.003 0.051 4339 Dihedral : 6.506 67.934 3565 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 6.11 % Allowed : 27.20 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3100 helix: 1.92 (0.23), residues: 543 sheet: -0.89 (0.28), residues: 339 loop : -0.69 (0.12), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 562 TYR 0.020 0.001 TYR C 424 PHE 0.016 0.001 PHE F 280 TRP 0.030 0.001 TRP B 541 HIS 0.007 0.001 HIS G 46 Details of bonding type rmsd covalent geometry : bond 0.00276 (24551) covalent geometry : angle 0.53367 (33298) SS BOND : bond 0.00234 ( 98) SS BOND : angle 0.98711 ( 196) hydrogen bonds : bond 0.02975 ( 738) hydrogen bonds : angle 4.58699 ( 2244) Misc. bond : bond 0.20558 ( 2) link_NAG-ASN : bond 0.00639 ( 9) link_NAG-ASN : angle 3.93145 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 174 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8143 (ttm) REVERT: A 163 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8224 (mtp85) REVERT: A 179 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8002 (mpp80) REVERT: A 485 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.8004 (pt) REVERT: A 597 GLU cc_start: 0.7875 (tp30) cc_final: 0.7620 (mm-30) REVERT: A 809 ARG cc_start: 0.6297 (OUTLIER) cc_final: 0.5882 (ttm170) REVERT: A 810 HIS cc_start: 0.7880 (m90) cc_final: 0.7054 (m90) REVERT: A 872 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8150 (mtmm) REVERT: A 888 MET cc_start: 0.7629 (ptp) cc_final: 0.7210 (ptp) REVERT: A 927 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7669 (t0) REVERT: A 1013 TRP cc_start: 0.8415 (m100) cc_final: 0.7907 (m100) REVERT: B 327 HIS cc_start: 0.7540 (OUTLIER) cc_final: 0.7058 (t70) REVERT: B 357 HIS cc_start: 0.7595 (OUTLIER) cc_final: 0.6580 (t-90) REVERT: B 467 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7585 (pt0) REVERT: B 548 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: B 615 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6198 (pt0) REVERT: B 630 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8219 (mt) REVERT: B 649 MET cc_start: 0.7642 (mtm) cc_final: 0.7283 (mtt) REVERT: B 785 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: B 809 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7875 (ttm170) REVERT: B 880 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.5616 (mt) REVERT: B 908 SER cc_start: 0.7266 (OUTLIER) cc_final: 0.6906 (p) REVERT: C 267 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.5083 (ptp-170) REVERT: C 319 VAL cc_start: 0.7520 (OUTLIER) cc_final: 0.7280 (m) REVERT: C 390 ILE cc_start: 0.9284 (mt) cc_final: 0.8772 (mm) REVERT: C 391 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: C 569 HIS cc_start: 0.7975 (OUTLIER) cc_final: 0.7166 (t-90) REVERT: C 778 THR cc_start: 0.8493 (m) cc_final: 0.8278 (t) REVERT: C 900 ASP cc_start: 0.8492 (p0) cc_final: 0.8224 (p0) REVERT: C 988 THR cc_start: 0.8474 (p) cc_final: 0.8130 (p) REVERT: C 999 LYS cc_start: 0.7292 (pttt) cc_final: 0.6934 (pttp) REVERT: C 1020 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.7299 (m-70) REVERT: D 57 LYS cc_start: 0.7949 (tppt) cc_final: 0.7520 (mmtt) REVERT: E 64 HIS cc_start: 0.7637 (t-170) cc_final: 0.7230 (t-170) REVERT: E 118 HIS cc_start: 0.7701 (OUTLIER) cc_final: 0.7397 (t-90) REVERT: E 144 HIS cc_start: 0.5262 (OUTLIER) cc_final: 0.4892 (m-70) REVERT: F 90 CYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6490 (t) REVERT: G 46 HIS cc_start: 0.4248 (OUTLIER) cc_final: 0.3981 (t-90) outliers start: 156 outliers final: 121 residues processed: 307 average time/residue: 0.1684 time to fit residues: 81.0872 Evaluate side-chains 319 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 172 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 457 TRP Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 809 ARG Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1015 HIS Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 808 CYS Chi-restraints excluded: chain B residue 809 ARG Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain C residue 267 ARG Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 640 LYS Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 808 CYS Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 853 SER Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 964 GLN Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain C residue 1018 CYS Chi-restraints excluded: chain C residue 1020 HIS Chi-restraints excluded: chain C residue 1028 CYS Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain G residue 46 HIS Chi-restraints excluded: chain G residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 198 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 221 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 196 optimal weight: 0.0770 chunk 134 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 268 optimal weight: 1.9990 chunk 278 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 HIS ** B 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.108868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.079105 restraints weight = 58631.886| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.99 r_work: 0.3146 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.323 24660 Z= 0.216 Angle : 0.625 12.986 33521 Z= 0.316 Chirality : 0.046 0.409 3535 Planarity : 0.004 0.050 4339 Dihedral : 6.824 68.624 3565 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.11 % Allowed : 27.24 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.14), residues: 3100 helix: 1.68 (0.23), residues: 542 sheet: -0.98 (0.27), residues: 353 loop : -0.84 (0.12), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 562 TYR 0.019 0.002 TYR C 424 PHE 0.031 0.002 PHE F 280 TRP 0.045 0.002 TRP B 541 HIS 0.011 0.001 HIS B 495 Details of bonding type rmsd covalent geometry : bond 0.00512 (24551) covalent geometry : angle 0.60831 (33298) SS BOND : bond 0.00400 ( 98) SS BOND : angle 1.20178 ( 196) hydrogen bonds : bond 0.03632 ( 738) hydrogen bonds : angle 4.87711 ( 2244) Misc. bond : bond 0.28540 ( 2) link_NAG-ASN : bond 0.00603 ( 9) link_NAG-ASN : angle 4.18170 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 175 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7970 (tpp) REVERT: A 163 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8179 (mtp85) REVERT: A 179 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7968 (mpp80) REVERT: A 485 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8084 (pt) REVERT: A 787 LYS cc_start: 0.9308 (tttp) cc_final: 0.9029 (mptt) REVERT: A 809 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.6007 (ttm170) REVERT: A 810 HIS cc_start: 0.7943 (m90) cc_final: 0.7077 (m90) REVERT: A 872 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8190 (mtmm) REVERT: A 886 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7812 (pt) REVERT: A 888 MET cc_start: 0.7700 (ptp) cc_final: 0.7184 (ptp) REVERT: A 927 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7768 (t0) REVERT: B 327 HIS cc_start: 0.7505 (OUTLIER) cc_final: 0.7061 (t70) REVERT: B 343 TRP cc_start: 0.8192 (OUTLIER) cc_final: 0.7574 (m100) REVERT: B 357 HIS cc_start: 0.7718 (OUTLIER) cc_final: 0.6637 (t-90) REVERT: B 467 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7630 (pt0) REVERT: B 548 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: B 615 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6227 (pt0) REVERT: B 630 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8246 (mt) REVERT: B 785 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: B 880 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.5849 (mt) REVERT: B 908 SER cc_start: 0.7365 (OUTLIER) cc_final: 0.7029 (p) REVERT: C 267 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.5015 (ptp-170) REVERT: C 319 VAL cc_start: 0.7575 (OUTLIER) cc_final: 0.7333 (m) REVERT: C 390 ILE cc_start: 0.9304 (mt) cc_final: 0.8815 (mm) REVERT: C 391 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.7864 (mp10) REVERT: C 569 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7206 (t-90) REVERT: C 778 THR cc_start: 0.8573 (m) cc_final: 0.8351 (t) REVERT: C 891 ASP cc_start: 0.8093 (t70) cc_final: 0.7751 (t0) REVERT: C 900 ASP cc_start: 0.8512 (p0) cc_final: 0.8240 (p0) REVERT: C 988 THR cc_start: 0.8489 (p) cc_final: 0.8198 (t) REVERT: C 1013 TRP cc_start: 0.8134 (m100) cc_final: 0.7817 (m100) REVERT: D 57 LYS cc_start: 0.8029 (tppt) cc_final: 0.7572 (mmtt) REVERT: E 64 HIS cc_start: 0.7746 (t-170) cc_final: 0.7329 (t-170) REVERT: E 118 HIS cc_start: 0.7718 (OUTLIER) cc_final: 0.7385 (t-90) REVERT: E 144 HIS cc_start: 0.5147 (OUTLIER) cc_final: 0.4741 (m-70) REVERT: F 90 CYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6506 (t) REVERT: G 46 HIS cc_start: 0.4947 (OUTLIER) cc_final: 0.3911 (t-170) outliers start: 156 outliers final: 119 residues processed: 309 average time/residue: 0.1643 time to fit residues: 79.9693 Evaluate side-chains 313 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 168 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 457 TRP Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 809 ARG Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1015 HIS Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 343 TRP Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 808 CYS Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain C residue 267 ARG Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 640 LYS Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 808 CYS Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 853 SER Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 964 GLN Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain C residue 1018 CYS Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain G residue 46 HIS Chi-restraints excluded: chain G residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 130 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 265 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 chunk 267 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 80 optimal weight: 0.0870 chunk 115 optimal weight: 0.8980 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 HIS ** B 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.109827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.080336 restraints weight = 58470.901| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.99 r_work: 0.3170 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.271 24660 Z= 0.146 Angle : 0.577 11.512 33521 Z= 0.290 Chirality : 0.044 0.399 3535 Planarity : 0.004 0.049 4339 Dihedral : 6.624 68.508 3563 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.75 % Allowed : 27.67 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3100 helix: 1.80 (0.23), residues: 542 sheet: -1.07 (0.27), residues: 362 loop : -0.79 (0.12), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 562 TYR 0.020 0.001 TYR C 424 PHE 0.018 0.001 PHE F 280 TRP 0.035 0.001 TRP A 612 HIS 0.008 0.001 HIS B 495 Details of bonding type rmsd covalent geometry : bond 0.00344 (24551) covalent geometry : angle 0.56154 (33298) SS BOND : bond 0.00278 ( 98) SS BOND : angle 1.04732 ( 196) hydrogen bonds : bond 0.03194 ( 738) hydrogen bonds : angle 4.71684 ( 2244) Misc. bond : bond 0.24102 ( 2) link_NAG-ASN : bond 0.00614 ( 9) link_NAG-ASN : angle 4.06798 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6137.31 seconds wall clock time: 105 minutes 40.34 seconds (6340.34 seconds total)